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Gromacs 3.3 Installation

posted Jun 7, 2011, 2:26 PM by Dong Xu
wget ftp://ftp.gromacs.org/pub/prerequisite_software/fftw-3.0.1.tar.gz

Or use system fftw installed from yast2

tar xzf Arch/fftw-3.0.1.tar.gz
tar xzf Arch/gromacs-3.3.1-062107.tgz
cd fftw-3.0.1/
./configure --enable-float --enable-threads --enable-fortran \
 --enable-type-prefix --prefix=/home/rok/pkg/Gromacs/fftw| tee
config-062107.log
make
make install

make distclean
./configure --enable-threads --enable-fortran --enable-type-prefix \
 --prefix=/home/rok/pkg/Gromacs/fftw| tee -a config-062107.log
make && make install

cd ../gmx
export CPPFLAGS=-I/home/rok/pkg/Gromacs/fftw/include
export LDFLAGS=-L/home/rok/pkg/Gromacs/fftw/lib
export LDFLAGS="-i-static -L/home/rok/pkg/Gromacs/fftw/lib"
./configure --prefix=/home/rok/pkg/Gromacs/bin
make && make install
make distclean
export MPICC=/usr/local/topspin/mpi/mpich/bin/mpicc.i
./configure --prefix=/home/rok/pkg/Gromacs/bin  --program-suffix=-mpi \
 --enable-mpi | tee configure-mpi.log

vim Makefile
make mdrun
make install-mdrun



== SGE script ==

#!/bin/bash
#
#$ -cwd
#$ -j y
#$ -S /bin/bash
#$ -pe mpich 8
#
#$ -l h_rt=01:00:00


echo Running on host `hostname`
echo Directory is `pwd`
echo This job runs on the following processors:
cat $TMPDIR/machines
echo This job has allocated $NSLOTS processors

cd /home/sjlee/Your_Working_Dir

export MDRUN=/home/sjlee/gromacs-3.3.1/bin/mdrun-mpi
export MPIRUN=/opt/mpich/intel/bin/mpirun

$MPIRUN -v -machinefile $TMPDIR/machines -nolocal -np $NSLOTS \
 $MDRUN -v -nice 0 -np $NSLOTS -s eq1.tpr

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