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Workspace Spectrum LSF
Components Administration
Created by Guest
Created on Apr 13, 2021

Add bkill option that will set the job status to DONE rather than EXIT

Currently all jobs terminated via bkill are set to status EXIT. With the growing usage of bioinformatics tools and applications that were traditionally run on dedicated servers being integrated into use on HPC resources there is a shifting paradigm from traditional batch processing. Specifically many tools will submit jobs with no fixed runtime but rather are checking a message queue of some type to acquire workunits then when there are no more workunits they will be bkilled to remove those worker processes.
because these are bkilled they are logged as EXIT rather than DONE and it results in jobs that did finish properly being included in metrics about failed jobs. As many of these tools will use large volumes of single core workers this can easily result in thousands of EXIT jobs and we have seen upwards of 50% of our 24 hour job throughput being tagged as Exit vs Done in RTM which makes it difficult to identify when there is a real issue.

  • Admin
    Bill McMillan
    Nov 15, 2021

    This RFE has been implemented and will be included in the next service pack. If you need it as a temporary patch before then, please let us know.

  • Guest
    Jun 8, 2021

    We hope to deliver this as a patch in the 2nd half of the year when resource is freed up from ongoing projects.

  • Guest
    May 10, 2021

    We are still reviewing this RFE and hope to have an update shortly.