modified: include/genUtil.h

	modified:   include/lmrcImageAddValue.h
	modified:   include/pdbFile.h
	modified:   src/Objects/DataManip/mrcImage/src/lmrcImageAddValue.c
	modified:   src/Objects/DataManip/pdbFile/src/pdbTrans.c
	modified:   src/Objects/DataManip/pdbFile/src/pdbTransCuda.cu
	modified:   src/Objects/General/genUtil/inc/genUtil.h

diff --git a/lib/X86LINUX64/libEosObjects.a b/lib/X86LINUX64/libEosObjects.a
index dbfda2d..c6c4ef3 100644 (file)
Binary files a/lib/X86LINUX64/libEosObjects.a and b/lib/X86LINUX64/libEosObjects.a differ

diff --git a/lib/X86LINUX64/libEosObjects.so b/lib/X86LINUX64/libEosObjects.so
index b570ab8..82a5317 100644 (file)
Binary files a/lib/X86LINUX64/libEosObjects.so and b/lib/X86LINUX64/libEosObjects.so differ

diff --git a/lib/X86LINUX64/libeosCuda.a b/lib/X86LINUX64/libeosCuda.a
index 3ea5e05..b7b4a76 100644 (file)
Binary files a/lib/X86LINUX64/libeosCuda.a and b/lib/X86LINUX64/libeosCuda.a differ

diff --git a/lib/X86LINUX64/libeosCuda.so b/lib/X86LINUX64/libeosCuda.so
index fd0d30b..aef5612 100644 (file)
Binary files a/lib/X86LINUX64/libeosCuda.so and b/lib/X86LINUX64/libeosCuda.so differ

diff --git a/lib/X86LINUX64/libmrcImage.a b/lib/X86LINUX64/libmrcImage.a
index 622328a..7f7f2a9 100644 (file)
Binary files a/lib/X86LINUX64/libmrcImage.a and b/lib/X86LINUX64/libmrcImage.a differ

diff --git a/lib/X86LINUX64/libpdbFile.a b/lib/X86LINUX64/libpdbFile.a
index 0f2127c..7ed6323 100644 (file)
Binary files a/lib/X86LINUX64/libpdbFile.a and b/lib/X86LINUX64/libpdbFile.a differ

diff --git a/lib/X86LINUX64/libpdbFile.so b/lib/X86LINUX64/libpdbFile.so
index 4b41577..f0b36d0 100644 (file)
Binary files a/lib/X86LINUX64/libpdbFile.so and b/lib/X86LINUX64/libpdbFile.so differ

diff --git a/lib/X86LINUX64/shared/eosCuda.sharedo b/lib/X86LINUX64/shared/eosCuda.sharedo
index 98df68c..bccbf78 100644 (file)
Binary files a/lib/X86LINUX64/shared/eosCuda.sharedo and b/lib/X86LINUX64/shared/eosCuda.sharedo differ

diff --git a/lib/X86LINUX64/shared/lmrcImageAddValue.sharedo b/lib/X86LINUX64/shared/lmrcImageAddValue.sharedo
index 8a956bf..0e958be 100644 (file)
Binary files a/lib/X86LINUX64/shared/lmrcImageAddValue.sharedo and b/lib/X86LINUX64/shared/lmrcImageAddValue.sharedo differ

diff --git a/lib/X86LINUX64/shared/lmrcImageAddValueCuda.sharedo b/lib/X86LINUX64/shared/lmrcImageAddValueCuda.sharedo
new file mode 100644 (file)
index 0000000..edaeff5
Binary files /dev/null and b/lib/X86LINUX64/shared/lmrcImageAddValueCuda.sharedo differ

diff --git a/lib/X86LINUX64/shared/pdbFileRead.sharedo b/lib/X86LINUX64/shared/pdbFileRead.sharedo
index 66f3537..2c9b12f 100755 (executable)
Binary files a/lib/X86LINUX64/shared/pdbFileRead.sharedo and b/lib/X86LINUX64/shared/pdbFileRead.sharedo differ

