MBG wiki: Editing 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) :
<code>
/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
</code>

* Prepare a submission script for SGE, say /SGE.sh/ :
<source>
#!/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
</source>

* 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).

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