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Status Functionality already exists
Workspace Spectrum LSF
Components Other
Created by Guest
Created on Sep 28, 2023

Clean left over job's daemon processes after job res finished

We have several workflows that the job script can run tools that will spawn processes in the backgroup or as daemons that will stay active once the job script ends. Since the job script ends, res will end with the exit code of the job script, but this is causing LSF to not consider the job as done until those processes also exit, which can never happen.

What we would like is for an option that when res gets the return status of the job script, to clean up the jobs enviroment of the leftover processes.

Needed By Yesterday (Let's go already!)
  • Guest
    Dec 5, 2023

    One solution is to use the "WATCHDOG" parameter in LSF application profile.

    LSF runs this watchdog script regularly and passes $LSB_JOB_PIDS to the script. The script can go through this pid list and check if job res is in it. If no, kill them all.

  • Admin
    Bill McMillan
    Oct 26, 2023

    Given the script above, it is unlikely that this will be make it to the top of the priority list in the near future. The idea will be left open and may be reconsidered if there is additional interest.

  • Admin
    Bill McMillan
    Oct 9, 2023

    There is a "zapit" utility that is included with LSF that can be used to clean up any processes that a job has created and still has lying around.

    It's typically added as the last line of the job script