wiki.chpc.ac.za

#!/bin/sh
#PBS -N eric.job
#PBS -l select=1:ncpus=12:mpiprocs=12
#PBS -l walltime=1:00:00
#PBS -q workq
#PBS -m abe
#PBS -o /export/home/username/amber/amber12/eric.out
#PBS -e /export/home/username/amber/amber12/eric.err
#PBS -M email@mail.com

cd $PBS_O_WORKDIR

pwd

source /etc/profile.d/modules.sh
module add intel-XE/13.0 openmpi/openmpi-1.6.5-intel amber/12

echo "My job starts here"
date

exe=sander.MPI

nproc=`cat $PBS_NODEFILE|wc -l`
time mpirun -np $nproc -machinefile $exe -O -i mdin -o mdout -p prmtop -c inpcrd
echo "My job ends here"
date