MBG wiki: Running one of the Gromacs' benchmarks

Download the gromacs lysozyme benchmark files.tar.gz.

Create a clean directory in /work/tmp and extract the files :
- cd /work/tmp
- mkdir gtest
- cd gtest/
- mv ~/gromacs_lysozyme_benchmark_files.tar.gz ./ (assuming the browser saved the file in your home directory).
- gunzip gromacs_lysozyme_benchmark_files.tar.gz
- tar xvf gromacs_lysozyme_benchmark_files.tar
- rm gromacs_lysozyme_benchmark_files.tar

Have a look at the system you will be simulating : vmd conf.gro

Preparation step (assuming you will run it on two processors) :

/usr/local/gromacs/i686-pc-linux-gnu/bin/grompp -f pme.mdp -c conf.gro -p topol.top -po mdout.mdp -shuffle -sort -np 2

Prepare a submission script for SGE, say SGE.sh :

#!/bin/tcsh -f
#

#
# The name of the job (MPI_job) ...
#
#$ -N GROtest

#
# The parallel environment (mpi_fast) and number of processors (9) ...
# 
#$ -pe mpi_fast 2

#
# The version of MPICH to use, transport protocol & a trick to delete cleanly
# running MPICH jobs ...
#
#$ -v MPIR_HOME=/usr/local/mpich-ssh
#$ -v P4_RSHCOMMAND=rsh
#$ -v MPICH_PROCESS_GROUP=no

#
# Nodes that can server as master queues
# 
#$ -masterq pc01.q,pc02.q,pc03.q,pc04.q,pc05.q,pc06.q,pc07.q,pc08.q,pc09.q,pc10.q,pc11.q,pc12.q,pc13.q,pc14.q,pc16.q

#
# Execute from the current working directory ...
#
#$ -cwd

#
# Standard error and output should go into the current working directory ...
#
#$ -e ./
#$ -o ./

echo "Got $NSLOTS slots."

$MPIR_HOME/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines /usr/local/gromacs/i686-pc-linux-gnu/bin/mdrun -s topol.tpr -o traj.trr -c confout.gro -e ener.edr -g md.lot

Run it : qsub SGE.sh followed by several qstat commands to confirm that the job started.

The Gromacs manual is available via the cluster's homepage (documents → computational biology → molecular dynamics).