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 kepla_k20
#PBS -m be
#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
echo "My job starts here"
date
source /etc/profile.d/modules.sh
module add intel-XE/c8000 cuda/5.0-c8000 mvapich2/c8000 amber/k20
module add amber/k20

exe=pmemd.cuda.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