feat: OpenMP + AVX-512 bindings and calcStructuresParallel() for trajectory analysis#41
Open
aminkvh wants to merge 1 commit into
Open
feat: OpenMP + AVX-512 bindings and calcStructuresParallel() for trajectory analysis#41aminkvh wants to merge 1 commit into
aminkvh wants to merge 1 commit into
Conversation
- OpenMP + SIMD flags in setup.py - calcStructuresParallel() Cython wrapper - Embed parallel C sources directly (replaces submodule) - 24/24 compatibility tests pass
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Summary
Adds OpenMP and SIMD compile flags to setup.py, and exposes the new
freesasa_calc_structures_parallel()C API ascalcStructuresParallel()in Python. This enables near-linear speedup for MD trajectory analysis.
All existing tests pass.
What Changed
setup.py— Auto-detects and enables-fopenmp,-march=native,-O3,-ffast-mathat build time. Graceful fallback if unavailable.src/freesasa.pyx— NewcalcStructuresParallel(structures, params)function. Takes a list of Structure objects, returns a list of Results.
src/cfreesasa.pxd— C declaration forfreesasa_calc_structures_parallellib/src/— Embedded parallel C sources (replaces submodule reference)from the companion fork: https://github.com/aminkvh/freesasa-parallel
Usage
Performance (8 frames × 58,674 atoms)
Tests
24/24 compatibility tests pass covering the full existing Python API.