2019/05/14 by Chen Yang, Yang, Chen, Tong Geng +19
Computer Science · Engineering · #Distributed #FOS: Computer and information sciences #Hardware Architecture (cs.AR) #Low-power high-performance VLSI design #Nanopore and Nanochannel Transport Studies #Parallel #Parallel Computing and Optimization Techniques #and Cluster Computing (cs.DC)
paper · pdf · doi:10.48550/arxiv.1905.05359
openalex publication_date 2019/05/14 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.