Biowulf

• Biowulf User Guide

Quota

checkquota

Single file - sbatch

Don't use swarm for a single file

sbatch --cpus-per-task=2 --mem=4g MYSCRIPT

Multiple files - swarm

• swarm
• Environment modules Note sbatch command does not support --module option. In sbatch case, the module command has to be put in the script file.

swarm -t 3 -g 20 -f run_seqtools_vc.sh --module samtools,picard,bwa --verbose 1 --devel
# 3 commands run in 3 subjobs, each command requiring 20 gb and 3 threads, allocating 6 cores and 12 cpus
swarm -t 3 -g 20 -f run_seqtools_vc.sh --module samtools,picard,bwa --verbose 1

# To change the default walltime, use --time=24:00:00

swarm -t 8 -g 24 --module tophat,samtools,htseq -f run_master.sh
cat sw3n17156.o

Monitor/Delete jobs

sjobs
scancel -u XXXXX
scancel NNNNN
scancel --state=PENDING
scancel --state=RUNNING
squeue -u XXXX

Interactive debugging

sinteractive --mem=8g -c 4