Fully Integrated On-FPGA Molecular Dynamics Simulations

• Published in: arXiv.org 2019-05
• Main Authors: Chen, Yang, Geng, Tong, Wang, Tianqi, Patel, Rushi, Xiong, Qingqing, Sanaullah, Ahmed, Sheng, Jiayi, Lin, Charles, Sachdeva, Vipin, Sherman, Woody, Herbordt, Martin C
• Format: Article
• Language: English
• Subjects: Computer simulation; Data storage; Migration; Molecular dynamics
• ISSN: 2331-8422

The implementation of Molecular Dynamics (MD) on FPGAs has received substantial attention. Previous work, however, has consisted of either proof-of-concept implementations of components, usually the range-limited force; full systems, but with much of the work shared by the host CPU; or prototype demonstrations, e.g., using OpenCL, that neither implement a whole system nor have competitive performance. In this paper, we present what we believe to be the first full-scale FPGA-based simulation engine, and show that its performance is competitive with a GPU (running Amber in an industrial production environment). The system features on-chip particle data storage and management, short- and long-range force evaluation, as well as bonded forces, motion update, and particle migration. Other contributions of this work include exploring numerous architectural trade-offs and analysis on various mappings schemes among particles/cells and the various on-chip compute units. The potential impact is that this system promises to be the basis for long timescale Molecular Dynamics with a commodity cluster.