[gmx-users] compilation of gmx-4.0.2

Xavier Periole X.Periole at rug.nl
Wed Nov 12 10:49:39 CET 2008

Thanks Mark and Justin,

I got the script of installation of gromacs3.3.1 from the system
manager. It works so far ... I attached it at the end (note: it is for
double precision), it might help others.

The mpicc was not found as mpcc was used instead.

# 32 or 64 bit version

export OBJECT_MODE=64
# C compiler

export CC='xlc_r -q64 -qsuppress=1506-229 '
export CFLAGS='-O3 -qhot -qarch=auto -qtune=auto -qmaxmem=-1'

# C++ compiler

export CXX='xlC_r -q64'
export CXXFLAGS='-O3 -qhot -qarch=auto -qtune=auto -qmaxmem=-1'

# Fortran compiler

export FC='xlf95_r -q64'
export FFLAGS='-O3 -qhot -qarch=auto -qtune=auto -qmaxmem=-1'

# MPI compilers

export MPICC='mpcc -q64 -compiler xlc_r'
export MPIF90='mpfort -q64 -compiler xlf95_r'

# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries in a
# nonstandard directory <lib dir>
# headers in a nonstandard directory <include dir>
# CPP C preprocessor

echo "Rootdir: $rootdir"
export MP_HOSTFILE=$rootdir/hostfile
cat > ${MP_HOSTFILE} << EOF

# make fftw3 available

echo "Loading ffwt3 version"
module load fftw3


mkdir -p ${builddir} || exit

cd ${dir} || exit

echo "Configuring double precision mpi parallel version"
echo "./configure --prefix=${builddir} --program-suffix="_mpi" --without-x 
--disable-float --enable-mpi"
./configure --prefix=${builddir} --program-suffix="_mpi" --without-x 
--disable-float --enable-mpi
make mdrun
make install-mdrun
---------end script-----------------
On Wed, 12 Nov 2008 11:20:22 +1100
  Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Xavier Periole wrote:
>> Dears,
>> my turn to ask a stupid question:
>> I am trying to install gmx402 on a IBM pSeries 575
>> CPUs: dual core IBM Power6
>> when running the command:
>> ./configure --enable-mpi --prefix==/home/XXXXX/gmx402/
>> I run very into the error:
>> .....
>> .....
>> checking size of int... configure: error: cannot compute sizeof (int)
>> See config.log for more details.
>> config.log did not help much.
>> Is this a known issue? I had never seen it.
> Yep there's at least one known cause. By default, configure assumes that you 
>are building on the same architecture on which your target will run. So when 
>testing for machine properties it can use either successful compilation or 
>successful execution. However in a cross-compilation environment, the latter 
>will fail.
> There are several work-arounds. There's a tool called yodconfigure that I 
>understand takes care of much of such issues, but I'm not sure how. Or you 
>can trick configure into running code on the target machine somehow - this is 
>tricky with GROMACS, because in src/gmxlib/nonbonded/nb_kernel you need to 
>make and run on the build machine to create the generic kernels. Or you can 
>tell configure you are cross-compiling with the --build and --host flag, so 
>that it uses only successful compilation as a diagnostic tool.
> I'm surprised that lack of mpicc caused such a problem and didn't cause a 
>problem when testing mpicc.
> Mark
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XAvier Periole - PhD

- Molecular Dynamics Group -
Computation and NMR
University of Groningen
The Netherlands

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