GROMACS 4.5.5, OpenMPI 1.6, And FFTW 3.3.2 Compilation Under Mountain Lion (OSX 10.8) With XCode (And A Little Help From Homebrew)

Minus a few glitches easily fixed with the right software, this build wasn’t bad at all (and thanks to Adam Lindsay for the title catch).

Now sitting in front of a new Core i7 MacBook Pro, one of the first compilations I wanted to have finished for new projects was GROMACS 4.5.5. As my procedure for compiling GROMACS 3.3.3 had been a highly-traveled page, I wanted to provide a brief summary of my successful 4.5.5 compilation.

A Few Piece Of Info

1. XCode

This used to be disc-download and install, now it’s available as a free download from the App Store (1.57 GB download, so plan to do something else while you wait for the download).

2. Homebrew

Having Homebrew installed in Mountain Lion made the installation of FFTW easy and OpenMPI trivial once gfortran was equally trivially installed. Therefore, to make your life easier, I can’t recommend a Homebrew installation enough. For additional install tweaks, I followed the following page: gist.github.com/1860902

Installation Procedure

1. Download gromacs 4.5.5

…and place it in your home folder (will go to Downloads most likely, drag it to your home folder for ease of building).

2. Extract into your home holder

…with a double-click, making ~/gromacs-4.5.5.

3. brew install fftw

With the install of Homebrew, you’ll simply run the following from a terminal window and produce the following output:

brew install fftw

==> Downloading http://www.fftw.org/fftw-3.3.2.tar.gz
######################################################################## 100.0%
==> ./configure --enable-single --enable-sse --enable-shared --disable-debug 
--prefix=/usr/local/Cellar/fftw/3.3.2 --enable-threads --disable-fortran
==> make install
==> make clean
==> ./configure --enable-sse2 --enable-shared --disable-debug 
--prefix=/usr/local/Cellar/fftw/3.3.2 --enable-threads --disable-fortran
==> make install
==> make clean
==> ./configure --enable-long-double --enable-shared --disable-debug 
--prefix=/usr/local/Cellar/fftw/3.3.2 --enable-threads --disable-fortran
==> make install
/usr/local/Cellar/fftw/3.3.2: 34 files, 13M, built in 2.7 minutes

4. brew install gfortran

If you don’t install gfortran FIRST and try to install OpenMPI, you’ll get the following error in Homebrew:

==> Downloading http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.tar.bz2
######################################################################## 100.0%
Error: This formula requires a fortran compiler, but we could not find one by
looking at the FC environment variable or searching your PATH for `gfortran`.
Please take one of the following actions:

  - Decide to use the build of gfortran 4.2.x provided by Homebrew using
        `brew install gfortran`

  - Choose another Fortran compiler by setting the FC environment variable:
        export FC=/path/to/some/fortran/compiler
    Using an alternative compiler may produce more efficient code, but we will
    not be able to provide support for build errors.

So don’t. Installing gfortran will produce the following:

brew install gfortran

==> Downloading http://r.research.att.com/tools/gcc-42-5666.3-darwin11.pkg
######################################################################## 100.0%
==> Installing gfortran 4.2.4 for XCode 4.2 (build 5666) or higher
==> Caveats
Brews that require a Fortran compiler should not use:
  depends_on 'gfortran'

The preferred method of declaring Fortran support is to use:
  def install
    ...
    ENV.fortran
    ...
  end

==> Summary
/usr/local/Cellar/gfortran/4.2.4-5666.3: 86 files, 72M, built in 39 seconds

5. brew install openmpi

This is what allows you to use all cores on your machine and is not in the default XCode install.

brew install openmpi

==> Downloading http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.tar.bz2
Already downloaded: /Library/Caches/Homebrew/open-mpi-1.6.tar.bz2
==> Using Homebrew-provided fortran compiler.
This may be changed by setting the FC environment variable.

==> ./configure --prefix=/usr/local/Cellar/open-mpi/1.6 --enable-ipv6
==> make all
==> make install
/usr/local/Cellar/open-mpi/1.6: 674 files, 21M, built in 5.9 minutes

6. cd gromacs-4.5.5

7. ./configure –enable-float –enable-mpi

You’ll produce output such as found in: 2012august29_gromacs455_configure.txt

You’ll also get two odd errors at the end of the ./configure run that do not affect the rest of the procedure:

./configure --enable-float --enable-mpi

...
./configure: line 29242: sort: No such file or directory
./configure: line 29239: sed: No such file or directory

So ignore them.

NOTE: If you’ve been going by my 3.3.3 procedure and used…

./configure --enable-mpi --enable-double

You’ll get the following error when you try to run make:

Making all in include
Making all in .
make[2]: Nothing to be done for `all-am'.
Making all in types
make[2]: Nothing to be done for `all'.

...

/bin/sh ../../libtool --tag=CC   --mode=compile mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\"   -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT genborn_sse2_double.lo -MD -MP -MF .deps/genborn_sse2_double.Tpo -c -o genborn_sse2_double.lo genborn_sse2_double.c
 mpicc -DHAVE_CONFIG_H -I. -I../../src -I/usr/include/libxml2 -I../../include -DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -O3 -fomit-frame-pointer -finline-functions -Wall -Wno-unused -msse2 -funroll-all-loops -std=gnu99 -MT genborn_sse2_double.lo -MD -MP -MF .deps/genborn_sse2_double.Tpo -c genborn_sse2_double.c  -fno-common -DPIC -o .libs/genborn_sse2_double.o
genborn_sse2_double.c:931: internal compiler error: Segmentation fault: 11
Please submit a full bug report,
with preprocessed source if appropriate.
See  for instructions.
make[3]: *** [genborn_sse2_double.lo] Error 1
make[2]: *** [all-recursive] Error 1
make[1]: *** [all] Error 2
make: *** [all-recursive] Error 1

So don’t do that, either. The proper flag is the enable-float.

8. make

This will produce the output available for download at: 2012august29_gromacs455_make.txt

9. make install

This will produce the output available for download at: 2012august29_gromacs455_make_install.txt

10. make links

This will produce the short piece of output reproduced below.

cd /usr/local/gromacs/bin && programs=`ls` && cd /usr/local/bin && \
	for i in $programs; do \
	   (test ! -f $i && ln -s /usr/local/gromacs/bin/$i . ; exit 0); \
	done

And with that, you should be able to run all programs from a terminal window.

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