View source for Using the PBS / Torque queueing environment

The main commands for interacting with the Torque environment are:

<source lang="c">
> qstat
</source>
View queued jobs.


<source lang="c">
> qsub
</source>
Submit a job to the scheduler.


<source lang="c">
> qdel
</source>
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:

<source lang="c">
#PBS -l nodes=1:ppn=14
</source>

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.

<source lang="c">
#PBS -l walltime=8:00:00
</source>

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:

<source lang="c">
#!/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
</source>


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

<source lang="c">
> qsub run_bowtie.sh
</source>


=== The different queues available ===
==== Single node jobs ====

{| class="wikitable"
!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
|-
|bigmem
|24
|2
|48:00:00
|Long queue with 48 hour time limit
|-
|massivemem
|24
|1
|48:00:00
|Long queue with 48 hour time limit
|}


* A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].