PBS job script for Parallel OPENMPI

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.