Regular Article
NAMD2: Greater Scalability for Parallel Molecular Dynamics

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Abstract

Molecular dynamics programs simulate the behavior of biomolecular systems, leading to understanding of their functions. However, the computational complexity of such simulations is enormous. Parallel machines provide the potential to meet this computational challenge. To harness this potential, it is necessary to develop a scalable program. It is also necessary that the program be easily modified by application–domain programmers. The NAMD2 program presented in this paper seeks to provide these desirable features. It uses spatial decomposition combined with force decomposition to enhance scalability. It uses intelligent periodic load balancing, so as to maximally utilize the available compute power. It is modularly organized, and implemented using Charm++, a parallel C++ dialect, so as to enhance its modifiability. It uses a combination of numerical techniques and algorithms to ensure that energy drifts are minimized, ensuring accuracy in long running calculations. NAMD2 uses a portable run-time framework called Converse that also supports interoperability among multiple parallel paradigms. As a result, different components of applications can be written in the most appropriate parallel paradigms. NAMD2 runs on most parallel machines including workstation clusters and has yielded speedups in excess of 180 on 220 processors. This paper also describes the performance obtained on some benchmark applications.

References (52)

  • S.J Plimpton

    Fast parallel algorithms for short-range molecular dynamics

    J. Comput. Phys.

    (March 1995)
  • E.L Pollock et al.

    Comments on P3

    Comput. Phys. Commun.

    (1996)
  • J.-P Ryckaert et al.

    Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics ofn

    J. Comput. Phys.

    (1977)
  • M.M Smith

    Histone structure and function

    Curr. Opinion Cell Biol.

    (1991)
  • W.L Smith et al.

    Prostaglandin endoperoxide H synthases-1 and -2

    Adv. Immunol.

    (1996)
  • J Barnes et al.

    A hierarchicalONN

    Nature

    (1986)
  • D.L Beveridge et al.

    Free energy via molecular simulation: Applications to chemical and biological systems

    Annu. Rev. Biophys. Biophys. Chem.

    (1989)
  • T.C Bishop et al.

    Difficulties with multiple time stepping and the fast multipole algorithm in molecular dynamics

    J. Comput. Chem.

    (1997)
  • B.R Brooks et al.

    Parallelization of CHARMM for MIMD machines

    Chemical Design Automation News

    (July 1992)
  • T.W Clark et al.

    Parallelizing molecular dynamics using spatial decomposition

    Proceedings, Scalable High-Performance Computing Conference

    (1994)
  • T.A Darden et al.

    Particle mesh Ewald. AnNN

    J. Chem. Phys.

    (1993)
  • U Essmann et al.

    A smooth particle mesh Ewald method

    J. Chem. Phys.

    (1995)
  • A Grama et al.

    Isoefficiency: Measuring the scalability of parallel algorithms and architectures

    IEEE Parallel & Distrib. Technol.

    (August 1993)
  • H Grubmüller et al.

    Ligand binding and molecular mechanics calculation of the streptavidin–biotin rupture force

    Science

    (1996)
  • J.L Gustafson

    Reevaluating Amdahl's law

    Comm. ACM

    (1988)
  • Cited by (0)

    P. DeuflhardJ. HermansB. LeimkuhlerA. E. MarkS. ReichR. D. Skeel

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    [email protected]

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