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

Authors:
Yongfeng Gu;Tom VanCourt;Martin C. Herbordt
Affiliations:
Computer Architecture and Automated Design Lab, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, United States;Computer Architecture and Automated Design Lab, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, United States;Computer Architecture and Automated Design Lab, Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, United States
Venue:
Parallel Computing
Year:
2008

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Abstract

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 256K 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.