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 -k oe
#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

If you receive an email with exit status "0", that would usually indicate that the job completed successfully.

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

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
normal	4	28	128 GB	08:00:00	Medium queue with 8 hour time limit
long	6	28	128 GB	168:00:00	Long queue with one week time limit
bigmem	3	24	750 GB	720:00:00	High memory queue with 30 day time limit
mpi	1	112	128 GB	72:00:00	Queue for mpi parallel jobs with 3 day time limit

• If you need to run MPI jobs, please advise the system administrator so that the necessary security access can be enabled for your login.
  • Both MPICH and openMPI are installed. Please select the relevant environment using the "module load" functionality.
  • The node list for MPI can be accessed as $PBS_NODEFILE.

Additional information

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