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'MDAnalysis.analysis.align' parallelization

Open talagayev opened this issue 4 months ago • 1 comments

Fixes #4659 attempt

Changes made in this Pull Request:

  • added backends and aggregators to AlignTraj and AverageStructure in analysis.align.
  • added the client_AlignTraj and client_AverageStructure in conftest.py
  • added client_AlignTraj and client_AverageStructure in run() in test_align.py

Currently for AlignTraj it only accepts serial and dask with multiprocessing leading to the pytests taking forever. An additional error that appears is the following:

OSError: File opened in mode: self.mode. Reading only allow in mode "r"

For AverageStructure the Failure that appears is the following:

AttributeError: 'numpy.ndarray' object has no attribute 'load_new'

Which leads me to believe that AverageStructure can not be parallelized, but I would need additional opinions on it and on AlignTraj :)

PR Checklist

  • [x] Tests?
  • [ ] Docs?
  • [ ] CHANGELOG updated?
  • [x] Issue raised/referenced?

Developers certificate of origin


📚 Documentation preview 📚: https://mdanalysis--4738.org.readthedocs.build/en/4738/

talagayev avatar Oct 18 '24 18:10 talagayev