Biowulf: Difference between revisions
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(Created page with "* [https://hpc.nih.gov/docs/userguide.html Biowulf User Guide] = Quota = <syntaxhighlight lang='bash'> checkquota </syntaxhighlight> = freen = = Single file - sbatch = <spa...") |
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| Line 16: | Line 16: | ||
= Multiple files - swarm = | = Multiple files - swarm = | ||
* [https://hpc.nih.gov/apps/swarm.html swarm] | * [https://hpc.nih.gov/apps/swarm.html swarm] | ||
* [https://hpc.nih.gov/apps/modules.html Environment modules] | * [https://hpc.nih.gov/apps/modules.html Environment modules] Note '''sbatch''' command does not support ''--module'' option. | ||
<syntaxhighlight lang='bash'> | <syntaxhighlight lang='bash'> | ||
swarm -t 3 -g 20 -f run_seqtools_vc.sh --module samtools,picard,bwa --verbose 1 --devel | swarm -t 3 -g 20 -f run_seqtools_vc.sh --module samtools,picard,bwa --verbose 1 --devel | ||
| Line 24: | Line 24: | ||
# To change the default walltime, use --time=24:00:00 | # To change the default walltime, use --time=24:00:00 | ||
swarm -t 8 -g 24 --module tophat samtools htseq -f run_master.sh | swarm -t 8 -g 24 --module tophat,samtools,htseq -f run_master.sh | ||
cat sw3n17156.o | cat sw3n17156.o | ||
</syntaxhighlight> | </syntaxhighlight> | ||
Revision as of 19:11, 15 May 2016
Quota
checkquota
freen
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.
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 10 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