Compute selection: deviceIndex & enforce 1 thread in vacuum

[IAlibay]

Fixes #739 #704

Checklist

• Added a news entry

Developers certificate of origin

• I certify that this contribution is covered by the MIT License here and the Developer Certificate of Origin at https://developercertificate.org/.

[pep8speaks]

Hello @IAlibay! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

• In the file openfe/protocols/openmm_afe/base.py:

Line 195:80: E501 line too long (93 > 79 characters)
Line 739:80: E501 line too long (81 > 79 characters)

• In the file openfe/protocols/openmm_md/plain_md_methods.py:

Line 620:80: E501 line too long (81 > 79 characters)
Line 623:80: E501 line too long (80 > 79 characters)

• In the file openfe/protocols/openmm_rfe/equil_rfe_methods.py:

Line 935:80: E501 line too long (81 > 79 characters)
Line 938:80: E501 line too long (80 > 79 characters)

• In the file openfe/protocols/openmm_utils/omm_compute.py:

Line 30:80: E501 line too long (136 > 79 characters)

• In the file openfe/protocols/openmm_utils/omm_settings.py:

Line 178:80: E501 line too long (132 > 79 characters)

Comment last updated at 2024-07-04 00:06:38 UTC

[codecov]

Codecov Report

Attention: Patch coverage is 83.33333% with 4 lines in your changes missing coverage. Please review.

Project coverage is 92.15%. Comparing base (ecc8a50) to head (48707e2).
Report is 120 commits behind head on main.

Files with missing lines	Patch %	Lines
openfe/protocols/openmm_utils/omm_compute.py	55.55%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #752      +/-   ##
==========================================
- Coverage   93.98%   92.15%   -1.84%     
==========================================
  Files         134      134              
  Lines        9790     9800      +10     
==========================================
- Hits         9201     9031     -170     
- Misses        589      769     +180     

Flag	Coverage Δ
fast-tests	92.15% <83.33%> (?)
slow-tests	?

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[IAlibay]

@mikemhenry when you get a chance please do have a look at this - I suspect it'll make life a bit easier in some cases.

[IAlibay]

Actually we should probably have a chat about how we handle this long term - this is a bit like MPI settings, where technically we shouldn't make this immutable but maybe something we pick up at run time?

How can we go about handling this properly?

[mikemhenry]

Something I don't think we abstracted well are "run time arguments". Like we have the split for settings that change thermo, but didn't consider a category of non-thermo settings that make the most sense to pick at runtime, I haven't looked at the code yet and will update this comment, but I suspect what we should do is

1. have some default
2. read this setting
3. read in an environmental variable

If we do things in that order, it means we don't break anything old, then when configuring your system you can make some choices, but then when running on HPC you can still set things if needed and override the settings

[mikemhenry]

good example of a nice changelog entry but since this was a private API, no symver major bump needed

[mikemhenry]

Do we want a private namespace or is this now in our public API?

Suggested change

	to `openfe.protocols.openmm_utils.omm_compute`.
	to `openfe.protocols.openmm_utils._omm_compute`.

[mikemhenry]

This one is good, have a few notes but nothing blocking.

[mikemhenry]

another argument we really should have an explicit way of saying this is a vacuum simulation. I propose we add a setting somewhere for that #904

In the meantime, this seems like a pretty good heuristic.

We could do more logging, I it would be nice to do a hackathon on it but in the mean time I will just suggest as I see it. It would be good to log what is going on here, maybe could be more verbose than what I suggest but this seems like a spot where if someone was like "why is this running on the CPU and not the GPU?" a log message could hep

Suggested change

	restrict_cpu = settings['forcefield_settings'].nonbonded_method.lower() == 'nocutoff'
	restrict_cpu = settings['forcefield_settings'].nonbonded_method.lower() == 'nocutoff'
	logging.info(f"{restrict_cpu=}")