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

The lines starting with #SBATCH are not interpreted by bash but are replaced with code by sbatch. The sbatch options do not support $1 vars (only %j and some others, replacing $1 by %1 will not work). When you don't have different sbatch processes running in parallel, you could try

#!/bin/bash

touch outFile${1}.txt errFile${1}.txt
rm link_out.sbatch link_err.sbatch 2>/dev/null # remove links from previous runs
ln -s outFile${1}.txt link_out.sbatch
ln -s errFile${1}.txt link_err.sbatch

#SBATCH -o link_out.sbatch
#SBATCH -e link_err.sbatch

hostname
# I do not know about the background processing of sbatch, are the jobs still running
# at this point? When they are, you can not delete the temporary symlinks yet.

exit 0

Alternative: As you said in a comment yourself, you could make a masterscript. This script can contain lines like

cat  exampleJob.sh.template | sed -e 's/File.txt/File'$1'.txt/' > exampleJob.sh
# I do not know, is the following needed with sbatch?
chmod +x exampleJob.sh

In your template the #SBATCH lines look like

#SBATCH -o "outFile.txt"
#SBATCH -e "errFile.txt"