Preliminary investigation of advanced electrostatics in molecular dynamics on reconfigurable computers

ABSTRACT

Scientific computing is marked by applications with very high performance demands. As technology has improved, reconfigurable hardware has become a viable platform to provide application acceleration, even for floating-point-intensive scientific applications. Now, reconfigurable computers---computers with general purpose microprocessors, reconfigurable hardware, memory, and high performance interconnect---are emerging as platforms that allow complete applications to be partitioned into parts that execute in software and parts that are accelerated in hardware. In this paper, we study molecular dynamics simulation. Specifically, we study the use of the smooth particle mesh Ewald technique in a molecular dynamics simulation program that takes advantage of the hardware acceleration capabilities of a reconfigurable computer. We demonstrate a 2.7-2.9xspeed-up over the corresponding software-only simulation program. Along the way, we note design issues and techniques related to the use of reconfigurable computers for scientific computing in general.

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INDEX TERMS

Primary Classification:
  B. Hardware
  B.7 INTEGRATED CIRCUITS
      B.7.1 Types and Design Styles
          Subjects: Gate arrays

Additional Classification:
  B. Hardware
  B.7 INTEGRATED CIRCUITS
      B.7.1 Types and Design Styles
          Subjects: Microprocessors and microcomputers; Algorithms implemented in hardware

  C. Computer Systems Organization
  C.0 GENERAL
      Subjects: Modeling of computer architecture

  I. Computing Methodologies
  I.6 SIMULATION AND MODELING
      I.6.7 Simulation Support Systems

  J. Computer Applications
  J.2 PHYSICAL SCIENCES AND ENGINEERING
      Subjects: Physics

General Terms:
Algorithms, Design

Keywords:
FPGA, electrostatics, molecular dynamics, reconfigurable