diff --git a/lib/X86LINUX64/shared/pdbRotation.sharedo b/lib/X86LINUX64/shared/pdbRotation.sharedo
index 022955a..ff272c7 100755 (executable)
Binary files a/lib/X86LINUX64/shared/pdbRotation.sharedo and b/lib/X86LINUX64/shared/pdbRotation.sharedo differ

diff --git a/lib/X86LINUX64/shared/pdbTrans.sharedo b/lib/X86LINUX64/shared/pdbTrans.sharedo
index ba0f840..e85161b 100755 (executable)
Binary files a/lib/X86LINUX64/shared/pdbTrans.sharedo and b/lib/X86LINUX64/shared/pdbTrans.sharedo differ

diff --git a/lib/X86LINUX64/shared/pdbTransCuda.sharedo b/lib/X86LINUX64/shared/pdbTransCuda.sharedo
new file mode 100644 (file)
index 0000000..f170f97
Binary files /dev/null and b/lib/X86LINUX64/shared/pdbTransCuda.sharedo differ

diff --git a/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Depend b/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Depend
index e2f8e73..fb9560a 100644 (file)
--- a/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Depend
+++ b/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Depend
@@ -380,19 +380,19 @@ lmrcImageAddValue.o: lmrcImageAddValue.c /usr/include/stdio.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
- /home/people/tacyas/Eos/include/eosCuda.h lmrcImageAddValue.h \
- ../inc/mrcImage.h /usr/include/math.h /usr/include/bits/huge_val.h \
- /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
- /usr/include/bits/inf.h /usr/include/bits/nan.h \
- /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
- /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
+ /home/people/tacyas/Eos/include/genUtil.h /usr/include/math.h \
+ /usr/include/bits/huge_val.h /usr/include/bits/huge_valf.h \
+ /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
+ /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
+ /usr/include/bits/mathcalls.h /usr/include/values.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
  /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
- /home/people/tacyas/Eos/include/ctfInfo.h \
+ /home/people/tacyas/Eos/include/eosCuda.h lmrcImageAddValue.h \
+ ../inc/mrcImage.h /home/people/tacyas/Eos/include/ctfInfo.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \

diff --git a/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Source b/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Source
index 81734b6..a665f67 100644 (file)
--- a/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Source
+++ b/src/Objects/DataManip/mrcImage/src/X86LINUX64/.Source
@@ -145,7 +145,8 @@ mrcImageWrite.c \
 mrcImageWrite2.c \
 mrcImagefuncmin.c \
 mrcRefUtil.c \
-lmrcImageAddValue.cu \
+lmrcImageAddValueCuda.cu \
+lmrcImageClusterAnalysis.cu \
 
 OBJ = \
 fftn.o \
@@ -294,7 +295,8 @@ mrcImageWrite.o \
 mrcImageWrite2.o \
 mrcImagefuncmin.o \
 mrcRefUtil.o \
-lmrcImageAddValue.o  \
+lmrcImageAddValueCuda.o  \
+lmrcImageClusterAnalysis.o  \
 
 SHAREDOBJ = \
 fftn.sharedo \
@@ -443,7 +445,8 @@ mrcImageWrite.sharedo \
 mrcImageWrite2.sharedo \
 mrcImagefuncmin.sharedo \
 mrcRefUtil.sharedo \
-lmrcImageAddValue.sharedo  \
+lmrcImageAddValueCuda.sharedo  \
+lmrcImageClusterAnalysis.sharedo  \
 
 REALOBJ = \
 X86LINUX64/fftn.o \
@@ -592,7 +595,8 @@ X86LINUX64/mrcImageWrite.o \
 X86LINUX64/mrcImageWrite2.o \
 X86LINUX64/mrcImagefuncmin.o \
 X86LINUX64/mrcRefUtil.o \
-X86LINUX64/lmrcImageAddValue.o \
+X86LINUX64/lmrcImageAddValueCuda.o \
+X86LINUX64/lmrcImageClusterAnalysis.o \
 
