Added AVX512 intrinsics-based Ungapped SW alignent kernel
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
- Implemented ungapped SW alignment kernel using AVX512 intrinsics.
- Added build-time flag
-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:
Steinegger M and Söding J.
MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets.
Nature Biotechnology, doi: 10.1038/nbt.3988 (2017). -
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:
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release -DHAVE_TESTS=0 -DHAVE_MPI=0 -DHAVE_AVX512=1 ..
make -j