Fully Integrated FPGA Molecular Dynamics Simulations

C Yang and T Geng and TQ Wang and R Patel and QQ Xiong and A Sanaullah and CS Wu and JY Sheng and C Lin and V Sachdeva and W Sherman and MC Herbordt, PROCEEDINGS OF SC19: THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS (2019).

DOI: 10.1145/3295500.3356179

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 of 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.

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