Day: February 9, 2013

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Running multiple copies of the same job at the same time on PBS

In some situation, you may have to run a job several times. This is true in situation of random number generators.

Single Copy

#!/bin/bash
.....
.....
## Use data1.ini as the input file for $file
cd $PBS_O_WORKDIR
mybinaryprogram 1> mybinaryprogram.out 2> mybinaryprogram.err
.....
.....

Multiple Copies

If we qsub the job more than once, the output will override the results from the previous jobs. You can use the PBS environment PBS_JOBID to create directory and redirect your output to the respective directory

#!/bin/bash
.....
.....
cd $PBS_O_WORKDIR
mkdir $PBS_JOBID
mybinaryprogram 1> $PBS_JOBID/mybinaryprogram.out 2> $PBS_JOBID/mybinaryprogram.err
.....
.....

This should prevent the output overwriting itself.

For above information is obtained from

  1. Michigan State University HPCC “Advanced Scripting Using PBS Environment Variables”