Bodhi LSF → SLURM Migration Guide

Questions?

Contact David Farrell with any questions about the Bodhi LSF-to-SLURM migration.

The Bodhi HPC cluster is migrating from IBM Spectrum LSF to SLURM. This guide helps you convert your existing LSF job scripts and workflows to SLURM.

Quick-start checklist

• 🔀 Replace #BSUB directives with #SBATCH equivalents (Directives)
• 🖥️ Update submission and monitoring commands (Commands)
• 🔤 Replace $LSB_* environment variables with $SLURM_* equivalents (Environment Variables)
• 🔢 Review job array syntax changes (Job Arrays)
• ✅ Test your converted scripts with a short run before submitting production jobs

Key differences at a glance

Concept	LSF	SLURM
Scheduler directive	#BSUB	#SBATCH
Submit a job	bsub < script.sh	sbatch script.sh
Job status	bjobs	squeue
Cancel a job	bkill	scancel
Interactive session	bsub -Is -q interactive bash	srun --pty bash
Array index variable	$LSB_JOBINDEX	$SLURM_ARRAY_TASK_ID

Use the converter script

We provide a sed-based helper script that handles the most common directive and variable substitutions automatically. It's a great starting point — just review the output before submitting.

What stays the same

• Shell scripts are still shell scripts. Only the scheduler directives and environment variables change; your actual commands (samtools, R, python, etc.) remain the same.
• Stdout/stderr are still captured to files — the default file naming just differs slightly.
• Module system (module load ...) is unchanged.

Where to get help

• Browse this guide using the sidebar navigation
• Check the Resources page for links to official SLURM documentation
• Contact the Bodhi HPC support team with migration questions