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

CPMD runscript if several nodes are needed

# PBS -q s32 

# PBS -l walltime=18:00:00

# PBS -l nodes=8:ppn=4

HERE=/home/mm695/whatever

file=dho2498_singlePoint

inpfile=${file}.inp

outfile=${file}.out

SCRATCH=/scratch/mm695/$file

nodes=`cat $PBS_NODEFILE | uniq`

for node in $nodes
 do
   rsh $node "rm -f $SCRATCH/*"
   rsh $node "rmdir $SCRATCH"
   rsh $node "mkdir $SCRATCH"
   rsh $node "cp ${HERE}/gromos*   $SCRATCH"
   rsh $node "cp ${HERE}/geom_end_of_sim.crd   $SCRATCH"
   rsh $node "cp ${HERE}/RESTART   $SCRATCH"
   rsh $node "cp ${HERE}/${inpfile}  $SCRATCH"
 done

exe=/home/mm695/SOURCE/cpmd.x

pp=/home/mm695/pseudopot

cd $SCRATCH
 
# Write out some helpful info to the output file

echo "Starting job $PBS_JOBID"
echo
echo "PBS assigned me this node:"
cat $PBS_NODEFILE
echo

mvapichwrapper  $exe $inpfile $pp > ${HERE}/${outfile}

for node in $nodes
 do
   rsh $node 'mv ${SCRATCH}/* ${HERE}'
   rsh $node 'rm -f ${SCRATCH}/*'       
   rsh $node 'rmdir /scratch/mm695/$file'
 done

qstat -f $PBS_JOBID