Editing Minnesota Supercomputing Institute (section)

==Example code to submit jobs on Mesabi==
First, submitting a job is easiest with a PBS batch script. The following script, called <code>kinship.pbs</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">
#!/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/genotypes.vcf.gz \
      --bn \
      --thread 10 \
      --out /home/vrie0006/hyoung/kinship
</syntaxhighlight>

That script can then be submitted for scheduling to the mesabi short queue on msi ([https://www.msi.umn.edu/queues MSI list of queues]) as follows:

<syntaxhighlight lang="bash">
qsub -q short kinship.sh
</syntaxhighlight>

You can then check the status of this job by running various commands.

To see when your job might start running use <code>showstart <jobid></code> like this:

<syntaxhighlight lang="bash">
[ln0006:hyoung] showstart 4560951
job 4560951 requires 10 procs for 10:00:00

Estimated Rsv based start in                 2:10:44 on Wed Nov 29 23:58:00
Estimated Rsv based completion in           12:10:44 on Thu Nov 30 09:58:00

Best Partition: mesabipar
</syntaxhighlight>

To check status use <code>qstat</code>:
<syntaxhighlight lang="bash">
[ln0006:hyoung] qstat
Job ID                    Name             User            Time Use S Queue
------------------------- ---------------- --------------- -------- - -----
4560955.mesabim3.msi.umn.edu kinship.sh       vrie0006        01:02:54 R small
</syntaxhighlight>

Here's an example of an array of 22 jobs to perform rvtests, with 1 job per chromosome. Note that in the script <code>${PBS_ARRAYID}</code> denotes the job number, and can be used to differentiate jobs.
<syntaxhighlight lang="bash">
#!/bin/bash

#PBS -l walltime=24:00:00,nodes=1:ppn=1,mem=2gb
#PBS -m abe
#PBS -M datt0019@umn.edu

/home/vrie0006/datt0019/tools/rvtests/executable/rvtest 
--inVcf /home/vrie0006/datt0019/mctfr/vcf_files/chr${PBS_ARRAYID}.withRS.filtered.PASS.beagled.MZadded.vcf.gz 
--boltPlink /home/vrie0006/datt0019/mctfr/bed/cpd_merged 
--pheno /home/vrie0006/datt0019/mctfr/phenotypes/residualized_phenotypes.ped 
--pheno-name cpd 
--meta bolt 
--inverseNormal --qtl 
--out /home/vrie0006/datt0019/mctfr/gwas/cpd/chr${PBS_ARRAYID} 
--boltPlinkNoCheck 
--siteMACMin 10

</syntaxhighlight>

That script can then be submitted for scheduling to mesabi as follows:

<syntaxhighlight lang="bash">
qsub -t 1-22 rvtests.sh
</syntaxhighlight>

=== Interactive job ===

<syntaxhighlight lang="bash">
qsub -I -l walltime=5:00:00,mem=10gb,nodes=1:ppn=1
</syntaxhighlight>