• DocumentCode
    3048106
  • Title

    Parallel implementation of the treecode Ewald method

  • Author

    Liu, Dongqing ; Duan, Zhong-Hui ; Krasny, Robert ; Zhu, Jianping

  • Author_Institution
    Dept. of Comput. Sci., Akron Univ., OH, USA
  • fYear
    2004
  • fDate
    26-30 April 2004
  • Firstpage
    236
  • Abstract
    Summary form only given. Here, we discuss an efficient parallel implementation of the treecode Ewald method for fast evaluation of long-range Coulomb interactions in a periodic system for molecular dynamics simulations. The parallelization is based on an adaptive decomposition scheme using the Morton order of the particles. This decomposition scheme takes advantage of the data locality and involves minimum changes to the original sequential code. The message passing interface (MPI) is used for interprocessor communications, making the code portable to a variety of parallel computing platforms. We also discuss communication and performance models for our parallel algorithm. The predicted communication time and parallel performance from these models match the measured results well. Timing results obtained using a system of water molecules on the IA32 Cluster at the Ohio Supercomputer Center demonstrate high speedup and efficiency of the parallel treecode Ewald method.
  • Keywords
    message passing; molecular dynamics method; parallel algorithms; sequential codes; tree codes; Coulomb interaction; IA32 Cluster; MPI; Morton order; Ohio Supercomputer Center; adaptive decomposition scheme; code portability; data locality; interprocessor communication; message passing interface; molecular dynamics simulation; parallel algorithm; parallel computing platform; parallel treecode Ewald method; Biological information theory; Biological system modeling; Biology computing; Clustering algorithms; Computational efficiency; Computational modeling; Computer science; Computer simulation; Costs; Mathematics;
  • fLanguage
    English
  • Publisher
    ieee
  • Conference_Titel
    Parallel and Distributed Processing Symposium, 2004. Proceedings. 18th International
  • Print_ISBN
    0-7695-2132-0
  • Type

    conf

  • DOI
    10.1109/IPDPS.2004.1303285
  • Filename
    1303285