{composition-setup}
{deck:id=PBS}
    {card:label=PBS Directives}
The filenames, paths, email addresses, and some values below are things you will probably _need_ to change.  In some cases, values/names have been used to demonstrate possibilities that you could employ (in a slightly different way).  Apart from the {{-l}} options, no option should appear on multiple lines.

||Directive(s)||Description of purpose||
|{{#PBS -c n}}
{{#PBS -c s}}
{{#PBS -c enabled}}|No checkpointing to be performed.
Checkpointing is to be done on a job at {{pbs_mom}} shutdown.
Checkpointing is allowed but must be explicitly invoked by a {{qhold}} or {{qchkpt}} command.|
|{{#PBS -d /fast/jc123456}}|Defines the working directory path to be used for the job.|
|{{#PBS -j oe}}
{{#PBS -o /tmp/output.$PBS_O_JOBID}}|Merge standard output and standard error streams into the named file.|
|{{#PBS -l pmem=8gb}}
{{#PBS -l nodes=1:ppn=2}}
{{#PBS -l walltime=24:00:00}}|Request that 4GB of memory be reserved for the batch job.
Request that 2 CPU cores on 1 host be reserved for the batch job.
Advise the scheduler that this job will have completed within 24 hours.|
|{{#PBS -l nodes=2 -I -X}}|Request 2 CPU cores that can be used for interactive job(s).
*Note*:  Our 2 login nodes each provide 18 CPU cores and 64GB of memory for running interactive jobs (without {{qsub}}).|
|{{#PBS -m ae}}
{{#PBS -M john.doe\@jcu.edu.au}}
{{#PBS -M joe.blogg\@my.jcu.edu.au}}|Send mail at batch job abort/exit to the Email address provided.|
|{{#PBS -N job\_name}}|Assign a name ({{job\_name}}) to the batch job|
|{{#PBS -q normal}}
{{#PBS -q bigmem}}|Specify the queue into which your job will be placed.
*Note*:  The {{bigmem}} queue targets two nodes only, long delays can be experienced before your job is run.|
|{{#PBS -V}}|Export environment variables to the batch job|

While defaults exist for many options, HPC staff ask researchers to specify CPU core, memory, and walltime requirements as accurately as possible.

A {{-W}} option can be used for more complicated tasks such as job dependencies, stage-in and stage-out.  Researchers may wish to consult with HPC staff with regard to use of the {{-W}} options.  A {{man qsub}} will provide more information and more options than provided above.

Users interested in protecting there job runs with checkpointing should realize that this feature comes at a cost (I/O operations).  Checkpoint restart of a job (using BLCR) will not work for all job types.  HPC staff advise use to test this feature on a _typical_ job first before using it on other similar jobs.  Generally speaking, checkpointing will only be a real benefit to jobs that run for over a week.
    {card}

    {card:label=PBS Variables}
The variables listed in the table below are _commonly_ used within a PBS script file.

||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|
|{{PBS_O_PATH}}     |Path variable used to locate executables within the job script|

*Note*:  On multi-core systems, a node (line in {{PBS_NODEFILE}}) will identify the hostname and a CPU core.
    {card}

    {card: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:
{noformat}
#!/bin/bash
#PBS -c s
#PBS -j oe
#PBS -m ae
#PBS -N jobname
#PBS -l pmem=5gb
#PBS -l walltime=500:00:00
#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: Job identifier is $PBS_JOBID"
echo "PBS: Job name is $PBS_JOBNAME"
echo "------------------------------------------------------"
 
cd $PBS_O_WORKDIR
source /etc/profile.d/modules.sh
module load paup
paup -n input.nex
{noformat}
To submit the job for execution on a HPRC compute node simply enter the command:
{noformat}qsub pbsjob{noformat}
If you know this job will require more than 4GB but less than 8GB of RAM, you could use the command:
{noformat}qsub -l nodes=1:ppn=2 pbsjob{noformat}
If you know this job will require more than 8GB but less than 16GB of RAM, you could use the command:
{noformat}qsub -l nodes=1:ppn=8 pbsjob{noformat}

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.
    {card}

    {card:label=Multiple 1-CPU Jobs}
h3. Using Job Arrays
Users with a knowledge of shell scripting (e.g., {{bash}}) may choose to take advantage of job arrays.  This feature significantly reduces load on our Torque/Maui server (compared to lots of individual job submissions).  The example below (assume the file name is {{pbsjob}}), will only be useful as a guide
{noformat}
#!/bin/bash
#PBS -c s
#PBS -j oe
#PBS -m ae
#PBS -N jobarray
#PBS -M your.name@jcu.edu.au
#PBS -l pmem=2gb
#PBS -l walltime=9:00:00

cd $PBS_O_WORKDIR
source /etc/profile.d/modules.sh
module load matlab
matlab -r myjob$PBS_ARRAYID
{noformat}
Issuing the command
{noformat}qsub -S /bin/bash -t 1-8 pbsjob{noformat}
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.

h3. 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
{noformat}
#!/bin/bash
#PBS -c s
#PBS -j oe
#PBS -m ae
#PBS -N jobname
#PBS -M your.name@jcu.edu.au
#PBS -l walltime=1000:00:00
#PBS -l nodes=1:ppn=8
#PBS -l pmem=32gb

ncpu=`wc -l $PBS_NODEFILE`
echo "------------------------------------------------------"
echo " This job is allocated "$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: Job identifier is $PBS_JOBID"
echo "PBS: Job name is $PBS_JOBNAME"
echo "------------------------------------------------------"

cd $PBS_O_WORKDIR
source /etc/profile.d/modules.sh
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.
{noformat}
To submit the job for execution on a HPRC compute node simply enter the command:
{noformat}qsub pbsjob{noformat}

*Note*: The {{echo}} commands in the PBS script example above are informational only.
    {card}

    {card:label=MPI/PVM/OpenMP Jobs}
{noformat}
#!/bin/bash
#PBS -V
#PBS -m abe
#PBS -N migrate
#PBS -l pmem=62GB
#PBS -l nodes=1:ppn=24
#PBS -l walltime=240:00:00
#PBS -M your.email@my.jcu.edu.au
cd #PBS_O_WORKDIR
module load openmpi
module load migrate
mpirun -np 24 -machinefile $PBS_NODEFILE migrate-n-mpi ...
{noformat}
    {card}
{deck}