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. Most HPC users will have scripts similar to Example 1 below.
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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 |
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#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N JobName1
#PBS -l pmem=2gb
#PBS -l nodes=ncpus=1:ppnmem=12gb
#PBS -l walltime=24:00:00
#PBS -M your.name@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, 40GB of memory, and 2 days of walltime for running of an MPI job. | No Format |
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#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N JobName3
#PBS -l pmem=2gb
#PBS -l nodes=1:ppn=20
#PBS -l walltime=240:00:00
#PBS -M your.name@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 openmpi
module load migrate
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, 24GB of memory, and 3 hours of walltime for running of 8 MATLAB jobs in parallel. | No Format |
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#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N JobName2
#PBS -l pmem=3gb
#PBS -l nodes=1:ppn=8
#PBS -l walltime=3:00:00
#PBS -M your.name@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 requests 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 |
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#!/bin/bash
#PBS -j oe
#PBS -m ae
#PBS -N ArrayJob
#PBS -l pmem=1gb
#PBS -l nodes=1:ppn=1
#PBS -l walltime=20:00
#PBS -M your.name@my.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. |
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Directive(s) | Description of purpose |
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#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
Variable | Description |
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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 |
Example CPU+Memory Resource Requests
| Your requirements |
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| CPU cores | Total Memory | PBS/Torque options |
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| 1 | 1200 MB | -l nodes=1:ppn=1 -l pmem=1200mb |
| 1 | 20 GB | -l nodes=1:ppn=1 -l pmem=20gb |
| 2 | 6 GB | -l nodes=1:ppn=2 -l pmem=3gb |
| 8 | 4 GB | -l nodes=1:ppn=8 -l pmem=512mb |
| 24 | 120 GB | -l nodes=1:ppn=24 -l pmem=5gb |
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