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Pymbar4 entropy enthalpy#785

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mikemhenry merged 15 commits into
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pymbar4-entropy_enthalpy
Aug 1, 2025
Merged

Pymbar4 entropy enthalpy#785
mikemhenry merged 15 commits into
mainfrom
pymbar4-entropy_enthalpy

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@ijpulidos

@ijpulidos ijpulidos commented Jul 31, 2025

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Description

This supersedes #758
Fixes #757

This just make the entropy and enthalpy test a separate more granular test that we can check independently.

Todos

  • Implement feature / fix bug
  • Add tests
  • Update documentation as needed
  • Update changelog to summarize changes in behavior, enhancements, and bugfixes implemented in this PR

Status

  • Ready to go

Changelog message

Add support for entropy and enthalpy calculations with pymbar4

@codecov

codecov Bot commented Jul 31, 2025

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Codecov Report

❌ Patch coverage is 78.18182% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.28%. Comparing base (59c14bf) to head (13e62c4).
⚠️ Report is 7 commits behind head on main.

🚀 New features to boost your workflow:
  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@ijpulidos

ijpulidos commented Jul 31, 2025

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@mikemhenry from the comment in #758 (comment) . I don't think it's that easy to use our wrapper for these changes. I think eventually we just have to drop support for pymbar 3 at some point.

@ijpulidos ijpulidos linked an issue Jul 31, 2025 that may be closed by this pull request
@ijpulidos

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One thing that I noticed is that this particular test fails with a rather cryptic XLA message when running in GPU with CUDA. The message is as follows

ERROR: Flag 'coordination_agent_recoverable' was defined more than once but with differing types. Defined in files 'external/xla/xla/tsl/distributed_runtime/coordination/coordination_service_agent.cc' and 'external/xla/xla/tsl/distributed_runtime/coordination/coordination_service_agent.cc'.

And just fails without much information. On CPU this works fine, hopefully it's just something with my local environment and nothing deeper to worry about.

@ijpulidos

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The test seems to be rather unstable even doubling the iterations. I guess we could have better results with more states, but that probably requires a bigger refactor and would affect the other tests as well. That said, re-running the failed jobs would probably just work if we want the green checks.

I wonder if we also want better or more robust of checking this instead of the hard 6.0 SIGMA line. For example, taking an average of the higher percentile or similar, and comparing that one with the 6 sigma. That is basically smooth the "worse" results and compare the smooth results.

@ijpulidos ijpulidos requested a review from mikemhenry July 31, 2025 21:55
@ijpulidos

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Hmm, ok, on a second thought, maybe doubling the iterations did help. I see a significantly higher number of CI workflows failing with the original number of iterations...

@mikemhenry mikemhenry merged commit de07551 into main Aug 1, 2025
40 of 42 checks passed
@mikemhenry mikemhenry deleted the pymbar4-entropy_enthalpy branch August 1, 2025 15:39
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Version 0.25.0 does not still support pymbar version 4* get_entropy() and get_enthalpy() does not work with pymbar4

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