 REALSHAREDOBJ = \
 X86LINUX64/fftn.sharedo \
@@ -741,7 +745,8 @@ X86LINUX64/mrcImageWrite.sharedo \
 X86LINUX64/mrcImageWrite2.sharedo \
 X86LINUX64/mrcImagefuncmin.sharedo \
 X86LINUX64/mrcRefUtil.sharedo \
-X86LINUX64/lmrcImageAddValue.sharedo \
+X86LINUX64/lmrcImageAddValueCuda.sharedo \
+X86LINUX64/lmrcImageClusterAnalysis.sharedo \
 
 OBJDEBUG = \
 fftn.debugo \
@@ -1038,7 +1043,8 @@ X86LINUX64/mrcImageWrite.debugo \
 X86LINUX64/mrcImageWrite2.debugo \
 X86LINUX64/mrcImagefuncmin.debugo \
 X86LINUX64/mrcRefUtil.debugo \
-X86LINUX64/lmrcImageAddValue.debugo \
+X86LINUX64/lmrcImageAddValueCuda.debugo \
+X86LINUX64/lmrcImageClusterAnalysis.debugo \
 
 OBJCUDAGDB = \
 fftn.cudagdb.o \
@@ -1187,7 +1193,8 @@ mrcImageWrite.cudagdb.o \
 mrcImageWrite2.cudagdb.o \
 mrcImagefuncmin.cudagdb.o \
 mrcRefUtil.cudagdb.o \
-lmrcImageAddValue.cudagdb.o  \
+lmrcImageAddValueCuda.cudagdb.o  \
+lmrcImageClusterAnalysis.cudagdb.o  \
 
 REALOBJCUDAGDB = \
 X86LINUX64/fftn.cudagdb.o \
@@ -1336,6 +1343,7 @@ X86LINUX64/mrcImageWrite.cudagdb.o \
 X86LINUX64/mrcImageWrite2.cudagdb.o \
 X86LINUX64/mrcImagefuncmin.cudagdb.o \
 X86LINUX64/mrcRefUtil.cudagdb.o \
-X86LINUX64/lmrcImageAddValue.cudagdb.o \
+X86LINUX64/lmrcImageAddValueCuda.cudagdb.o \
+X86LINUX64/lmrcImageClusterAnalysis.cudagdb.o \
 
 

diff --git a/src/Objects/DataManip/mrcImage/src/X86LINUX64/Makefile b/src/Objects/DataManip/mrcImage/src/X86LINUX64/Makefile
index 28e9069..a429553 100755 (executable)
--- a/src/Objects/DataManip/mrcImage/src/X86LINUX64/Makefile
+++ b/src/Objects/DataManip/mrcImage/src/X86LINUX64/Makefile
@@ -22,6 +22,8 @@ $(SHAREDLIB): $(SHAREDOBJ)
        @COMPILEDOBJ=`ls $(SHAREDOBJ)` ; echo "#### Compiled Objects"; echo $${COMPILEDOBJ};  echo "################"; \
        $(SHARED) $(SHAREDLIB) $${COMPILEDOBJ} 
 
+debug: $(LIBNAMEDEBUG) $(LIBNAMECUDAGDB)
+
 $(LIBNAMEDEBUG): $(OBJDEBUG)
        @echo LIBNAME:$(LIBNAMEDEBUG)
        $(AR) rs $(LIBNAMEDEBUG) $(OBJDEBUG)

diff --git a/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a b/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a
index 56316fa..7f7f2a9 100644 (file)
Binary files a/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a and b/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.a differ

diff --git a/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a b/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a
index 591c135..9045513 100644 (file)
Binary files a/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a and b/src/Objects/DataManip/mrcImage/src/X86LINUX64/libmrcImage.debug.a differ

diff --git a/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValue.sharedo b/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValue.sharedo
index 7a81668..0e958be 100644 (file)
Binary files a/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValue.sharedo and b/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValue.sharedo differ

