Pass command line arguments via sbatch

Question

Suppose that I have the following simple bash script which I want to submit to a batch server through SLURM:

#!/bin/bash

#SBATCH -o \"outFile\"$1\".txt\"
#SBATC         


        

Answer 1

I thought I'd offer some insight because I was also looking for the replacement to the -v option in qsub, which for sbatch can be accomplished using the --export option. I found a nice site here that shows a list of conversions from Torque to Slurm, and it made the transition much smoother.

You can specify the environment variable ahead of time in your bash script:

$ var_name='1'
$ sbatch -D `pwd` exampleJob.sh --export=var_name

Or define it directly within the sbatch command just like qsub allowed:

$ sbatch -D `pwd` exampleJob.sh --export=var_name='1'

Whether this works in the # preprocessors of exampleJob.sh is also another question, but I assume that it should give the same functionality found in Torque.