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[CI] tests related to guessers are slow #4842

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orbeckst opened this issue Dec 18, 2024 · 3 comments · May be fixed by #4893
Open

[CI] tests related to guessers are slow #4842

orbeckst opened this issue Dec 18, 2024 · 3 comments · May be fixed by #4893
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Component-Topology Continuous Integration performance testing

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@orbeckst
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Expected behavior

Tests run reasonably quickly in our CI (let's say, faster than ~20 seconds).

Actual behavior

The top 3 slowest tests are all related to guessing functionality and take between 25 and 100 seconds. E.g. from https://github.com/MDAnalysis/mdanalysis/actions/runs/12399640935/job/34615007364?pr=4729 :

100.18s call     MDAnalysisTests/guesser/test_base.py::TestBaseGuesser::test_guessing_angles_respects_bond_kwargs
25.62s call     MDAnalysisTests/guesser/test_base.py::TestBaseGuesser::test_guess_topology_objects_out_of_order_init
25.50s call     MDAnalysisTests/guesser/test_base.py::TestBaseGuesser::test_guess_topology_objects_out_of_order_guess
@tanishy7777
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So should the tests for these three functions be rewritten to speed it up? @orbeckst

@orbeckst
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You are asking a very good question, @tanishy7777 .

I haven't looked at tests or the code, I only noticed that they seem to take a very long time compared to other tests. Given that the new guesser code is a recent addition (in 2.8.0), we should look at the impact that this code has. The first step would be understanding why they take so long: are the tests written in a complicated way and could be shortened or is the underlying guesser code slow?

@tanishy7777
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tanishy7777 commented Dec 24, 2024 •
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I ran cProfiler(thrice to make sure of the results) on these test functions on my local system
The test_guess_topology_objects_out_of_order_init and test_guess_topology_objects_out_of_order_guess take about 5 seconds each and test_guessing_angles_respects_bond_kwargs takes about 25 seconds.
I have attached the output below. I am not sure what is causing it to take so long on github CI.
@orbeckst

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@yuxuanzhuang yuxuanzhuang linked a pull request Jan 14, 2025 that will close this issue
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Test on smaller pdb for guesser to reduce test duration yuxuanzhuang/mdanalysis
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@orbeckst @tanishy7777