'MDAnalysis.analysis.diffusionmap' parallelization

[talagayev]

Fixes #4679 attempt

Changes made in this Pull Request:

• added backends and aggregators to DistanceMatrix in analysis.diffusionmap
• added the client_DistanceMatrix in conftest.py
• added client_DistanceMatrix in run() in test_diffusionmap.py

Here is the Problem:

From what I see currently self.results.dist_matrix = np.zeros((self.n_frames, self.n_frames)) has the problem, that when it uses parallelization the self.n_frames value gets divided, which leads with the ndarray_sum and ndarray_mean to:

E AssertionError: E Arrays are not almost equal to 4 decimals E (shapes (2,), (4,) mismatch) E ACTUAL: array([1., 1.]) E DESIRED: array([1, 1, 1, 1])

and with the use of ndarray_vstack or ndarray_hstack it leads to the following error: numpy.linalg.LinAlgError: Last 2 dimensions of the array must be square

so I am not sure if this can be somehow adjusted, I also encountered a similar case also while trying to parallelize analysis.msd

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.

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📚 Documentation preview 📚: https://mdanalysis--4745.org.readthedocs.build/en/4745/

[pep8speaks]

Hello @talagayev! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! :beers:

Comment last updated at 2024-10-19 23:05:04 UTC