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MDAnalysis.analysis.hydrogenbonds.hbond_analysis: Implement parallelization or mark as unparallelizable #4664

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marinegor opened this issue Aug 20, 2024 · 0 comments · Fixed by #4718
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MDAnalysis.analysis.hydrogenbonds.hbond_analysis: Implement parallelization or mark as unparallelizable #4664

marinegor opened this issue Aug 20, 2024 · 0 comments · Fixed by #4718
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@talagayev
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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.hydrogenbonds.hbond_analysis 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.hydrogenbonds.hbond_analysis 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_hydrogenbond_analysis.py, and modify the way run() method is called
@talagayev talagayev mentioned this issue Sep 25, 2024
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orbeckst added a commit that referenced this issue Oct 7, 2024
@talagayev @yuxuanzhuang @orbeckst
Implementation of Parallelization to analysis.hydrogenbonds.hbond_ana…
474be5b 
…lysis (#4718)

- Fixes #4664 
- Parallelization of the backend support to the class HydrogenBondAnalysis in hbond_analysis.py
- Moved setting up of donors and acceptors from _prepare() to __init__() (needed to make
  parallel processing work)
- Addition of parallelization tests in test_hydrogenbonds_analysis.py and fixtures in conftest.py
- Updated Changelog

---------

Co-authored-by: Yuxuan Zhuang <[email protected]>
Co-authored-by: Oliver Beckstein <[email protected]>
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Implementation of Parallelization to analysis.hydrogenbonds.hbond_analysis talagayev/mdanalysis
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@RMeli @marinegor @talagayev