Using the PBS / Torque queueing environment

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:

#!/bin/bash
#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 bowtie2-2.3.4.1
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 memory	Max time	Description
veryshort	28	4	64 GB	00:15:00	Very short queue with 15 minute time limit
short	28	2	64 GB	01:00:00	Short queue with 1 hour time limit
medium	28	2	64 GB	08:00:00	Medium queue with 8 hour time limit
long	28	1	64 GB	48:00:00	Long queue with 48 hour time limit
verylong	14	1	64 GB	96:00:00	Long queue with 96 hour time limit
bigmem	24	2	256 GB	48:00:00	Long queue with 48 hour time limit
massivemem	24	1	1024 GB	48:00:00	Long queue with 48 hour time limit

Multi-node jobs

Queue Name	Max cores	Max nodes running	Max memory	Max time	Description
wide	28	2	128 GB	24:00:00	Queue to enable MPI-type jobs with up to 56 cores with 48 hour time limit
verywide	28	4 128 GB	08:00:00	Queue to enable MPI-type jobs with up to 112 cores with 24 hour time limit

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