diff --git a/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValueCuda.sharedo b/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValueCuda.sharedo
new file mode 100644 (file)
index 0000000..edaeff5
Binary files /dev/null and b/src/Objects/DataManip/mrcImage/src/X86LINUX64/lmrcImageAddValueCuda.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/.Depend b/src/Objects/DataManip/pdbFile/src/X86LINUX64/.Depend
index 34497a8..f052922 100644 (file)
--- a/src/Objects/DataManip/pdbFile/src/X86LINUX64/.Depend
+++ b/src/Objects/DataManip/pdbFile/src/X86LINUX64/.Depend
@@ -16,11 +16,12 @@ X86LINUX64/pdbUtil.o:pdbUtil.o
 lpdb2mrc2d.o: lpdb2mrc2d.c /usr/include/stdlib.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
- /usr/include/sys/types.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h /home/people/tacyas/Eos/include/genUtil.h \
@@ -29,15 +30,15 @@ lpdb2mrc2d.o: lpdb2mrc2d.c /usr/include/stdlib.h /usr/include/features.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h ../inc/pdbFile.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h ../inc/pdbFile.h \
  /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \
  /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -49,11 +50,12 @@ lpdb2mrc2d.o: lpdb2mrc2d.c /usr/include/stdlib.h /usr/include/features.h \
 lpdb2mrc3d.o: lpdb2mrc3d.c /usr/include/stdlib.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
- /usr/include/sys/types.h /usr/include/bits/types.h \
- /usr/include/bits/typesizes.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/bits/types.h /usr/include/bits/typesizes.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h /home/people/tacyas/Eos/include/genUtil.h \
@@ -62,15 +64,15 @@ lpdb2mrc3d.o: lpdb2mrc3d.c /usr/include/stdlib.h /usr/include/features.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h ../inc/pdbFile.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h ../inc/pdbFile.h \
  /usr/include/stdio.h /usr/include/libio.h /usr/include/_G_config.h \
  /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -82,14 +84,15 @@ lpdb2mrc3d.o: lpdb2mrc3d.c /usr/include/stdlib.h /usr/include/features.h \
 lpdbCoord.o: lpdbCoord.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h lpdbCoord.h \
@@ -102,12 +105,12 @@ lpdbCoord.o: lpdbCoord.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/ctfInfo.h \
  /home/people/tacyas/Eos/include/Matrix3D.h
 lpdbCoordInfo.o: lpdbCoordInfo.c \
@@ -119,17 +122,17 @@ lpdbCoordInfo.o: lpdbCoordInfo.c \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h lpdbCoordInfo.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h lpdbCoordInfo.h \
  ../inc/pdbFile.h /usr/include/stdio.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -142,14 +145,15 @@ lpdbSelectedAtom.o: lpdbSelectedAtom.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -158,12 +162,12 @@ lpdbSelectedAtom.o: lpdbSelectedAtom.c /usr/include/stdio.h \
  /usr/include/bits/huge_vall.h /usr/include/bits/inf.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/String.h ../inc/pdbFile.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -181,17 +185,17 @@ lpdbSurface.o: lpdbSurface.c /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h pdbInfoGet.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h pdbInfoGet.h \
  ../inc/pdbFile.h /usr/include/stdio.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -205,14 +209,15 @@ lpdbSurface.o: lpdbSurface.c /home/people/tacyas/Eos/include/genUtil.h \
 pdbFileRead.o: pdbFileRead.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -222,12 +227,12 @@ pdbFileRead.o: pdbFileRead.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/string.h /usr/include/xlocale.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/Memory.h ../inc/pdbFile.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -240,15 +245,16 @@ pdbFileWrite.o: pdbFileWrite.c /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /usr/include/string.h /usr/include/xlocale.h /usr/include/stdlib.h \
- /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h /home/people/tacyas/Eos/include/genUtil.h \
@@ -257,12 +263,12 @@ pdbFileWrite.o: pdbFileWrite.c /usr/include/stdio.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h ../inc/pdbFile.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h ../inc/pdbFile.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
  /home/people/tacyas/Eos/include/Array.h \
@@ -273,21 +279,22 @@ pdbFileWrite.o: pdbFileWrite.c /usr/include/stdio.h \
 pdbGet.o: pdbGet.c /usr/include/string.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/xlocale.h /home/people/tacyas/Eos/include/Memory.h \
  /usr/include/stdio.h /usr/include/bits/types.h \
  /usr/include/bits/typesizes.h /usr/include/libio.h \
  /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h /usr/include/stdlib.h \
- /usr/include/sys/types.h /usr/include/time.h /usr/include/endian.h \
- /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
- /usr/include/sys/select.h /usr/include/bits/select.h \
+ /usr/include/bits/waitflags.h /usr/include/bits/waitstatus.h \
+ /usr/include/endian.h /usr/include/bits/endian.h \
