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When using etapfs you should acess these filesystem only within your job and not indicate paths on the command line with SLURM commands (e.g. sbatch). Especially stdout should not be directed to /etapfs as this can prevent a job to be ended (even if the wall clock time limit is hit), if one such filesystem “hangs”.

This means that the -o, -e and -D/--workdir=<path> parameters of sbatch should not point to etapfs. However, copying within your script to etapfs is ok, e.g.:

  # bash code + statements
  <application call + options>
} > <outputfile on etapfs>

Likewise, pointing the output of subshells to etapfs is an alternate solution. This helps the scheduler to clean up jobs.

Also, you should not submit jobs when your actual working directory at the time of submit is on an etapfs. Instead,

#SBATCH --workdir=<path outside etapfs>

can intentionally be used to avoid the mentioned problems, whilst submitting from a working directory in etapfs.

etap.txt · Last modified: 2017/06/30 08:38 by meesters