CODEWITHSUNDEEP
pythonsungridengine
Cholts
Cholts

Reputation: 101

How can I pass command line arguments containing braces using sun grid engine qsub?

I have a Python script that I would like to run on sun grid engine, and this script accepts a string command line argument that might contain braces. For instance, the script could be script.py:

import sys
print(sys.argv[1])

If I run python script.py aaa{ the output is aaa{, and if I run python script.py aaa{} the output is aaa{}. These are both the desired behavior.

However, if I run qsub -b y -cwd python script.py aaa{ the job fails with error Missing }., and if I run qsub -b y -cwd python script.py aaa{} the job succeeds but outputs aaa. This is not the desired behavior.

My hypothesis is that qsub does some preprocessing of the command line arguments to my script, but I don't want it to do this. Is there any way to make qsub pass command line arguments to my script as is, regardless of whether they contain braces or not?

Upvotes: 0

Views: 771

Answers (2)

Cholts
Cholts

Reputation: 101

I was able to solve my problem by running qsub -b y -cwd -shell no python script.py aaa{} instead of qsub -b y -cwd python script.py aaa{}. On my system, -shell yes seemed to be enabled by default, which initiated some preprocessing. Adding -shell no appears to fix this.

Upvotes: 0

Thomas Kainrad
Thomas Kainrad

Reputation: 2830

The simplest solution would be to use

echo "python script.py aaa{}" | qsub -cwd

You could also create submit file containing the following:

#!/bin/bash
#$ -cwd

python ./script.py ${input}

Then, you can pass your input via qsub -v input=aaa{} script.submit

Both variants require to omit -b y.

Upvotes: 0

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