CODEWITHSUNDEEP
shellcluster-computing
FalafelPita
FalafelPita

Reputation: 293

PBS directive with variable resource request

I use a shell script to launch several jobs on a computing cluster by calling qsub inside a loop. I use the loop to give each job a different starting value. I wanted to specify the number of cores for each job to request by simply passing a number to the shell script when I run it from the command line. For example

./lauchJobs.sh 8

would launch jobs which requests 8 cores per node. I attempted to do this with 

#!/bin/tcsh
#check that all input arguments are there
if ($# != 3) then
    echo "This script requires three input arguments: (i) number of cores per job, (ii) starting guessNum, (iii) ending guessNum"
else
    foreach iNum (`seq $2 1 $3`) #loop over guess numbers
        qsub  -v iGuess=${iNum} estimate.pbs
    end
endif

(yes, technically my first example should have been something like ./launchJobs.sh 8 1 50 because I expect three arguments)

And estimate.pbs began with

#!/bin/tcsh 
#PBS -l pmem=1gb,nodes=1:ppn=${nCores},walltime=60:00:00

The problem is that ${nCores} did not resolve to the value I passed from the shell script because it is inside the PBS directive.

Is it possible to write a script file and PBS file that will allow me to specify the number of cores to request by passing it to the script, as in ./lauchJobs.sh 8 ?

Upvotes: 0

Views: 552

Answers (1)

Fex
Fex

Reputation: 332

You don't have to specify nodes=1:ppn=${nCores} in estimate.pbs.

You can also invoke qsub in this way:

qsub -l nodes=1:ppn=${1} -v iGuess=${iNum} estimate.pbs

Upvotes: 3

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