Fully Integrated FPGA Molecular Dynamics Simulations

Authors: Chen Yang (Boston University), Tong Geng (Boston University), Tianqi Wang (Boston University), Rushi Patel (Boston University), Qingqing Xiong (Boston University), Ahmed Sanaullah (Boston University), Chunshu Wu (Boston University), Jiayi Sheng (Falcon Computing Solutions Inc), Charles Lin (Silicon Therapeutics), Vipin Sachdeva (Silicon Therapeutics), Woody Sherman (Silicon Therapeutics), Martin Herbordt (Boston University)

Abstract: 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.


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