Appendix A — LSF Quick Reference Guide

This page summarises the most relevant information to work with the HPC, to be used as a quick-reference guide.

This is used in the examples that follow:

A.1 LSF Commands

Command Description
bsub simulation.sh submit script to scheduler
bjobs jobs currently in the queue
bkill JOBID cancel the job with the specified ID (get the ID from the command above)
bkill -u xyz123 cancel all your jobs at once
bhist JOBID basic information about the job
bacct JOBID custom information about your job

A.2 Submission Script Template

At the top of the submission shell script, you should have your #BSUB options. Use this as a general template for your scripts:

#!/bin/bash
#BSUB -J my_simulation                        # a job name for convenience
#BSUB -cwd /home/xyz123/scratch/simulations   # your working directory
#BSUB -o logs/simulation.out    # standard output (and standard error if omitting -e) will be saved in this file
#BSUB -q normal                 # partition
#BSUB -n2                       # number of CPUs
#BSUB -R"select[mem>1000] rusage[mem=1000]"   # RAM memory part 1
#BSUB -M1000                                  # RAM memory part 2 
#BSUB -W15                          # Time for the job in (hh:)mm