High-throughput drug discovery on the Fujitsu A64FX architecture

Research Paper

EUPEX partner CINECA presented this research paper at HPC Asia 2024, the International Conference on High Performance Computing in Asia-Pacific Region, that was held in Nagoya, Japan, form 25 to 27 January 2024.

Abstract

High-performance computational kernels that optimally exploit modern vector-capable processors are critical in running large-scale drug discovery campaigns efficiently and promptly compatible with the constraints posed by urgent computing needs. Yet, state-of-the-art virtual screening workflows focus either on the broadness of features provided to the drug researcher or performance on high-throughput accelerators, leaving the task of deploying efficient CPU kernels to the compiler. We ported the key parts of the LiGen drug discovery pipeline, based on molecular docking, to the Fujitsu A64FX platform and leveraged its vector processing capabilities via an industry-proven retargetable SIMD programming model. By rethinking and optimizing key geometrical docking algorithms to leverage SVE instructions, we are able to provide efficient, high throughput execution on SVE-capable platforms.

Authors: Filippo Barbari, Federico Ficarelli, Daniele Cesarini (CINECA)

DOI: 10.1145/3636480.3637095