parameter for shell scripts that is started with qsub

Question

how can I parametrize a shell script that is executed on a grid (started with qsub) ? I have a shell script, where I use getopts to read the parameters.

When I start (qsub script.sh -r firstparam -s secondparam ..) this working script with qsub I receive error messages,

qsub: invalid option -- s

qsub: illegal -r value

as qsub thinks the parameter are for itself. Yet I have not found any solution.

Thanks

Answer 1

Using the qsub -v option is the proper way:

qsub -v par_name=par_value[,par_name=par_value...] script.sh 

par_name can be used as variable in the shell script.

Answer 2

In addition to volk's answer, in order to reference the variables in the list (designated by -v) you simply use the name you define in your call. So, say you made a call to qsub as follows

qsub -v foo='qux' myRunScript.sh

Then myRunScript.sh could look something like this:

#!/bin/bash #PBS -l nodes=1:ppn=16,walltime=0:00:59 #PBS -l mem=62000mb #PBS -m abe  bar=${foo} echo "${bar}" 

Where the output would be

qux 

Hope this helps!