wiki.chpc.ac.za

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Before running your scripts remember to run:

user@login01:~ $ module add gromacs/4.6.3

Then your job script called my_job.msub will look something like this:

#/bin/sh
#MSUB -l procs=64
#MSUB -l feature=dell
#MSUB -l walltime=10:00:00
#MSUB -m be
#MSUB -V
#MSUB -o ${HOME}/scratch5/GROMACS/stdout.txt
#MSUB -e ${HOME}/scratch5/GROMACS/stderr.txt
#MSUB -d ${HOME}/scratch5/GROMACS/
#MSUB -N MyGromacsJob
#MSUB -mb
 
NP=`cat ${PBS_NODEFILE} | wc -l`
 
EXE=mdrun
ARGS="-s input.tpr -deffnm input.tpr"
 
mpirun -np ${NP} -machinefile ${PBS_NODEFILE} ${EXE} ${ARGS}

Finally submit your job using:

user@login01:~ $ msub my_job.msub