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MDAnalysis.analysis.density: Implement parallelization or mark as unparallelizable #4677

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marinegor opened this issue Aug 20, 2024 · 0 comments · Fixed by #4729
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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.density 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.density 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_density.py, and modify the way run() method is called
orbeckst added a commit that referenced this issue Dec 18, 2024
* Fixes #4677
* parallelize DensityAnalysis
* Changes made in this Pull Request:
    - added backends and aggregators to DensityAnalysis in analysis.density
    - added client_DensityAnalysis in conftest.py
    - added client_DensityAnalysis to the tests in test_density.py
* Update CHANGELOG

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Co-authored-by: Yuxuan Zhuang <yuxuan.zhuang@dbb.su.se>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
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