#PBS -S /bin/bash
#PBS -l nodes=4,walltime=1:00:00
#PBS -m abe
#PBS -M username@your.address.here
#PBS -N jobname

# Change to working directory
cd $HOME/working_directory

# Create scratch directory
mkdir -p /scratch/serial/$USER/$PBS_JOBID

# Copy data files scratch directory
cp $HOME/working_directory/data_files /scratch/serial/$USER/$PBS_JOBID

# Execute serial or mpi job
# This uses standard MPICH compiled with GNU/Pathscale located in
# /uufs/icebox/sys/pkg/mpich/std
# For executables compiled with PGI compilers, use /uufs/icebox/sys/pkg/mpich/std_pgi
mpirun -np 4 -machinefile $PBS_NODEFILE ./a.out > outputfile
# In case of using MPICH2, make sure you are setting up the environment as specified
# on our Software-MPI webpage and then:
# mpdboot -n 2 -r rsh -f $PBS_NODEFILE
# mpiexec -n 4 ./a.out > outputfile
 
# Copy files back home and cleanup
cp * $HOME/working_directory && cd .. && rm -rf /scratch/serial/$USER/$PBS_JOBID