How to Pass Parameters from QSub to Bash Script?

parameter-passing qsub
user2800589 picture user2800589 · Sep 20, 2013 · Viewed 14.5k times · Source

I'm having an issue passing variables to a Bash script using QSub.

Assume I have a Bash script named example. The format of example is the following:

#!/bin/bash
# (assume other variables have been set)

echo $1 $2 $3 $4

So, executing "bash example.sh this is a test" on Terminal (I am using Ubuntu 12.04.3 LTS, if that helps) produces the output "this is a test".

However, when I enter "qsub -v this,is,a,test example.sh", I get no output. I checked the output file that QSub produces, but the line "this is a test" is nowhere to be found.

Any help would be appreciated.

Thank you.

Answer

Scott Gigante picture Scott Gigante · Jan 5, 2017

Using PBSPro or SGE, arguments can simply be placed after the script name as may seem intuitive.

qsub example.sh hello world

In Torque, command line arguments can be submitted using the -F option. Your example.sh will look something like this:

#!/bin/bash echo "$1 $2"

and your command like so:

qsub -F "hello world" example.sh

Alternatively, environment variables can be set using -v with a comma-separated list of variables.

#!/bin/bash echo "$FOO $BAR"

and your command like so:

qsub -v FOO="hello",BAR="world" example.sh

(This may be better phrased as a comment on @William Hay's answer, but I don't have the reputation to do so.)

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