+ /usr/include/bits/byteswap.h /usr/include/sys/types.h \
+ /usr/include/time.h /usr/include/sys/select.h /usr/include/bits/select.h \
  /usr/include/bits/sigset.h /usr/include/bits/time.h \
  /usr/include/sys/sysmacros.h /usr/include/bits/pthreadtypes.h \
  /usr/include/alloca.h ../inc/pdbFile.h \
@@ -300,7 +307,7 @@ pdbGet.o: pdbGet.c /usr/include/string.h /usr/include/features.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/ctfInfo.h \
  /home/people/tacyas/Eos/include/Matrix3D.h
 pdbInfoGet.o: pdbInfoGet.c /home/people/tacyas/Eos/include/genUtil.h \
@@ -311,17 +318,17 @@ pdbInfoGet.o: pdbInfoGet.c /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h pdbInfoGet.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h pdbInfoGet.h \
  ../inc/pdbFile.h /usr/include/stdio.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -334,10 +341,10 @@ pdbRotation.o: pdbRotation.c ../inc/pdbFile.h /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -348,39 +355,40 @@ pdbRotation.o: pdbRotation.c ../inc/pdbFile.h /usr/include/stdio.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/ctfInfo.h \
  /home/people/tacyas/Eos/include/Matrix3D.h
 pdbSecondaryStructure.o: pdbSecondaryStructure.c /usr/include/string.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/xlocale.h /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/math.h /usr/include/bits/huge_val.h \
  /usr/include/bits/huge_valf.h /usr/include/bits/huge_vall.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/Memory.h /usr/include/stdio.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -396,10 +404,10 @@ pdbSet.o: pdbSet.c ../inc/pdbFile.h /usr/include/stdio.h \
  /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
  /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/Vector.h \
@@ -410,12 +418,12 @@ pdbSet.o: pdbSet.c ../inc/pdbFile.h /usr/include/stdio.h \
  /usr/include/bits/nan.h /usr/include/bits/mathdef.h \
  /usr/include/bits/mathcalls.h /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/ctfInfo.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/genUtil.h \
@@ -423,14 +431,15 @@ pdbSet.o: pdbSet.c ../inc/pdbFile.h /usr/include/stdio.h \
 pdbTrans.o: pdbTrans.c /usr/include/stdio.h /usr/include/features.h \
  /usr/include/sys/cdefs.h /usr/include/bits/wordsize.h \
  /usr/include/gnu/stubs.h /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/bits/types.h /usr/include/bits/typesizes.h \
  /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h \
@@ -444,17 +453,19 @@ pdbTrans.o: pdbTrans.c /usr/include/stdio.h /usr/include/features.h \
  /home/people/tacyas/Eos/include/Array.h \
  /home/people/tacyas/Eos/include/mrcImage.h \
  /home/people/tacyas/Eos/include/genUtil.h /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /home/people/tacyas/Eos/include/ctfInfo.h \
  /home/people/tacyas/Eos/include/Matrix3D.h \
  /home/people/tacyas/Eos/include/String.h \
+ /home/people/tacyas/Eos/include/eosCuda.h \
  /home/people/tacyas/Eos/include/genUtil.h \
- /home/people/tacyas/Eos/include/Vector.h
+ /home/people/tacyas/Eos/include/Vector.h \
+ /home/people/tacyas/Eos/include/Memory.h
 pdbUtil.o: pdbUtil.c /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/math.h /usr/include/features.h /usr/include/sys/cdefs.h \
  /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
@@ -463,23 +474,24 @@ pdbUtil.o: pdbUtil.c /home/people/tacyas/Eos/include/genUtil.h \
  /usr/include/bits/inf.h /usr/include/bits/nan.h \
  /usr/include/bits/mathdef.h /usr/include/bits/mathcalls.h \
  /usr/include/values.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/limits.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include-fixed/syslimits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/limits.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/syslimits.h \
  /usr/include/limits.h /usr/include/bits/posix1_lim.h \
  /usr/include/bits/local_lim.h /usr/include/linux/limits.h \
  /usr/include/bits/posix2_lim.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/float.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/float.h \
  /usr/include/string.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stddef.h \
  /usr/include/xlocale.h /home/people/tacyas/Eos/include/Memory.h \
  /usr/include/stdio.h /usr/include/bits/types.h \
  /usr/include/bits/typesizes.h /usr/include/libio.h \
  /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
+ /usr/lib/gcc/x86_64-redhat-linux/4.4.7/include/stdarg.h \
  /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h \
- /usr/include/stdlib.h /usr/include/sys/types.h /usr/include/time.h \
- /usr/include/endian.h /usr/include/bits/endian.h \
- /usr/include/bits/byteswap.h /usr/include/sys/select.h \
+ /usr/include/stdlib.h /usr/include/bits/waitflags.h \
+ /usr/include/bits/waitstatus.h /usr/include/endian.h \
+ /usr/include/bits/endian.h /usr/include/bits/byteswap.h \
+ /usr/include/sys/types.h /usr/include/time.h /usr/include/sys/select.h \
  /usr/include/bits/select.h /usr/include/bits/sigset.h \
  /usr/include/bits/time.h /usr/include/sys/sysmacros.h \
  /usr/include/bits/pthreadtypes.h /usr/include/alloca.h ../inc/pdbFile.h \

