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  How to build Molby
  Version 0.6.5
  Toshi Nagata
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Building Molby is somewhat complicated because you need static libraries of wxWidgets and Ruby (and CLAPACK in Windows). The procedures are described below for each platform.
In the following, $MOLBY represents the Molby source directory, which should reside within a directory like $HOME/Development or something like that.

(1) Mac OS X

(i) Xcode, gfortran

Install Xcode, if you have not done so yet. The Xcode project included in the source distribution is for Xcode 3.0 and later, thus you need Mac OS 10.5.

To build AmberTools, you need to have gfortran installed. The author uses a binary build available at the "R for Mac OS X" website (http://r.research.att.com/tools/, gfortran-4.2.3.dmg).

We need static linking of libgfortran.a. For that purpose, the following modification should be done after installation of gfortran.

% cd /usr/local/lib
% sudo cp libgfortran.a libgfortran-static.a  #  Copy as a different name
% sudo strip -S libgfortran-static.a  #  Remove the symbols
% sudo ranlib libgfortran-static.a

The last two lines are necessary to avoid linker warnings saying "Can't find atom for N_GSYM stabs."

(ii) wxWidgets

Get wxWidgets-3.0.0 from the wxWidgets official page in sourceforge.net (http://sourceforge.net/projects/wxwindows/files/). Newer versions may work, but they are not tested.

Unpack wxWidgets-3.0.0.tar.gz. Move the resulting directory wxWidgets-3.0.0 to $MOLBY/../.

Build wxWidgets. The commands will be as follows. Take care of the configure options.
$ cd $MOLBY/../wxWidgets-3.0.0
$ mkdir osx-build
$ cd osx-build
$ ../configure --with-macosx-sdk=/Developer/SDKs/MacOSX10.5.sdk --with-macosx-version-min=10.5 --enable-universal_binary=ppc,i386 --disable-shared --with-opengl --enable-monolithic
$ make
(It will take quite long. You do not need to do "sudo make install".)

(iii) Ruby

Get ruby-2.0.0-p353.tar.gz, unpack it, and move the resulting directory ruby-2.0.0-p353 to $MOLBY/../.
$ cd $MOLBY/../ruby-2.0.0-p353
$ CFLAGS='-isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -O2' ./configure --prefix=$PWD/osx-build --with-arch=i386,ppc --disable-shared --with-ext=date --disable-install-rdoc --with-static-linked-ext
$ make && make install
$ cp enc/libenc.a enc/libtrans.a osx-build/lib  #  We need this for encoding support

The osx-build directory contains lib (which contains libruby-static.a) and include (which contains include files). (There are also bin and share directories, but these are not used for building Molby.)
$ make clean  #  Remove configure files and intermediates; the osx-build directory remains intact

---- Old description (ruby 1.8.7) ----
Get ruby-1.8.7-p160.tar.gz from the Molby source distribution site. Unpack it, and move the resulting directory ruby-1.8.7-p160 to $MOLBY/../. Rename it to ruby-1.8.7-static (or make a symbolic link).
$ cd $MOLBY/..
$ mv somewhere/ruby-1.8.7-p160.tar.gz ./
$ tar xvzf ruby-1.8.7-p160.tar.gz
$ ln -s ruby-1.8.7-p160 ruby-1.8.7-static

If you want to place ruby-1.8.7-static in another place (and/or another name) than $MOLBY/../, you will need to change the build settings in Xcode.

Patch the Ruby source.
$ cd $MOLBY/../ruby-1.8.7-static
$ patch --backup -p1 < $MOLBY/ruby-1.8.7-p160-tn.patch
($MOLBY is the location of the Molby source.)

Build Ruby with --disable-shared option.
$ CFLAGS='-isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -arch i386 -arch ppc -O2' ./configure --disable-shared --disable-thread
$ make
---- end old description (ruby 1.8.7) ----

(iv) FFTW

Get fftw-3.3.2.tar.gz, unpack it, and move the resulting directory fftw-3.3.2 to $MOLBY/../. $ cd $MOLBY/../fftw-3.3.2
$ ./configure --prefix=$PWD/osx-build --disable-fortran CFLAGS="-isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -arch i386 -O2"
$ make && make install  #  sudo is not necessary
$ ./configure --prefix=$PWD/osx-ppc-build --disable-fortran CFLAGS="-isysroot /Developer/SDKs/MacOSX10.5.sdk -mmacosx-version-min=10.5 -arch ppc -O2"
$ make && make install  #  sudo is not necessary
$ cd osx-build/lib
$ mv libfftw3.a libfftw3.i386.a
$ lipo -create libfftw3.i386.a ../../osx-ppc-build/lib/libfftw3.a -output libfftw3.a
ranlib libfftw3.a

(v) Build on Xcode

Open xcode-build/Molby.xcodeproj, and build. Note that there are two configurations, Debug and Release. In the "Release" build, the Ruby scripts update_version.rb and Documents/makedoc.rb are executed before compilation; update_version.rb modifies the version strings in the source files (by looking up the file Version), and makedoc.rb creates the HTML docments in the doc directory.

(2) Windows

The Windows binary is built by using tdm-gcc/msys. If you use VC++ or Cygwin, you need to help yourself. I use Windows only occasionally, so there may be errors and misunderstandings in the following descriptions. Feedback is welcome!

