Difference between revisions of "PBS job script for Parallel OPENMPI"
From Computational Biophysics and Materials Science Group
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Latest revision as of 12:11, 31 July 2014
Sample job script for Parallel OPENMPI
#PBS -S /bin/bash #PBS -N namd_outf_unsym #PBS -l nodes=4 ppn=16 #PBS -m e # NAMD_PATH=/share/apps/NAMD_2.9_Linux-x86_64-multicore NAMD=$NAMD_PATH/namd2 CHARMRUN=$NAMD_PATH/charmrun cd /share/data/kevin/BAR-PH/raw/unsym/oforce_qsub cat $PBS_NODEFILE >> /tmp/nodefile.$$ NP=`cat $PBS_NODEFILE | wc -l` NN=`cat $PBS_NODEFILE | sort | uniq | tee /tmp/nodes.$$ | wc -l` mpirun -n $NP $NAMD NPT-outputf.namd > ./output/unsym_outf.log wait
Save the above script to a job.sh,
qsub job.sh
submits the job. Simple as it seems.
