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    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:

    #!/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 jc123456@jcu.edu.au
    
    echo "------------------------------------------------------"
    echo " This job is allocated 1 cpu on "
    cat $PBS_NODEFILE
    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
    

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

    qsub pbsjob

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

    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:

    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.

    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

    #!/bin/bash
    #PBS -c s
    #PBS -j oe
    #PBS -m ae
    #PBS -N jobarray
    #PBS -M jc123456@jcu.edu.au
    #PBS -l walltime=9:00:00
    
    cd $PBS_O_WORKDIR
    source /etc/profile.d/modules.sh
    module load matlab
    matlab -r myjob$PBS_ARRAYID.m
    

    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

    #!/bin/bash
    #PBS -c s
    #PBS -j oe
    #PBS -m ae
    #PBS -N jobname
    #PBS -M jc123456@jcu.edu.au
    #PBS -l walltime=1000:00:00
    #PBS -l nodes=1:ppn=8:pmem=4gb
    
    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.m &
    matlab -r myjob2.m &
    matlab -r myjob3.m &
    matlab -r myjob4.m &
    matlab -r myjob5.m &
    matlab -r myjob6.m &
    matlab -r myjob7.m &
    matlab -r myjob8.m &
    wait    # Wait for background jobs to finish.
    

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

    qsub pbsjob

    Note: The echo commands in the PBS script example above are informational only.

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