Update slurm_submit to capture job ID

[bio-boris]

Modify sbatch command to output job ID

[MrCreosote]

I don't really have a ton of expertise here, but I'm assuming the changes are just to

• ensure that sbatch is in the path
• modify the output from sbatch so the script spits out the job ID only

Assuming that's correct this seems fine to me

[MrCreosote]

I generally don't think paths should be hardcoded in scripts, but it seems unlikely this script is ever going to be used for anything other than hipmer so it's probably fine

[Copilot]

Pull Request Overview

This PR modifies the Slurm submission wrapper script to capture and return the job ID from the sbatch command output. The change allows downstream processes to programmatically obtain the job ID for tracking and monitoring purposes.

Key Changes

• Modified sbatch command to parse and return only the job ID number
• Added documentation comments about PATH requirements for both scripts

Reviewed Changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
scripts/slurm_submit	Updated sbatch command to extract job ID from output using sed
scripts/slurm_checkjob	Added documentation comment about PATH requirements

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[Copilot]

There's an extra space in 'that slurm_submit' - should be 'that slurm_submit' with only one space.

Suggested change

	# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated
	# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated

[Copilot]

There's an extra space after the # character - should be '# Ensure' instead of '# Ensure' for consistency with other comments.

Suggested change

	# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated
	# Ensure that slurm_submit and slurm_checkjob are in the PATH . ~/.local_settings may need to be updated

[Copilot]

The sed command assumes sbatch will always output 'Submitted batch job ' prefix. Consider adding error handling to verify the command succeeded and the output format is as expected before parsing.

Suggested change

	sbatch -o $LOGFILE -e $ERRFILE $SUBMIT|sed 's/Submitted batch job //'
	# Submit the job and capture output
	SBATCH_OUTPUT=$(sbatch -o "$LOGFILE" -e "$ERRFILE" "$SUBMIT")
	SBATCH_EXIT=$?
	# Check if sbatch succeeded
	if [ $SBATCH_EXIT -ne 0 ]; then
	echo "Error: sbatch failed with exit code $SBATCH_EXIT" >&2
	echo "$SBATCH_OUTPUT" >&2
	exit $SBATCH_EXIT
	fi
	# Extract job ID from output
	if [[ "$SBATCH_OUTPUT" =~ ^Submitted\ batch\ job\ ([0-9]+) ]]; then
	echo "${BASH_REMATCH[1]}"
	else
	echo "Error: Unexpected sbatch output format:" >&2
	echo "$SBATCH_OUTPUT" >&2
	exit 1
	fi

[bio-boris]

Looks like the tests are failing. I don't know what the special tests are actually doing or how they work yet, I haven't gone in depth with them.