Clean up dhfr nonbonded tests

proteneer / timemachine

Differentiate all the things!

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Clean up dhfr nonbonded tests #1322

Closed badisa closed 2 months ago

badisa commented 2 months ago

Seen by @mcwitt that these would occasionally OOM in the CI. Separated into pytest.mark.parameterize test both to better align with our common way of writing tests as well as make it easier to tell which set of parameters triggered the OOMs.
This may fix the issue if it was accumulation of memory and slow garbage collection, but doubtful. May need to reduce the number of atoms passed in the reference platform.

badisa commented 2 months ago

@mcwitt @maxentile I noticed that after https://github.com/proteneer/timemachine/pull/1290 we had changed test_nonbonded.py to test cutoff=1.2 but that setup_dhfr uses cutoff=1.0 which meant that for any tests that don't override the cutoff could use the wrong cutoff.

Changed to set the cutoff to 1.2 in https://github.com/proteneer/timemachine/pull/1322/commits/f46d0e8d51582daf27bf8ddffcb1d83248ad6d11