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Improve libdcd cython #3888

Merged
merged 42 commits into from
Nov 29, 2022
Merged

Improve libdcd cython #3888

merged 42 commits into from
Nov 29, 2022

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hmacdope
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@hmacdope hmacdope commented Oct 27, 2022 •
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Fixes #3882 #3923

Improves the cython in the DCD reader to be more compiled.

Changes made in this Pull Request:

  • Improves the cython in the DCD reader.

PR Checklist

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

hmacdope
hmacdope commented Oct 27, 2022
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package/MDAnalysis/coordinates/DCD.py Outdated
@@ -191,7 +191,7 @@ def _read_next_timestep(self, ts=None):
if ts is None:
# use a copy to avoid that ts always points to the same reference
# removing this breaks lammps reader
ts = self.ts.copy()
ts = self.ts.copy() # why is this copy required ??
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@orbeckst @MDAnalysis/coredevs does anyone know specifically why this copy is required? None of the other readers use this pattern and it is ~30% overhead but removing it breaks a bunch of tests. I will keep working on it but if anyone has a quick answer would be appreciated.

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@hmacdope hmacdope Oct 27, 2022 •
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I will keep working on it in the meantime but the behaviour seems to be inconsistent with the other readers.

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I am going to move discussion to an issue.

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Moved to #3889

@hmacdope hmacdope added the CZI-performance performance track of CZIEOSS4 grant label Oct 27, 2022
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codecov bot commented Oct 27, 2022 •
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Codecov Report

Base: 94.36% // Head: 94.39% // Increases project coverage by +0.03% 🎉

Coverage data is based on head (64ad08a) compared to base (497f45e).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files 
@@             Coverage Diff             @@
##           develop    #3888      +/-   ##
===========================================
+ Coverage    94.36%   94.39%   +0.03%     
===========================================
  Files          194      194              
  Lines        25109    25146      +37     
  Branches      3398     3398              
===========================================
+ Hits         23694    23737      +43     
+ Misses        1366     1360       -6     
  Partials        49       49
Impacted Files Coverage Δ
package/MDAnalysis/coordinates/DCD.py 100.00% <100.00%> (ø)
package/MDAnalysis/lib/formats/libdcd.pyx 91.11% <100.00%> (+2.58%) ⬆️
package/MDAnalysis/coordinates/base.py 94.78% <0.00%> (+0.17%) ⬆️
MDAnalysisTests/coordinates/base.py 94.42% <0.00%> (+0.17%) ⬆️

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@hmacdope hmacdope mentioned this pull request Oct 28, 2022
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orbeckst
orbeckst requested changes Oct 28, 2022
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Looking fine. Just minor question and

  • docs (versionchanged)
  • Changelog update

thanks.

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orbeckst
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orbeckst commented Oct 28, 2022 •
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@hmacdope for my first review I only saw one set of changes. You clearly have a change log entry. For other things I just added comments. (Sorry for bad typing, reviewing from phone is not ideal)

IAlibay
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IAlibay
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@hmacdope hmacdope added this to the Release 3.0 milestone Oct 28, 2022
richardjgowers
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@hmacdope can probably use a shared scratch buffer. You can raise an issue about deprecating that timeseries helper method

This was referenced Nov 21, 2022
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orbeckst
orbeckst approved these changes Nov 22, 2022
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only minimal doc/changelog updates — please do them but I'll approve as to not hold up

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@hmacdope can probably use a shared scratch buffer. You can raise an issue about deprecating that timeseries helper method

Performance improvement of ~ 12% with use of shared scratch buffer

image

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Windows C++ compiler seems to be complaining about libdcd, I'll revert it back to compiling as C sometime tommorow.

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hmacdope commented Nov 24, 2022 •
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@MDAnalysis/coredevs I think we are good to roll here?

@orbeckst orbeckst self-assigned this Nov 29, 2022
@orbeckst orbeckst linked an issue Nov 29, 2022 that may be closed by this pull request
Improve deprecation warning for DCDReader copying timestep #3923
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@orbeckst orbeckst merged commit d63cd6d into MDAnalysis:develop Nov 29, 2022
This was referenced Feb 28, 2023
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@IAlibay IAlibay IAlibay left review comments

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@richardjgowers richardjgowers richardjgowers approved these changes

@orbeckst orbeckst orbeckst approved these changes

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Component-lib Component-Readers CZI-performance performance track of CZIEOSS4 grant enhancement
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CZI Performance track
Status: Done
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2.4.0
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Successfully merging this pull request may close these issues.

Improve deprecation warning for DCDReader copying timestep Improve DCD reader typing and performance.
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@hmacdope @orbeckst @kain88-de @richardjgowers @IAlibay