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

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|48:00:00
 
|48:00:00
 
|Long queue with 48 hour time limit
 
|Long queue with 48 hour time limit
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==== Multi-node jobs ====
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==== Single node jobs ====
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{| class="wikitable"
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!Queue Name
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!Max cores
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!Max nodes running
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!Max time
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!Description
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|-
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|wide
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|28
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|2
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|24:00:00
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|Queue to enable MPI-type jobs with up to 56 cores with 48 hour time limit
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|-
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verywide
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|28
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|4
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|08:00:00
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|Queue to enable MPI-type jobs with up to 112 cores with 24 hour time limit
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* A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].
 
* A useful Torque tutorial can be found at [https://kb.iu.edu/d/avmy this link].

Revision as of 11:44, 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: 

#!/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 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

Multi-node jobs

Single node jobs

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