Difference between revisions of "LSF to Slurm quick reference"

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The commands for Slurm are similar to the ones used in LSF. You can find a mapping of the relevant commands below.
 
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==
+
==Submitting a batch job==
 
{| class="wikitable" border="1" style="width:80%;text-align:left;"
 
{| class="wikitable" border="1" style="width:80%;text-align:left;"
 
! LSF !! Slurm
 
! LSF !! Slurm

Latest revision as of 13:55, 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 batch 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=2000
#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

Check resource usage of a job

LSF Slurm
bbjobs [JOBID] sacct -j JOBID