Useful PBS scripts

If you have put some effort into writing a PBS job script for a particular type of job, please consider adding it here.

Job script with signal handler

# This is an example PBS job script that can carry out an action to clean up
# after itself when the queueing system terminates the job. You could use it to
# make your code checkpoint or similar.


#PBS -q s4
#PBS -l walltime=2:00:00

WD=/scratch/cen1001/work
OUT=$WD/output

# A shell function to clean up after an imaginary job. Replace with whatever's
# appropriate for your job.
cleanup() {
    cp $OUT /home/cen1001 && rm $OUT
}

# This function gets called when PBS tells your job to exit. PBS gives a job 60
# seconds to run its exit handler and then terminates it, so whatever this does
# must happen in less than 60 seconds.
exithandler() {
    echo "Job was killed" >> $OUT
    cleanup
    exit
}

trap exithandler SIGTERM

# The main script starts here

mkdir -p $WD

# do some busy work that generates output
i=0
while [ $i -lt 100 ]
do
 echo $i >> $OUT
 sleep 2
 i=$((i+1))
done

# call the cleanup function
cleanup

# get our PBS stats
qstat -f $PBS_JOBID