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MDAnalysis.analysis.pca: Implement parallelization or mark as unparallelizable #4680

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marinegor opened this issue Aug 20, 2024 · 1 comment · Fixed by #4684
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MDAnalysis.analysis.pca: Implement parallelization or mark as unparallelizable #4680

marinegor opened this issue Aug 20, 2024 · 1 comment · Fixed by #4684
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@orbeckst
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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.pca 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.pca 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_pca.py, and modify the way run() method is called
@orbeckst
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PCA is not easily parallelizable as far as I know so I will just mark it as not parallelizable for now.

@orbeckst orbeckst self-assigned this Aug 23, 2024
orbeckst added a commit that referenced this issue Aug 23, 2024
@orbeckst
mark analysis.pca.PCA as not parallelizable
4db6f27 
- fix #4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
@orbeckst orbeckst mentioned this issue Aug 23, 2024
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orbeckst added a commit that referenced this issue Aug 26, 2024
@orbeckst
mark analysis.pca.PCA as not parallelizable (#4684)
d73995a 
- fix #4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG
yuxuanzhuang pushed a commit to yuxuanzhuang/mdanalysis that referenced this issue Sep 9, 2024
@orbeckst @yuxuanzhuang
mark analysis.pca.PCA as not parallelizable (MDAnalysis#4684)
dc9654e 
- fix MDAnalysis#4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG
hmacdope pushed a commit that referenced this issue Sep 10, 2024
@yuxuanzhuang @MattTDavies
@IAlibay @orbeckst
Remove GSD from optional test dependencies (#4707)
319b667 
* Fixed high dimensional GroupBase indexing.

* fixed pep8 issues

* Removed sanitisation

* Fix #4687 -- rdkit values in azure CI (#4688)

* Investigate rdkit issue

* Update azure-pipelines.yml

* fix numpy 2.0 import block

* fix imports

* mark analysis.pca.PCA as not parallelizable (#4684)

- fix #4680
- PCA explicitly marked as not parallelizable (at least not with
  simple split-apply-combine)
- add tests
- update CHANGELOG

* disable gsd

* disable gsd in azure

* reduce timeout and set logical

* fix azure

* restore timeout to 200

---------

Co-authored-by: Matthew Davies <128810112+MattTDavies@users.noreply.github.com>
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>
Co-authored-by: Oliver Beckstein <orbeckst@gmail.com>
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mark analysis.pca.PCA as not parallelizable MDAnalysis/mdanalysis
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@orbeckst @RMeli @marinegor