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Add subshell to hide resource monitor #5091

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merged 3 commits into from
Sep 16, 2024
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adamnovak
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This will fix #5090 by hiding the resource monitor process from Bash's job system.

Changelog Entry

To be copied to the draft changelog by merger:

  • toil-wdl-runner will no longer hang when running workflows using Bash wait on Docker

Reviewer Checklist

  • Make sure it is coming from issues/XXXX-fix-the-thing in the Toil repo, or from an external repo.
    • If it is coming from an external repo, make sure to pull it in for CI with:
      contrib/admin/test-pr otheruser theirbranchname issues/XXXX-fix-the-thing
      
    • If there is no associated issue, create one.
  • Read through the code changes. Make sure that it doesn't have:
    • Addition of trailing whitespace.
    • New variable or member names in camelCase that want to be in snake_case.
    • New functions without type hints.
    • New functions or classes without informative docstrings.
    • Changes to semantics not reflected in the relevant docstrings.
    • New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
    • New features without tests.
  • Comment on the lines of code where problems exist with a review comment. You can shift-click the line numbers in the diff to select multiple lines.
  • Finish the review with an overall description of your opinion.

Merger Checklist

  • Make sure the PR passes tests.
  • Make sure the PR has been reviewed since its last modification. If not, review it.
  • Merge with the Github "Squash and merge" feature.
    • If there are multiple authors' commits, add Co-authored-by to give credit to all contributing authors.
  • Copy its recommended changelog entry to the Draft Changelog.
  • Append the issue number in parentheses to the changelog entry.

@adamnovak adamnovak marked this pull request as ready for review September 13, 2024 22:53
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@DailyDreaming DailyDreaming left a comment

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This looks good to me. Thanks for adding the test.

@DailyDreaming DailyDreaming merged commit 8faca0f into master Sep 16, 2024
1 check was pending
@DailyDreaming DailyDreaming deleted the issues/5090-wdl-wait branch September 16, 2024 20:53
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Successfully merging this pull request may close these issues.

Toil resource monitoring will break wait in WDL scripts
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