mdanalysis
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'MDAnalysis.analysis.align' parallelization
Fixes #4659 attempt
Changes made in this Pull Request:
- added
backends
andaggregators
toAlignTraj
andAverageStructure
inanalysis.align
. - added the
client_AlignTraj
andclient_AverageStructure
inconftest.py
- added
client_AlignTraj
andclient_AverageStructure
inrun()
intest_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
- [x] I certify that this contribution is covered by the LGPLv2.1+ license as defined in our LICENSE and adheres to the Developer Certificate of Origin.
📚 Documentation preview 📚: https://mdanalysis--4738.org.readthedocs.build/en/4738/