(i) MinGW, MSYS, gfortran

Install msys and tdm-gcc. The author uses msys-1.0.11, tdm-gcc-4.7.1-2, and gcc-4.7.1-tdm-1-fortran.tar.lzma.
Read instructions carefully in installing tdm-gcc. 
In installing msys-1.0.11, please make sure findutils is installed. Otherwise, find.exe of Windows is invoked from make and cause strange errors.

(ii) wxWidgets

Get wxWidgets-3.0.0 from the wxWidgets official page in sourceforge.net (http://sourceforge.net/projects/wxwindows/files/). Newer versions may work, but they are not tested.

Unpack wxWidgets-3.0.0.tar.gz. Move the resulting directory wxWidgets-3.0.0 to $MOLBY/../.

Build wxWidgets. The commands will be as follows. Take care of the configure options.
$ cd $MOLBY/../wxWidgets-3.0.0
$ mkdir msw-build
$ cd msw-build
$ ../configure --with-msw --with-opengl --disable-shared --with-libjpeg=builtin --with-zlib=builtin --enable-monolithic
$ make
(It will take quite long. You do not need to do "sudo make install".)

(iii) Ruby

Get ruby-2.0.0-p353.tar.gz, unpack it, and move the resulting directory ruby-2.0.0-p353 to $MOLBY/../.
$ cd $MOLBY/../ruby-2.0.0-p353

If you use gcc 4.6 or later, comment out the following line in cygwin/GNUmakefile.in
#  DLLWRAP += -mno-cygwin
(gcc 4.x deprecates the -mno-cygwin option, and from 4.6 it causes 'unrecognized option' error.)

$ ./configure --prefix=$PWD/msw-build --disable-shared --with-ext=date --disable-install-rdoc --with-static-linked-ext
$ make && make install
$ cp enc/libenc.a enc/libtrans.a msw-build/lib  #  We need this for encoding support

The msw-build directory contains lib (which contains libmsvcrt-ruby200-static.a and libmsvcrt-rubuy200.a) and include (which contains include files). (There are also bin and share directories, but these are not used for building Molby.)
$ make clean  #  Remove configure files and intermediates; the msw-build directory remains intact

--- Old description (ruby 1.8.7) ---
Get ruby-1.8.7-p160.tar.gz from the Molby source distribution site. Unpack it, and move the resulting directory ruby-1.8.7-p160 to $HOME. Rename it to ruby-1.8.7-static.
$ cd $HOME
$ mv somewhere/ruby-1.8.7-p160.tar.gz ./
$ tar xvzf ruby-1.8.7-p160.tar.gz
$ mv ruby-1.8.7-p160 ruby-1.8.7-static

Patch the Ruby source.
$ cd $HOME/ruby-1.8.7-static
$ patch --backup -p1 < $MOLBY/ruby-1.8.7-p160-tn.patch
($MOLBY is the location of the Molby source.)

Build Ruby with --disable-shared option.
$ ./configure --disable-shared --disable-thread
$ make

(iv) CLAPACK

Get clapack-3.1.1.1.tar.gz from the CLAPACK official site (http://www.netlib.org/clapack/) and unpack it. (clapack-3.2.1 may cause trouble because it uses symbolic links.)
$ cd $MOLBY/..
$ mv somewhere/clapack-3.1.1.1.tgz ./
$ tar xvzf clapack-3.1.1.1.tgz

Patch the clapack source.
$ patch -p0 <$MOLBY/clapack-3.1.1.1-mingw.patch

Build CLAPACK.
$ cd CLAPACK-3.1.1.1
$ make

In my case, uninit.c caused an error. It turned out that float.h in GCC needed modification. In c:/tdm-gcc-32-471/lib/gcc/mingw32/4.7.1/include/float.h, a line "#include_next <float.h>" was inserted just before the last "#endif".

Modify libf2c.a, so that the 'main' entry does not interfere the main program.
$ cd F2CLIBS
$ cp libf2c.a libf2c_nomain.a
$ ar d libf2c_nomain.a main.o
$ cd ..

Copy the library and header files to CLAPACK-3.1.1.1/lib
$ mkdir lib
$ cp F2CLIBS/libf2c_nomain.a lib
$ cp blasMinGW.a lib/libblasMinGW.a
$ cp lapackMinGW.a lib/liblapackMinGW.a

(v) FFTW

Get fftw-3.3.2.tar.gz and unpack it. Move the resulting directory fftw-3.3.2 to $MOLBY/../. $ ./configure --prefix=$PWD/msw-build --disable-fortran CFLAGS="-O2"
$ make
$ make install  #  sudo is not necessary

(vi) Inno Setup 5

Install Inno Setup 5 (http://www.jrsoftware.org/isinfo.php). This is necessary to create the Molby Installer.

(vii) Build

Now you can start building Molby! Go to the project directory and do make.
$ cd somewhere/Molby/msw-build
$ make
$ make setup  #  To make the installer


2010.1.21.
2010.1.31. Added notice on AmberTools1.3
2010.4.29. Update description for MinGW/MSYS
2011.8.3.  Added notice on static linking of libgfortran for Mac
2012.11.23. Added notice on FFTW

Toshi Nagata