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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 LSF commands (e.g. bsub). 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 -cwd parameters of bsub 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.

Also, a jobscript should not be started within a directory belonging to etapfs.

The reason is that a “hanging” etapfs (e.g. lost mount) will cause the scheduler to be unable to clean up the job, while a job unable to write to etapfs can still be cleaned up, if the scheduler's daemons do not have file handles there.

  • etap.1434466410.txt.gz
  • Last modified: 2015/06/16 16:53
  • by meesters