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/.Source b/src/Objects/DataManip/pdbFile/src/X86LINUX64/.Source
index 7394b36..7dd9d2d 100644 (file)
--- a/src/Objects/DataManip/pdbFile/src/X86LINUX64/.Source
+++ b/src/Objects/DataManip/pdbFile/src/X86LINUX64/.Source
@@ -14,6 +14,7 @@ pdbSecondaryStructure.c \
 pdbSet.c \
 pdbTrans.c \
 pdbUtil.c \
+pdbTransCuda.cu \
 
 OBJ = \
 lpdb2mrc2d.o \
@@ -31,6 +32,7 @@ pdbSecondaryStructure.o \
 pdbSet.o \
 pdbTrans.o \
 pdbUtil.o \
+pdbTransCuda.o  \
 
 SHAREDOBJ = \
 lpdb2mrc2d.sharedo \
@@ -48,6 +50,7 @@ pdbSecondaryStructure.sharedo \
 pdbSet.sharedo \
 pdbTrans.sharedo \
 pdbUtil.sharedo \
+pdbTransCuda.sharedo  \
 
 REALOBJ = \
 X86LINUX64/lpdb2mrc2d.o \
@@ -65,6 +68,7 @@ X86LINUX64/pdbSecondaryStructure.o \
 X86LINUX64/pdbSet.o \
 X86LINUX64/pdbTrans.o \
 X86LINUX64/pdbUtil.o \
+X86LINUX64/pdbTransCuda.o \
 
 REALSHAREDOBJ = \
 X86LINUX64/lpdb2mrc2d.sharedo \
@@ -82,6 +86,7 @@ X86LINUX64/pdbSecondaryStructure.sharedo \
 X86LINUX64/pdbSet.sharedo \
 X86LINUX64/pdbTrans.sharedo \
 X86LINUX64/pdbUtil.sharedo \
+X86LINUX64/pdbTransCuda.sharedo \
 
