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Enable FUSE for privileged Toil clusters

Open stxue1 opened this issue 11 months ago • 0 comments

This should close #4806 This is also related to #4807

The Dockerfile pulls from Github releases for now, but I will change it to a Debian mirror once the package managers get around to updating Singularity.

I think the namespace rules might not be needed now from my basic testing. My guess is the new version of Singularity now is able to handle it, but I'll test it more thoroughly later.

Changelog Entry

To be copied to the draft changelog by merger:

  • Allow toil-wdl-runner to use FUSE in unprivileged environments if possible
  • Set Toil-managed clusters to run in privileged mode by default
    • Allow Toil-managed Kubernetes clusters support FUSE
    • Added option in the Kubernetes batchsystem to ask for privileged pods
    • Added option in launch-cluster to enable FUSE support
  • Reduced configuration debug spam

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.

stxue1 avatar Mar 09 '24 01:03 stxue1