Two Algorithms Designed for Realizing Efficient Combination of Fast Multipole Method and Dedicated Hardware for Molecular Dynamics Simulations

Takashi AMISAKIa*, Shinjiro TOYODAb, Hiroh MIYAGAWAc and Kunihiro KITAMURAc

aFaculty of Medicine, Tottori University,
86 Nishi-machi, Yonago 683-8503, Japan
bNBC Fuji Xerox Co., Ltd.
430 Sakai, Nakai-machi, Ashigarakami-gun 259-0157, Japan
cTaisho Pharmaceutical Co., Ltd.
1-403 Yoshino-cho, Saitama 330-8530, Japan

(Received: April 8, 2002; Accepted for publication: May 23, 2002; Published on Web: July 5, 2002)

This paper concerns two algorithms designed for acceleration of molecular dynamics simulations using the fast multipole method (FMM) and special-purpose machine (MD-Engine II) for calculating pair interactions. One algorithm is based on a three-dimensional cyclic buffer, which enables efficient cooperation between FMM and MD-Engine II. The algorithm is implemented as part of the particle-processor of MD-Engine II. The processor specifically extracts a set of particles which are contained in nearby regions defined in FMM. The other algorithm is based on a recursive bisection for static load-balancing technique. The efficacy of these algorithms was confirmed by numerical tests.

Keywords: molecular dynamics, special-purpose machine, fast multipole method, parallel algorithm, load-balancing

Abstract in Japanese

Text in Japanese

PDF file(154kB)