 OBJDEBUG = \
 lpdb2mrc2d.debugo \
@@ -116,6 +121,7 @@ X86LINUX64/pdbSecondaryStructure.debugo \
 X86LINUX64/pdbSet.debugo \
 X86LINUX64/pdbTrans.debugo \
 X86LINUX64/pdbUtil.debugo \
+X86LINUX64/pdbTransCuda.debugo \
 
 OBJCUDAGDB = \
 lpdb2mrc2d.cudagdb.o \
@@ -133,6 +139,7 @@ pdbSecondaryStructure.cudagdb.o \
 pdbSet.cudagdb.o \
 pdbTrans.cudagdb.o \
 pdbUtil.cudagdb.o \
+pdbTransCuda.cudagdb.o  \
 
 REALOBJCUDAGDB = \
 X86LINUX64/lpdb2mrc2d.cudagdb.o \
@@ -150,5 +157,6 @@ X86LINUX64/pdbSecondaryStructure.cudagdb.o \
 X86LINUX64/pdbSet.cudagdb.o \
 X86LINUX64/pdbTrans.cudagdb.o \
 X86LINUX64/pdbUtil.cudagdb.o \
+X86LINUX64/pdbTransCuda.cudagdb.o \
 
 

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/Makefile b/src/Objects/DataManip/pdbFile/src/X86LINUX64/Makefile
index 28e9069..a429553 100755 (executable)
--- a/src/Objects/DataManip/pdbFile/src/X86LINUX64/Makefile
+++ b/src/Objects/DataManip/pdbFile/src/X86LINUX64/Makefile
@@ -22,6 +22,8 @@ $(SHAREDLIB): $(SHAREDOBJ)
        @COMPILEDOBJ=`ls $(SHAREDOBJ)` ; echo "#### Compiled Objects"; echo $${COMPILEDOBJ};  echo "################"; \
        $(SHARED) $(SHAREDLIB) $${COMPILEDOBJ} 
 
+debug: $(LIBNAMEDEBUG) $(LIBNAMECUDAGDB)
+
 $(LIBNAMEDEBUG): $(OBJDEBUG)
        @echo LIBNAME:$(LIBNAMEDEBUG)
        $(AR) rs $(LIBNAMEDEBUG) $(OBJDEBUG)

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.a b/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.a
index 0f2127c..7ed6323 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.a and b/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.a differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.debug.a b/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.debug.a
index 97352bc..764b2cf 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.debug.a and b/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.debug.a differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.so b/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.so
index 4b41577..f0b36d0 100755 (executable)
Binary files a/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.so and b/src/Objects/DataManip/pdbFile/src/X86LINUX64/libpdbFile.so differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbFileRead.sharedo b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbFileRead.sharedo
index 66f3537..2c9b12f 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbFileRead.sharedo and b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbFileRead.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbRotation.sharedo b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbRotation.sharedo
index 022955a..ff272c7 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbRotation.sharedo and b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbRotation.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTrans.sharedo b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTrans.sharedo
index ba0f840..e85161b 100644 (file)
Binary files a/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTrans.sharedo and b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTrans.sharedo differ

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTransCuda.cu b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTransCuda.cu
new file mode 120000 (symlink)
index 0000000..a2f7509
--- /dev/null
+++ b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTransCuda.cu
@@ -0,0 +1 @@
+../pdbTransCuda.cu
\ No newline at end of file

diff --git a/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTransCuda.sharedo b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTransCuda.sharedo
new file mode 100644 (file)
index 0000000..f170f97
Binary files /dev/null and b/src/Objects/DataManip/pdbFile/src/X86LINUX64/pdbTransCuda.sharedo differ

