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Example 1:

The following PBS script requests 1 CPU core, 2GB of memory, and 24 hours of walltime for the running of "paup -n input.nex".

#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N JobName1
#PBS -M FIRSTNAME.LASTNAME@jcu.edu.au
#PBS -l walltime=24:00:00
#PBS -l select=1:ncpus=1:mem=2gb

cd $PBS_O_WORKDIR
shopt -s expand_aliases
source /etc/profile.d/modules.sh
echo "Job identifier is $PBS_JOBID"
echo "Working directory is $PBS_O_WORKDIR"

module load paup
paup -n input.nex

If the file containing the above content has a name of JobName1.pbs, you simply execute qsub JobName1.pbs to place it into the queueing system.

Example 3:

The following PBS script requests 20 CPU cores, 60GB of memory, and 10 days of walltime for running of an MPI job.

#!/bin/bash
#PBS -c s
#PBS -j oe
#PBS -m ae
#PBS -N jobnameJobName3
#PBS -l pmem=5gbM FIRSTNAME.LASTNAME@my.jcu.edu.au
#PBS -l nodeswalltime=1:ppn=1240:00:00
#PBS -l walltimeselect=1681:00:00
#PBS -M your.name@jcu.edu.au

ncpu=`wc -l $PBS_NODEFILE | awk '{print $1}'`
echo "------------------------------------------------------"
echo " This job is allocated "$ncpu" CPU cores on "
cat $PBS_NODEFILE | uniq
echo "------------------------------------------------------"
echo "PBS: Submitted to $PBS_QUEUE@$PBS_O_HOST"
echo "PBS: Working directory is $PBS_O_WORKDIR"
echo "PBS: ncpus=20:mem=60gb

cd $PBS_O_WORKDIR
shopt -s expand_aliases
source /etc/profile.d/modules.sh
echo "Job identifier is $PBS_JOBID"
echo "Working directory is $PBS_O_WORKDIR"

module load migrate
module load mpi/openmpi
mpirun -np 20 -machinefile $PBS_NODEFILE migrate-n-mpi ...

If the file containing the above content has a name of JobName3.pbs, you simply execute qsub JobName3.pbs to place it into the queueing system.

Example 2:

The following PBS script requests 8 CPU cores, 32GB of memory, and 3 hours of walltime for running of 8 MATLAB jobs in parallel.

#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N JobName2
#PBS -M FIRSTNAME.LASTNAME@my.jcu.edu.au
#PBS -l walltime=3:00:00
#PBS -l select=1:ncpus=8:mem=32gb

cd $PBS_O_WORKDIR
shopt -s expand_aliases
source /etc/profile.d/modules.sh
echo "Job identifier is $PBS_JOBID"
echo "PBS:Working Jobdirectory name is $PBS_JOBNAMEO_WORKDIR"
echo "------------------------------------------------------"
 
cd $PBS_O_WORKDIR
source /etc/profile.d/modules.sh
module load paup
paup -n input.nex

To submit the job for execution on a HPRC compute node simply enter the command:

qsub pbsjob

Using Job Arrays

module load matlab
matlab -r myjob1 &
matlab -r myjob2 &
matlab -r myjob3 &
matlab -r myjob4 &
matlab -r myjob5 &
matlab -r myjob6 &
matlab -r myjob7 &
matlab -r myjob8 &
wait    # Wait for background jobs to finish.

If the file containing the above content has a name of JobName2.pbs, you simply execute qsub JobName2.pbs to place it into the queueing system.

Example 4:

The following PBS script request uses job arrays. If you aren't proficient with bash scripting, using job arrays could be painful. The example below has each sub-job requesting 1 CPU core, 1 GB of memory, and 80 minutes of walltime.

#!/bin/bash
#PBS -c s
#PBS -j oe
#PBS -m ae
#PBS -N jobarrayArrayJob
#PBS -M yourFIRSTNAME.name@jcuLASTNAME@jcu.edu.au
#PBS -l pmem=2gbwalltime=1:20:00
#PBS -l walltimeselect=91:00:00ncpus=1:mem=1gb

cd $PBS_O_WORKDIR
shopt -s expand_aliases
source /etc/profile.d/modules.sh

module load matlab
matlab -r myjob$PBS_ARRAYID

Issuing the command

qsub -S /bin/bash -t 1-8 pbsjob

will see 8 jobs run under one major identifier. To view status of individual jobs in the array. The above example is identical (in terms of what jobs would be executed) to the one in the "Do It Yourself" section below.

Chances are you may need more advanced features of the scripting language than what is shown above. HPRC staff will endeavour to provide assistance with job arrays, if requested.

Do It Yourself

There are several legitimate reasons for wanting to run multiple single processor jobs in parallel within a single PBS script. For example, you may want to run 8 MATLAB jobs which require a toolbox that only has 4 licensed users. Only 1 MATLAB license is checked out if all 8 jobs are run on the same system. An example PBS script to do this task would look like

If the file containing the above content has a name of ArrayJob.pbs and you will be running 32 sub-jobs, you simply use qsub -t 1-32 ArrayJob.pbs to place it into the queueing system.

Note: I haven't done extensive testing of job arrays.