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What do {script,stdout,stderr}.kill files indicate?

mmahmmah Member, Broadie ✭✭

If {script,stdout,stderr}.kill files are present in a task's execution directory, does this indicate that Cromwell has intentionally killed a task due to some error condition? If so, Is this error condition necessarily related to the killed task?

Best Answer


  • jsotojsoto Broad InstituteMember, Broadie, Dev ✭✭

    Cromwell does add the "kill" extension to those files when a user tries to abort a workflow when using certain backends. Did you or any other user try to abort a workflow while it was running?

    Could you also explain what environment you are running Cromwell in, namely what backend you are using.

  • mmahmmah Member, Broadie ✭✭

    This is running on an LSF backend. I have an error message about running out of memory for the parent Cromwell job with 12 GB of memory, which results in LSF killing the parent Cromwell job. I am trying to determine whether the .kill files for the task also indicate there is a problem with the task resource allocation, or if the problem simply stems from the parent resource allocation.

  • mmahmmah Member, Broadie ✭✭

    Yes, the Cromwell parent job runs the java process running Cromwell. The Cromwell server is running in single workflow mode.

  • jsotojsoto Broad InstituteMember, Broadie, Dev ✭✭

    Great that means what I said earlier still holds. Your Cromwell resources are the cause, not your task resources.

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