Difference between revisions of "LSF to Slurm quick reference"

From ScientificComputing
Jump to: navigation, search
(Monitoring a job)
(Environment variables)
Line 59: Line 59:
 
! LSF !! Slurm  
 
! LSF !! Slurm  
 
|-
 
|-
| style="width:50%;" | <tt>$LSB_JOBID</tt> || <tt>$SLURM_JOBID</tt>
+
| style="width:50%;" | <tt>$LSB_JOBID</tt> || <tt>$SLURM_JOB_ID</tt>
 
|-
 
|-
 
| <tt>$LSB_SUBCWD</tt> || <tt>$SLURM_SUBMIT_DIR</tt>
 
| <tt>$LSB_SUBCWD</tt> || <tt>$SLURM_SUBMIT_DIR</tt>
 
|}
 
|}

Revision as of 08:54, 31 March 2022

Introduction

The commands for slurm are similar to the ones used in LSF. You can find a mapping of the relevant commands below.

Submitting a job

LSF Slurm
bsub < jobscript.sh sbatch jobscript.sh
jobscript.sh:
#!/bin/bash

#BSUB -n 4
#BSUB -W 08:00
#BSUB -R "rusage[mem=2000]"
#BSUB -J analysis1
#BSUB -o analysis1.out
#BSUB -e analysis1.err

# load modules
# run command
jobscript.sh:
#!/bin/bash

#SBATCH -n 4
#SBATCH --time=8:00
#SBATCH --mem-per-cpu=2G
#SBATCH --job-name=analysis1
#SBATCH --output=analysis1.out
#SBATCH --error=analysis1.err

# load modules
# run command

Interactive job

LSF Slurm
bsub -Is [LSF options] bash srun --pty bash

Monitoring a job

LSF Slurm
bjobs [JOBID] squeue [-j JOBID]

Killing a job

LSF Slurm
bkill [JOBID] scancel [JOBID]

Environment variables

LSF Slurm
$LSB_JOBID $SLURM_JOB_ID
$LSB_SUBCWD $SLURM_SUBMIT_DIR