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.
Best,
XAvier
------------script------------
# 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
rootdir=$PWD
echo "Rootdir: $rootdir"
export MP_HOSTFILE=$rootdir/hostfile
echo $MP_HOSTFILE
cat > ${MP_HOSTFILE} << EOF
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
localhost
EOF
# make fftw3 available
echo "Loading ffwt3 version"
module load fftw3
builddir=$PWD/build-dp
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 <[EMAIL PROTECTED]> 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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