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Submitting jobs on the theory cluster

Job Submission

To submit a 4 processor job on the cluster run the following command

qsub -N jobname -pe openmpi 4 submit_gromacs.bash

where submit_gromacs.bash is the following file in your work directory

#!/bin/bash -x
echo "Directory: $PWD"
mpirun -np $NSLOTS mdrun_mpi
echo "Run is finished on host $HOSTNAME"

In addition you should check manpages man qsub and homepage of Sun Gridengine. The maximum number of cpus per job is 12 for newer nodes. Sequential jobs are submitted using command

qsub submit_script.bash