Porting and Optimizing Molecular Docking onto the SX-Aurora TSUBASA Vector Computer
| Autor: | Erich Focht, Andreas Koch, Leonardo Solis-Vasquez |
|---|---|
| Rok vydání: | 2021 |
| Předmět: |
Computer Networks and Communications
Computer science Parallel computing AutoDock Porting Field (computer science) Computer Science Applications Vector processor Acceleration Computational Theory and Mathematics Hardware and Architecture Docking (molecular) Server Performance efficiency Software Information Systems |
| Zdroj: | Supercomputing Frontiers and Innovations. 8 |
| ISSN: | 2313-8734 |
| Popis: | In computer-aided drug design, the rapid identification of drugs is critical for combating diseases. A key method in this field is molecular docking, which aims to predict the interactions between two molecules. Molecular docking involves long simulations running compute-intensive algorithms, and thus, can profit a lot from hardware-based acceleration. In this work, we investigate the performance efficiency of the SX-Aurora TSUBASA vector computer for such simulations. Specifically, we present our methodology for porting and optimizing AutoDock, a widely-used molecular docking program. Using a number of platform-specific code optimizations, we achieved executions on the SX-Aurora TSUBASA that are in average 3.6× faster than on modern 128-core CPU servers, and up to a certain extent, competitive to V100 and A100 GPUs. To the best of our knowledge, this is the first molecular docking implementation for the SX-Aurora TSUBASA. |
| Databáze: | OpenAIRE |
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