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WIP: create Universes with Merge in encore #2579

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lilyminium
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Fixes #2578
Fixes MDAnalysis/mdaencore#32

Changes made in this Pull Request:

  • transfer Universes to memory before getting coordinates in encore
  • create new Universes with mda.Merge instead of mda.Universe in encore
  • pass select into merge_universe to avoid the create_subverse() shenanigans in Clustering ensemble of in memory universes mdaencore#32, which are necessary if you have Universes with different atoms
  • improved performance a bit

Tests to come...

PR Checklist

  • Tests?
  • Docs?
  • CHANGELOG updated?
  • Issue raised/referenced?

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codecov bot commented Mar 4, 2020

Codecov Report

Merging #2579 into develop will decrease coverage by 0.01%.
The diff coverage is n/a.

Impacted file tree graph

@@             Coverage Diff             @@
##           develop    MDAnalysis/mdanalysis#2579      +/-   ##
===========================================
- Coverage    90.45%   90.43%   -0.02%     
===========================================
  Files          173      173              
  Lines        23381    23399      +18     
  Branches      3038     3037       -1     
===========================================
+ Hits         21149    21162      +13     
- Misses        1605     1609       +4     
- Partials       627      628       +1     

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@lilyminium
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These functions are hardly the bottleneck in encore, but every bit helps.

Original:
Screenshot 2020-03-04 at 5 05 29 PM

New:

Screenshot 2020-03-04 at 5 13 47 PM

merge_universes is strictly slower when the inputs are the same, but when select does not choose all the atoms, performance improves. This has the added benefit of being able to pass in universes with different atoms, so long as the selection is the same.

@richardjgowers richardjgowers changed the title create Universes with Merge in encore WIP: create Universes with Merge in encore Mar 6, 2020
@lilyminium
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Closed due to being superceded by newer work (related to #2664).

@lilyminium lilyminium closed this May 19, 2021
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