I don’t think you can turn them into command-line arguments to your script
since Bash treats the #SBATCH lines as comments and can’t see “into” them, but
you can, as I’m sure you know, override any #SBATCH options by putting them on
the sbatch command-line before specifying the command to run. If it were to
work at all, Slurm (probably in sbatch) would have to find such command line
arguments and expand them for you in the #SBATCH directives in, say, its copy
of your script before running it, and even before parsing the directives.
Technically feasible unless your command-line arguments to your sbatch scripts
are generated outside that script when sbatch is invoked. If that’s what you’re
doing, probably better to just override the option on the sbatch command line:
foo.sh:
#!/bin/bash
…
#SBATCH –n 50
…
for i in 50 100 1000; do
sbatch –n $i ./foo.sh
done
Is that what you were thinking? Doing:
bar.sh:
#!/bin/bash
…
#SBATCH –n $1
…
for i in 50 100 1000; do
sbatch bar.sh $i
done
Would be more challenging for Slurm to handle since it would have to understand
and parse the command-line arguments of the command handed to it to be run as
the job. That parsing is going to depend on the shebang line (as to what’s
being invoked) bash? csh? python? perl? /usr/bin/env X? So, I’d be surprised if
there was a mode for this. Also, would you expect Slurm to delete any options
it used from your command line or leave them?
Best,
Bill.
--
Bill Barth, Ph.D., Director, HPC
bba...@tacc.utexas.edu | Phone: (512) 232-7069
Office: ROC 1.435 | Fax: (512) 475-9445
On 3/18/18, 12:44 PM, "slurm-users on behalf of Jessie Poquérusse"
<slurm-users-boun...@lists.schedmd.com on behalf of
jessie.poqueru...@gmail.com> wrote:
Hello,
In trying to modularize and genericize my Bash scripts as much as possible,
I was wondering if there was a way to turn #SBATCH options (mainly walltime,
mem, and output and error file directories)
into externally defined script parameters (e.g. in the same command line
as during sbatch job submission).
Thank-you!
