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MDAnalysis.analysis.rdf: Implement parallelization or mark as unparallelizable #4675

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marinegor opened this issue Aug 20, 2024 · 3 comments · May be fixed by #4884
Open

MDAnalysis.analysis.rdf: Implement parallelization or mark as unparallelizable #4675

marinegor opened this issue Aug 20, 2024 · 3 comments · May be fixed by #4884
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Component-Analysis help wanted parallelization

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@marinegor
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Given a newly implemented parallelization (https://docs.mdanalysis.org/dev/documentation_pages/analysis/parallelization.html), implement it for all classes in analysis.rdf module. You may use analysis.RMSD in develop as a reference.

You need to add:

  • appropriate implementation of result aggregation for AnalysisBase subclasses in analysis.rdf module (or explicitly limit available backends if the classes aren't parallelizable)
  • a boilerplate fixture(s) to testsuite/analysis/conftest.py, analogous with existing ones
  • a client_... fixtures to all tests using in testsuite/MDAnalysisTests/analysis/test_rdf.py, and modify the way run() method is called
@tanishy7777
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can I work on this @RMeli ?

@marinegor
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hey @tanishy7777 just start working on it and submit your PR, I don't think there's a need to ask for a permission.

it's not that big of an issue (like maybe 20-30 LOC, you can check other issues marked parallelization), so there's no need to struggle to prevent double work.

this comment goes also on #4676

@tanishy7777
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hey @tanishy7777 just start working on it and submit your PR, I don't think there's a need to ask for a permission.

it's not that big of an issue (like maybe 20-30 LOC, you can check other issues marked parallelization), so there's no need to struggle to prevent double work.

Got it! Thanks for your reply

@tanishy7777 tanishy7777 linked a pull request Jan 7, 2025 that will close this issue
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mark analysis.rdf.InterRDF and analysis.rdf.InterRDF_s as not parallizable tanishy7777/mdanalysis
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@RMeli @marinegor @tanishy7777