Skip to content

Add PME parameter options and automatic PME tuning - #235

Merged
lohedges merged 3 commits into
develfrom
feature_pme_parameters
Oct 1, 2026
Merged

lohedges merged 3 commits into
develfrom
feature_pme_parameters

Conversation

@lohedges

@lohedges lohedges commented Oct 1, 2026

Copy link
Copy Markdown
Contributor

Profiling showed that OpenMM's default PME parameters often use a much finer reciprocal-space grid than the requested accuracy needs. Choosing them more carefully gives a decent speedup at the same or better accuracy. This PR uses the new Sire support to add pme_alpha, pme_grid and pme_spacing options for setting the PME parameters directly, and a pme_tolerance option for the Ewald error tolerance, whose default is unchanged. It also adds a tune_pme option, on by default. On the CUDA and OpenCL platforms it chooses the fastest PME parameters that are at least as accurate as those OpenMM would choose from pme_tolerance. Tuning runs once at setup, takes tens of seconds, and logs the chosen parameters and their relative force error. The result is saved to pme_parameters.yaml in the output directory and reused on restart, so a run keeps the same parameters even if it's restarted on different hardware. Restarts of runs from before this feature carry on with the default parameters. Tuning is skipped when explicit PME options are given, and on the CPU platform. This depends on OpenBioSim/sire#499.

@lohedges
lohedges force-pushed the feature_pme_parameters branch from 1863dd3 to 337d74a Compare October 1, 2026 15:42
@lohedges
lohedges deployed to somd2-build October 1, 2026 15:42 — with GitHub Actions Active
@lohedges
lohedges deployed to somd2-build October 1, 2026 15:42 — with GitHub Actions Active
@lohedges
lohedges deployed to somd2-build October 1, 2026 15:42 — with GitHub Actions Active
@lohedges
lohedges deployed to somd2-build October 1, 2026 17:17 — with GitHub Actions Active
@lohedges
lohedges merged commit 0b5a4fd into devel Oct 1, 2026
10 of 12 checks passed
@lohedges
lohedges deleted the feature_pme_parameters branch October 1, 2026 17:34

This branch was successfully deployed

1 active deployment
somd2-build — 337d74a8 Deployed Oct 1, 2026 by lohedges via build (3.11, linux) #117
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

enhancement New feature or request

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant