Difference between revisions of "Using the PBS / Torque queueing environment"
From Centre for Bioinformatics and Computational Biology
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!Max cores | !Max cores | ||
!Max nodes running | !Max nodes running | ||
| + | !Max memory | ||
!Max time | !Max time | ||
!Description | !Description | ||
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|28 | |28 | ||
|4 | |4 | ||
| + | |64 GB | ||
|00:15:00 | |00:15:00 | ||
|Very short queue with 15 minute time limit | |Very short queue with 15 minute time limit | ||
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|28 | |28 | ||
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|01:00:00 | |01:00:00 | ||
|Short queue with 1 hour time limit | |Short queue with 1 hour time limit | ||
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|28 | |28 | ||
|2 | |2 | ||
| + | |64 GB | ||
|08:00:00 | |08:00:00 | ||
|Medium queue with 8 hour time limit | |Medium queue with 8 hour time limit | ||
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|28 | |28 | ||
|1 | |1 | ||
| + | |64 GB | ||
|48:00:00 | |48:00:00 | ||
|Long queue with 48 hour time limit | |Long queue with 48 hour time limit | ||
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|14 | |14 | ||
|1 | |1 | ||
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|96:00:00 | |96:00:00 | ||
|Long queue with 96 hour time limit | |Long queue with 96 hour time limit | ||
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|24 | |24 | ||
|2 | |2 | ||
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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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|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 ==== | ==== Multi-node jobs ==== | ||
| − | |||
| − | |||
{| class="wikitable" | {| class="wikitable" | ||
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!Max cores | !Max cores | ||
!Max nodes running | !Max nodes running | ||
| + | !Max memory | ||
!Max time | !Max time | ||
!Description | !Description | ||
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|28 | |28 | ||
|2 | |2 | ||
| + | |128 GB | ||
|24:00:00 | |24:00:00 | ||
|Queue to enable MPI-type jobs with up to 56 cores with 48 hour time limit | |Queue to enable MPI-type jobs with up to 56 cores with 48 hour time limit | ||
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|28 | |28 | ||
|4 | |4 | ||
| + | 128 GB | ||
|08:00:00 | |08:00:00 | ||
|Queue to enable MPI-type jobs with up to 112 cores with 24 hour time limit | |Queue to enable MPI-type jobs with up to 112 cores with 24 hour time limit | ||
| − | |||
|} | |} | ||
* 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 11:47, 11 April 2018
The main commands for interacting with the Torque environment are:
> qstatView queued jobs.
> qsubSubmit a job to the scheduler.
> qdelDelete one of your jobs from queue.
Contents
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=14sets 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=8:00:00sets 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.
