Explicit design of FPGA-based coprocessors for short-range force computations in molecular dynamics simulations

• Published in: Parallel computing Vol. 34; no. 4; pp. 261 - 277
• Main Authors: Gu, Yongfeng, VanCourt, Tom, Herbordt, Martin C.
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier B.V 01.05.2008
• Subjects: Accelerator; Coprocessor; FPGA; High performance reconfigurable computing; Molecular dynamics; Molecular dynamics; Coprocessor; FPGA; High performance reconfigurable computing; Accelerator
• ISSN: 0167-8191; 1872-7336; 1872-7336
• DOI: 10.1016/j.parco.2008.01.007

FPGA-based acceleration of molecular dynamics simulations (MD) has been the subject of several recent studies. The short-range force computation, which dominates the execution time, is the primary focus. Here we combine: a high level of FPGA-specific design including cell-lists, systematically determined interpolation and precision, handling of exclusion, and support for MD simulations of up to 256 K particles. The target system consists of a standard PC with a 2004-era COTS FPGA board. There are several innovations: new microarchitectures for several major components, including the cell-list processor and the off-chip memory controller; and a novel arithmetic mode. Extensive experimentation was required to optimize precision, interpolation order, interpolation mode, table sizes, and simulation quality. We obtain a substantial speed-up over a highly tuned production MD code.