broadinstitute
Docs HPCSlurmWithLocalScratch.md redundant?
This is a remark on https://github.com/broadinstitute/cromwell/blob/master/docs/tutorials/HPCSlurmWithLocalScratch.md there is a feature on slum config to edit the sbatch command. You could add in a find and replace in the config to do the same as the tutorial.
you can skip the first part of the tutorial by editing the slurm backend config (somewhat hotpatching the scripts on submission time).
old submit submit = """ sbatch -J ${job_name} -D ${cwd} -o ${out} -e ${err} -t ${runtime_minutes} -p ${queue} ${"-c " + cpu} --mem ${memory_mb} --wrap "/bin/bash ${script}" """
new submit for slurm auto configured job dir:
submit = """
perl -i.bak -wpe 's/^tmpDir=.*/tmpdir="$TMPDIR"/g' ${script} &&
sbatch -J ${job_name} --tmp=${disk} -D ${cwd} -o ${out} -e ${err} -t ${runtime_minutes} -p ${queue} ${"-c " +
cpu} --mem ${memory_mb} --wrap "/bin/bash ${script}"
"""
new submit for /genomics/local/ (not tested tough):
submit = """
perl -i.bak -wpe 's/^tmpDir=.*/tmpdir="$(mkdir -p "/genomics_local/$PID_$HOSTNAME"/" && echo "/genomics_local/$PID_$HOSTNAME"/"/g' ${script} &&
sbatch -J ${job_name} --tmp=${disk} -D ${cwd} -o ${out} -e ${err} -t ${runtime_minutes} -p ${queue} ${"-c " +
cpu} --mem ${memory_mb} --wrap "/bin/bash ${script}"
"""
The backend I'm running on is Slurm hpc with a version 1.0 workflow. This alternative workflow has its downsides but also benefits it is up to the hpc(user) to decide what works best in their own situation.
