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 -o /path/to/stdout.log
#PBS -e /path/to/stderr.log
#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

Interactive jobs

• If you need an interactive terminal session on one of the servers (e.g. to compile code, setup jobs, test jobs), you can do this by using the qsub interactive mode, for example:

> qsub -I -q queue_name -l nodes=1:ppn=1 -l walltime=01:00:00

The different queues available

Single node jobs

Queue Name	Max user jobs running	Max user cores running per job	Max memory	Max walltime	Description
short	6	28	128 GB	00:05:00	Short queue with 5 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	Very 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

Additional information

• A useful Torque tutorial can be found at this link.
• Detailed reference documentation for queue submission is available here.