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Directives: #BSUB → #SBATCH

Every #BSUB directive in your LSF scripts has a SLURM equivalent using #SBATCH. The table below covers the most common mappings.

Directive mapping table

Purpose LSF (#BSUB) SLURM (#SBATCH) Notes
Job name -J myJob --job-name=myJob
Queue / Partition -q normal --partition=normal LSF "queues" are SLURM "partitions"
Wall-clock time limit -W 60 or -W 1:00 --time=01:00:00 SLURM uses HH:MM:SS or D-HH:MM:SS
Stdout file -o output.%J --output=output.%j See filename patterns below
Stderr file -e error.%J --error=error.%j
Combine stdout/stderr -o output.%J (default) --output=output.%j SLURM merges by default when --error is omitted
Memory per job -M 4000 --mem=4G LSF uses KB by default; SLURM uses MB (suffix G for GB)
Memory per core -R "rusage[mem=4000]" --mem-per-cpu=4G
Number of cores -n 4 --ntasks=4 or --cpus-per-task=4 Use --cpus-per-task for threaded jobs
Number of nodes -R "span[hosts=1]" --nodes=1
Exclusive node -x --exclusive
GPU request -R "rusage[ngpus_physical=1]" --gpus=1 or --gres=gpu:1 Syntax varies by cluster config
GPU type -R "select[ngpus_physical>0] rusage[ngpus_physical=1]" -q gpu --gpus=a100:1 or --gres=gpu:a100:1
Job array -J "myJob[1-100]" --array=1-100 See Job Arrays
Array concurrency limit -J "myJob[1-100]%10" --array=1-100%10 Max simultaneous tasks
Dependency (after OK) -w "done(12345)" --dependency=afterok:12345
Dependency (after any) -w "ended(12345)" --dependency=afterany:12345
Email address -u user@example.com --mail-user=user@example.com
Email on start -B --mail-type=BEGIN
Email on end -N --mail-type=END
Email on start and end -B -N --mail-type=BEGIN,END
Project / Account -P myproject --account=myproject
Working directory (submit from dir) --chdir=/path/to/dir LSF runs from submission dir by default; so does SLURM
Hold job -H --hold
Requeue on failure -r --requeue

Output filename patterns

LSF and SLURM use different tokens for dynamic filenames:

Meaning LSF SLURM
Job ID %J %j
Array index %I %a
Job name %J %x
Array Job ID %J %A
Node (first) — %N

Case matters

LSF uses uppercase %J and %I. SLURM uses lowercase %j and %a. Forgetting to change the case will result in literal %J appearing in your filenames.

Example

#!/bin/bash
#BSUB -J alignment
#BSUB -q normal
#BSUB -W 4:00
#BSUB -n 8
#BSUB -M 16000
#BSUB -o alignment.%J.out
#BSUB -e alignment.%J.err

module load samtools
samtools sort -@ 8 input.bam -o sorted.bam

#!/bin/bash
#SBATCH --job-name=alignment
#SBATCH --partition=normal
#SBATCH --time=04:00:00
#SBATCH --cpus-per-task=8
#SBATCH --mem=16G
#SBATCH --output=alignment.%j.out
#SBATCH --error=alignment.%j.err

module load samtools
samtools sort -@ 8 input.bam -o sorted.bam

Memory units

LSF's -M typically specifies KB. SLURM's --mem defaults to MB, but you can use suffixes: --mem=16G for 16 GB. Always double-check units when converting.