Difference between revisions of "Minnesota Supercomputing Institute"
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(Created page with "MSI uses a PBS scheduler. It's easy to find a lot of information online about how to use PBS, but here are some commonly used functions First, submitting a job is easiest wit...") |
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MSI uses a PBS scheduler. It's easy to find a lot of information online about how to use PBS, but here are some commonly used functions | MSI uses a PBS scheduler. It's easy to find a lot of information online about how to use PBS, but here are some commonly used functions | ||
| − | First, submitting a job is easiest with a PBS batch script. The following script runs a program called vcf2kinship to create a kinship matrix on MCTFR genotypes. It requests a single node and 12 processors on that node. It requests 25 GB of memory. | + | First, submitting a job is easiest with a PBS batch script. The following script, called <code>kinship.sh</code>, runs a program called vcf2kinship to create a kinship matrix on MCTFR genotypes. It requests a single node and 12 processors on that node. It requests 25 GB of memory. |
<syntaxhighlight lang="bash"> | <syntaxhighlight lang="bash"> | ||
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/home/vrie0006/hyoung/software/rvtests/executable/vcf2kinship --inVcf /home/vrie0006/hyoung/gedi5-660WQuad-b37-forwardstrand-correctreferenceallele-final-vcf.vcf.gz --bn -\ | /home/vrie0006/hyoung/software/rvtests/executable/vcf2kinship --inVcf /home/vrie0006/hyoung/gedi5-660WQuad-b37-forwardstrand-correctreferenceallele-final-vcf.vcf.gz --bn -\ | ||
-thread 10 --out MCTFR | -thread 10 --out MCTFR | ||
| + | </syntaxhighlight> | ||
| + | |||
| + | That script can then be submitted for scheduling to the mesabi short queue on msi ([https://www.msi.umn.edu/queues]) as follows: | ||
| + | |||
| + | <syntaxhighlight lang="bash"> | ||
| + | qsub -t short kinship.sh | ||
</syntaxhighlight> | </syntaxhighlight> | ||
Revision as of 03:58, 30 November 2017
MSI uses a PBS scheduler. It's easy to find a lot of information online about how to use PBS, but here are some commonly used functions
First, submitting a job is easiest with a PBS batch script. The following script, called kinship.sh, runs a program called vcf2kinship to create a kinship matrix on MCTFR genotypes. It requests a single node and 12 processors on that node. It requests 25 GB of memory.
#!/bin/bash -l
#PBS -l walltime=10:00:00,nodes=1:ppn=12,mem=25gb
/home/vrie0006/hyoung/software/rvtests/executable/vcf2kinship --inVcf /home/vrie0006/hyoung/gedi5-660WQuad-b37-forwardstrand-correctreferenceallele-final-vcf.vcf.gz --bn -\
-thread 10 --out MCTFR
That script can then be submitted for scheduling to the mesabi short queue on msi ([1]) as follows:
qsub -t short kinship.sh