diff --git a/src/Objects/General/eosCuda/src/X86LINUX64/.Depend b/src/Objects/General/eosCuda/src/X86LINUX64/.Depend
index 3ea863b..e69de29 100644 (file)
--- a/src/Objects/General/eosCuda/src/X86LINUX64/.Depend
+++ b/src/Objects/General/eosCuda/src/X86LINUX64/.Depend
@@ -1,10 +0,0 @@
-X86LINUX64/eosCuda.o:eosCuda.o
-eosCuda.o: eosCuda.c ../inc/eosCuda.h /usr/include/stdio.h \
- /usr/include/features.h /usr/include/sys/cdefs.h \
- /usr/include/bits/wordsize.h /usr/include/gnu/stubs.h \
- /usr/include/gnu/stubs-64.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stddef.h \
- /usr/include/bits/types.h /usr/include/bits/typesizes.h \
- /usr/include/libio.h /usr/include/_G_config.h /usr/include/wchar.h \
- /usr/lib64/gcc/x86_64-suse-linux/4.4/include/stdarg.h \
- /usr/include/bits/stdio_lim.h /usr/include/bits/sys_errlist.h

diff --git a/src/Objects/General/eosCuda/src/X86LINUX64/.Source b/src/Objects/General/eosCuda/src/X86LINUX64/.Source
index 46459f6..6ddf7c1 100644 (file)
--- a/src/Objects/General/eosCuda/src/X86LINUX64/.Source
+++ b/src/Objects/General/eosCuda/src/X86LINUX64/.Source
@@ -1,11 +1,11 @@
 SRC = \
-eosCuda.c \
+eosCuda.cu \
 
 OBJ = \
-eosCuda.o \
+eosCuda.o  \
 
 SHAREDOBJ = \
-eosCuda.sharedo \
+eosCuda.sharedo  \
 
 REALOBJ = \
 X86LINUX64/eosCuda.o \
@@ -14,13 +14,12 @@ REALSHAREDOBJ = \
 X86LINUX64/eosCuda.sharedo \
 
 OBJDEBUG = \
-eosCuda.debugo \
 
 REALOBJDEBUG = \
 X86LINUX64/eosCuda.debugo \
 
 OBJCUDAGDB = \
-eosCuda.cudagdb.o \
+eosCuda.cudagdb.o  \
 
 REALOBJCUDAGDB = \
 X86LINUX64/eosCuda.cudagdb.o \

diff --git a/src/Objects/General/eosCuda/src/X86LINUX64/Makefile b/src/Objects/General/eosCuda/src/X86LINUX64/Makefile
index 28e9069..a429553 100755 (executable)
--- a/src/Objects/General/eosCuda/src/X86LINUX64/Makefile
+++ b/src/Objects/General/eosCuda/src/X86LINUX64/Makefile
@@ -22,6 +22,8 @@ $(SHAREDLIB): $(SHAREDOBJ)
        @COMPILEDOBJ=`ls $(SHAREDOBJ)` ; echo "#### Compiled Objects"; echo $${COMPILEDOBJ};  echo "################"; \
        $(SHARED) $(SHAREDLIB) $${COMPILEDOBJ} 
 
+debug: $(LIBNAMEDEBUG) $(LIBNAMECUDAGDB)
+
 $(LIBNAMEDEBUG): $(OBJDEBUG)
        @echo LIBNAME:$(LIBNAMEDEBUG)
        $(AR) rs $(LIBNAMEDEBUG) $(OBJDEBUG)

diff --git a/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.cu b/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.cu
new file mode 120000 (symlink)
index 0000000..5b1347d
--- /dev/null
+++ b/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.cu
@@ -0,0 +1 @@
+../eosCuda.cu
\ No newline at end of file

diff --git a/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.sharedo b/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.sharedo
index 98df68c..bccbf78 100644 (file)
Binary files a/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.sharedo and b/src/Objects/General/eosCuda/src/X86LINUX64/eosCuda.sharedo differ

diff --git a/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.a b/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.a
index 3ea5e05..b7b4a76 100644 (file)
Binary files a/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.a and b/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.a differ

diff --git a/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.debug.a b/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.debug.a
index 7308f08..8b277f0 100644 (file)
Binary files a/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.debug.a and b/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.debug.a differ

diff --git a/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.so b/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.so
index fd0d30b..aef5612 100755 (executable)
Binary files a/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.so and b/src/Objects/General/eosCuda/src/X86LINUX64/libeosCuda.so differ