AFtest.pbs

#!/bin/bash
### set the number of nodes
### set the number of PEs per node
#PBS -l nodes=1:ppn=2:xe
### set the wallclock time
#PBS -l walltime=00:10:00
### set the job name
#PBS -N AFtest
### set the job stdout and stderr
#PBS -e $PBS_JOBID.err
#PBS -o $PBS_JOBID.out
### set email notification
##PBS -m bea
##PBS -M <EmailId>@illinois.edu

# NOTE: lines that begin with "#PBS" are not interpreted by the shell but ARE
# used by the batch system, wheras lines that begin with multiple # signs,
# like "##PBS" are considered "commented out" by the batch system
# and have no effect.

# If you launched the job in a directory prepared for the job to run within,
# you'll want to cd to that directory
# [uncomment the following line to enable this]
cd $PBS_O_WORKDIR

# Alternatively, the job script can create its own job-ID-unique directory
# to run within.  In that case you'll need to create and populate that
# directory with executables and perhaps inputs
# [uncomment and customize the following lines to enable this behavior]
# mkdir -p /scratch/sciteam/$USER/$PBS_JOBID
# cd /scratch/sciteam/$USER/$PBS_JOBID
# cp /scratch/job/setup/directory/* .

# To add certain modules that you do not have added via ~/.modules
. /opt/modules/default/init/bash # NEEDED to add module commands to shell

#Load HDF5 1.8.16 
module load cray-hdf5/1.8.16

#To load HDF5 1.10, comment out the above line and uncomment out the following line
#module load cray-hdf5/1.10.2

# export APRUN_XFER_LIMITS=1  # to transfer shell limits to the executable

### launch the application
### redirecting stdin and stdout if needed

#To run the AF tool, needs to add the GDAL library to the LD_LIBRARY_PATH
#Specify the GDAL library at your own system
export LD_LIBRARY_PATH="/projects/sciteam/jq0/TerraFusion/gdal/lib:$LD_LIBRARY_PATH"
# if run with OMP
#export OMP_NUM_THREADS=2
#aprun -n 1 -d 2  ./AFtool ./inputParameters_MISR2MODIS.txt
# run serial
aprun -n 1  ./AFtool ./inputParameters_MISR2MODIS.txt

### For more information see the man page for aprun