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id	PBS

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label	Single 1-CPU Job

This example runs PAUP on the input file input.nex that resides in the current working directory. A file (here we'll name it pbsjob) is created with the contents:

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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. For a brief description of PBS directives provided in examples below, see the "Brief Explanation of PBS directive used in examples above" section immediately following the final example PBS script.

HPC staff should be able to assist researchers needing help with PBS scripts.

Singularity Example

The following PBS script requests 1 CPU core, 2GB of memory, and 24 hours of walltime

No Format

#!/bin/bash
#PBS -c s
#PBS -j oe
#PBS -m ae
#PBS -N jobnameJobName1
#PBS -M jc123456@jcuFIRSTNAME.LASTNAME@jcu.edu.au
#PBS -l walltime=200024:00:00
#PBS -l select=1:ncpus=1:mem=2gb

echo "------------------------------------------------------"
echo " This job is allocated 1 cpu on "
cat $PBS_NODEFILE
echo "------------------------------------------------------"
echo "PBS: Submitted to $PBS_QUEUE@$PBS_O_HOST"
echo "PBS: cd $PBS_O_WORKDIR

# Add this to all of your scripts
shopt -s expand_aliases
source /etc/profile.d/modules.sh
 
# Output some useful information about
# the job we are running
echo "Job identifier is $PBS_JOBID"
echo "Working directory is $PBS_O_WORKDIR"

# Load the container we want to use
# It is a good idea to always specify the version number 
module load R/4.1.2u1

# Run your code
R ...    # Replace ... with your arguments & options.

Module Examples

PBS

Section

Card

Single 1-CPU Job Single 1-CPU Job

Card

label	Multiple 1-CPU Jobs

Card

Multiple 1-CPU Jobs Multiple 1-CPU Jobs

Card

label	MPI/PVM/OpenMP Jobs

Card

MPI/PVM/OpenMP Jobs MPI/PVM/OpenMP Jobs

Deck of Cards

PBS

Column

width	50%

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 -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"

echo "PBS:



module load paup/4b10
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 -M FIRSTNAME.LASTNAME@my.jcu.edu.au
#PBS -l walltime=240:00:00
#PBS -l select=1: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 "

PBS:

Working

Job

directory

name

is $PBS_

JOBNAME" echo "------------------------------------------------------"

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.

Column

width	50%

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 -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 "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 80 minutes of walltime.

No Format

#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N ArrayJob
#PBS -M FIRSTNAME.LASTNAME@jcu.edu.au
#PBS -l walltime=1:20:00
#PBS -l select=1:ncpus=1:mem=1gb

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

module load

paup

matlab

paup

matlab -

n input.nex

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

No Format
qsub pbsjob

If you know this job will require more than 4GB but less than 8GB of RAM, you could use the command:

No Format
qsub -l nodes=1:ppn=2 pbsjob

If you know this job will require more than 8GB but less than 16GB of RAM, you could use the command:

No Format
qsub -l nodes=1:ppn=8 pbsjob

The reason for the special cases (latter two) is to guarantee memory resources for your job. If memory on a node is overallocated, swap will be used. Job(s) that are actively using swap (disk) to simulate memory could take more than 1000 times longer to finish than a job running on dedicated memory. In most cases, this will mean your job will never finish.

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.

Example 5:

The following script is a rework of Example 2 to use the /fast/tmp filesystem for a hyperthetical workflow that is I/O intensive. This example assumes 1 output file per job.

Note

Usage of /fast/tmp

Please make sure you first create an place all files in a folder that matches your jc number eg: jcXXXXXXXX

No Format

#!/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 "Working directory is $PBS_O_WORKDIR"

mkdir -p /fast/tmp/jc012345/myjobs
cp -a myjob1.m myjob2.m myjob3.m myjob4.m myjob5.m myjob6.m myjob7.m myjob8.m /fast/tmp/jc012345/myjobs/
pushd /fast/tmp/jc012345/myjobs

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.

cp -a out1.mat out2.mat out3.mat out4.mat out5.mat out6.mat out7.mat out8.mat $PBS_O_WORKDIR/
popd
rm -rf /fast/tmp/jc012345/myjobs

Consider the possibility that you may be running more than one workflow at any given time. Using subdirectories is a good way of segregating workflows (at a storage layer).

Brief Explanation of PBS directive used in examples above

Directive	Description of impact
`#PBS -j oe`	Merge STDOUT & STDERR streams into a single file
`#PBS -m ae`	Send an Email upon job abort/exit.
`#PBS -N ...`	Assign a meaningful name to the job (replace `...` with 1 "word" - e.g., test_job).
`#PBS -M ...`	Email address that PBSPro will use to provide job information (if desired)
`#PBS -l walltime=HH:MM:SS`	Amount of clock time that your job is likely to required.
`#PBS -l select=1:ncpus=X:mem=Ygb`	Request 1 chunk of "X CPU cores" & "Y GB of RAM". The "select=1:" is not really required as it is the default. Due to JCU cluster size, requests for more than 1 chunk should/will be rejected.

Brief Details on some extra PBS/Torque directives

Directive(s)	Description of purpose
`#PBS -d <PATH_TO_DIRECTORY>`	Sets the working directory for you job to <PATH>.
`#PBS -o <OUTPUT_FILE_PATH>`	Explicit specification of file that will hold the standard output stream from you job.
`#PBS -V`	Export environment variables to the batch job

For full details on directives that can be used, use "man qsub" on a HPC login node or look at online documentation for Torque.

PBS/Torque Variables

The following variables can be useful within your PBS job script. Some are present in the examples above.

Variable	Description
`PBS_JOBNAME`	Job name specified by the user
`PBS_O_WORKDIR`	Working directory from which the job was submitted
`PBS_O_HOME`	Home directory of user submitting the job
`PBS_O_LOGNAME`	Name of user submitting the job
`PBS_O_SHELL`	Script shell
`PBS_O_JOBID`	Unique PBS job id
`PBS_O_HOST`	Host on which job script is running
`PBS_QUEUE`	Name of the job queue
`PBS_NODEFILE`	File containing line delimited list on nodes allocated to the job (may be required for MPI jobs).
`PBS_O_PATH`	Path variable used to locate executables within the job script

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Singularity Example

Module Examples

Example 1:

Example 3:

Example 2:

Example 4:

Example 5:

Brief Explanation of PBS directive used in examples above

Brief Details on some extra PBS/Torque directives

PBS/Torque Variables