Difference between revisions of "Using the PBS / Torque queueing environment"

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Much of this content has been adapted from the [http://wiki.chpc.ac.za/quick:start Quick Start Guide] at CHPC.
* A usef ul Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].

Revision as of 11:11, 11 April 2018

The main commands for interacting with the Torque environment are:

  • qstat View queued jobs.
  • qsub Submit a job to the scheduler.
  • qdel Delete one of your jobs from queue.

Job script parameters

Parameters for any job submission are specified as #PBS comments in the job script file or as options to the qsub command. The essential options for the cluster include:

#PBS -l nodes=1:ppn=14

sets the size of the job in number of processors:

nodes=N sets the number of nodes needed.

ppn=N sets the number of cores per node.

#PBS -l walltime=8:00:00

sets the total expected wall clock time in hours:minutes:seconds. Note the wall clock limits for each queue.

Example job scripts

A program using 14 cores on a single node:

#PBS -l nodes=1:ppn=14
#PBS -l walltime=8:00:00
#PBS -q normal
#PBS -m ae
#PBS -M your.email@address
module load bowtie2-
bowtie2 -x /path/to/genome -p 14 -1 /path/to/forwardreads.fastq -2 /path/to/reversereads.fastq -S /path/to/outputfile.sam

Assuming the above job script is saved as the text file run_bowtie.sh, the command to submit it to the Torque scheduler is:

> qsub run_bowtie.sh

  • A usef ul Torque tutorial can be found at this link.