Minnesota Supercomputing Institute

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 (MSI list of queues) as follows:

qsub -t short kinship.sh