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disable nsgrid neighbor search #2930

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orbeckst opened this issue Sep 2, 2020 · 2 comments
Closed

disable nsgrid neighbor search #2930

orbeckst opened this issue Sep 2, 2020 · 2 comments
Labels
Component-Analysis Component-Core Component-lib PBC performance Priority-High
Projects
backport
Milestone
1.0.1

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@orbeckst
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orbeckst commented Sep 2, 2020

Expected behavior

neighbor search with capped_distance returns reliable and consistent results

Actual behavior

It doesn't.

See #2229 (comment) for detailed analysis of problems.

Course of action

Disable nsgrid-based neighbor search until we have a stable solution. Use PBC-pkdtree instead.

Impact

  • slower distance-based searches and analysis (e.g. RDF)
  • correct results in all cases

Code to reproduce the behavior

See linked issues.

Current version of MDAnalysis

  • Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)") 1.0.x, 2.0.0-dev
  • Which version of Python (python -V)? any
  • Which operating system? any
@orbeckst orbeckst added this to the 1.0.x milestone Sep 2, 2020
@orbeckst orbeckst mentioned this issue Sep 2, 2020
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@orbeckst orbeckst mentioned this issue Sep 4, 2020
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@orbeckst orbeckst added this to To do in backport Sep 19, 2020
@IAlibay
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IAlibay commented Oct 23, 2020

I'm working on a quick fix for this given the discussion in #2768

Do we want to solely remove nsgrid from 1.0.1 (i.e. only target master), or do we want to do so for develop too?

IAlibay added a commit to IAlibay/mdanalysis that referenced this issue Oct 23, 2020
@IAlibay
Temporarily disable nsgrid (Issue MDAnalysis#2930)
ce11aeb
@IAlibay IAlibay mentioned this issue Oct 23, 2020
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@orbeckst orbeckst moved this from To do to In progress in backport Oct 24, 2020
@IAlibay IAlibay mentioned this issue Nov 9, 2020
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4 tasks
lilyminium pushed a commit that referenced this issue Dec 22, 2020
@IAlibay
Temporarily disable nsgrid (Issue #2930) (#3004)
6e2d8e7 
Fixes #2930
 - Temporarily replaces nsgrid with pkdtree
 - Adds note on the use of nsgrid
@lilyminium
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Closed in #3004.

backport automation moved this from In progress to Done Dec 23, 2020
@MohitKumar020291 MohitKumar020291 mentioned this issue Jan 21, 2023
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Labels
Component-Analysis Component-Core Component-lib PBC performance Priority-High
Projects
backport
  
Done
Milestone
1.0.1
Development

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3 participants
@orbeckst @IAlibay @lilyminium