Issue
I'm working towards setting up a script for batch submission to an HPC system which uses software in an apptainer image. Here's what I have in mind:
apptainer run container.sif runjob.sh
runjob.sh
--------------------
./loadenv.sh
python3 job.py
Where loadenv.sh is ~160 line script that sets up paths/etc and launches a new shell with:
$NEW_SHELL "$@"
With the new shell being launched, bash commands stop being processed until the shell exits. Is there a way to pass the job to the new shell without editing loadenv.sh?
Solution
the "$@" accepts command line arguments entered after it as variables.
editing runjob.sh to:
./loadenv.sh python3 job.py
runs the job in the environment. I found this only works for 1 argument, with the shell exiting on completion. So to run multiple jobs in the same batch submission it needs to be structured as:
apptainer run container.sif runjob.sh
runjob.sh
--------------------
./loadenv.sh python3 job1.py
./loadenv.sh python3 job2.py
./loadenv.sh python3 job3.py
...
Answered By - Arland Answer Checked By - Willingham (WPSolving Volunteer)