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Important:  Most software will only consume 1 CPU core - e.g., requesting 8 CPU cores for a PAUP job blocks other people using the unused 7 CPU cores.  Example 1 below would likely be the most users should be basing their job scripts from.  If in doubt, contact HPRC staff.


For more information about PBSPro please click to see guide.

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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".

No Format
#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N JobName1
#PBS -l walltime=24:00:00
#PBS -l select=1:ncpus=1:mem=2gb
#PBS -M FIRSTNAME.LASTNAME@jcu.edu.au

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.

No Format
#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N JobName3
#PBS -l walltime=240:00:00
#PBS -l select=1:ncpus=20:mem=60gb
#PBS -M FIRSTNAME.LASTNAME@my.jcu.edu.au

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.


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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.

No Format
#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N JobName2
#PBS -l walltime=3:00:00
#PBS -l select=1:ncpus=8:mem=32gb
#PBS -M FIRSTNAME.LASTNAME@my.jcu.edu.au

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 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 20 minutes of walltime.

No Format
#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N ArrayJob
#PBS -l pmem=1gb
#PBS -l walltime=20:00
#PBS -l select=1:ncpus=1:mem=1gb
#PBS -M FIRSTNAME.LASTNAME@jcu.edu.au

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

module load matlab
matlab -r myjob$PBS_ARRAYID

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.


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