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

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|Short queue with 1 hour time limit
|Short queue with 1 hour time limit

Revision as of 11:38, 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

The different queues available

Single node jobs

Queue Name Max cores Max nodes running Max time Description
veryshort 28 4 00:15:00 Very short queue with 15 minute time limit
short 28 2 01:00:00 Short queue with 1 hour time limit
medium 28 2 08:00:00 Medium queue with 8 hour time limit
long 28 1 48:00:00 Long queue with 48 hour time limit
verylong 14 1 96:00:00 Long queue with 96 hour time limit

  • A useful Torque tutorial can be found at this link.