Added AVX512 intrinsics-based Ungapped SW alignent kernel #983
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Outdated suggestions cannot be applied.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
This PR adds support for an AVX512 intrinsics-based ungapped Smith-Waterman (SW) alignment kernel to MMseqs2, enabling higher performance on supported hardware.
Changes
-DHAVE_AVX512=1to enable AVX512 kernel.Performance
On 2 socket Intel® Xeon® Platinum 8592+ CPU, the AVX512 kernel shows an end-to-end speedup of ~1.25× for
easy-searchcompared to the AVX2 version.Benchmarking was performed using the dataset from:
The dataset contains 6370 query sequences and ~30M database sequences.
A batch size of 1 was used for both AVX2 and AVX512 runs to ensure fair comparison.
Build Instructions
To build the MMseqs2 binary with AVX512 support: