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Move to Parsl HighThroughputExecutor for default workflow execution #97

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merged 17 commits into from
Sep 15, 2023

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@d33bs d33bs commented Sep 8, 2023

Description

This PR makes the Parsl HighThroughputExecutor (HTE) the default executor / config for running CytoTable convert. This change comes about to help conserve memory usage based on findings in #75 .

Notes:

  • I found that Moto is not compatible with HTE and so decided to split Parsl configurations by test module and continue using S3 tests through the ThreadPoolExecutor. See this ref for more.
  • I changed the port used by Moto in tests to 5001 to avoid the potential for an obscure MacOS issue with port 5000 and local development testing
  • test_convert_hte_cellprofiler_csv has been ported to test non-S3 ThreadPoolExecutor capabilities alongside the S3 tests.
  • I updated a number of dependencies which were related to this work in an effort towards general maintenance

What is the nature of your change?

  • Bug fix (fixes an issue).
  • Enhancement (adds functionality).
  • Breaking change (fix or feature that would cause existing functionality to not work as expected).
  • This change requires a documentation update.

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  • I have read the CONTRIBUTING.md guidelines.
  • My code follows the style guidelines of this project.
  • I have performed a self-review of my own code.
  • I have commented my code, particularly in hard-to-understand areas.
  • I have made corresponding changes to the documentation.
  • My changes generate no new warnings.
  • New and existing unit tests pass locally with my changes.
  • I have added tests that prove my fix is effective or that my feature works.
  • I have deleted all non-relevant text in this pull request template.

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@falquaddoomi falquaddoomi left a comment

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Neat to see you changing over to the HTExecutor; very curious to see how that impacts performance. I made a small comment, but IMHO it's not a blocker, so I'll approve for now.

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d33bs commented Sep 15, 2023

Thank you @falquaddoomi for your review on this! I've addressed the comment you provided and will now merge this in.

@d33bs d33bs merged commit ce3f752 into cytomining:main Sep 15, 2023
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@d33bs d33bs deleted the parsl-hte-default branch September 15, 2023 14:19
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2 participants