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  1. B200 工学部/工学研究科
  2. B200a 雑誌掲載論文
  3. 学術雑誌

Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations

http://hdl.handle.net/2237/0002000044
http://hdl.handle.net/2237/0002000044
233a35c9-e57f-4f2c-8a36-a9f3f08c7471
名前 / ファイル ライセンス アクション
JCC_mtd_final.pdf JCC_mtd_final.pdf (3.8 MB)
Item type itemtype_ver1(1)
公開日 2021-05-18
タイトル
タイトル Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations
言語 en
著者 Andoh, Yoshimichi

× Andoh, Yoshimichi

en Andoh, Yoshimichi

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Ichikawa, Shin‐ichi

× Ichikawa, Shin‐ichi

en Ichikawa, Shin‐ichi

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Sakashita, Tatsuya

× Sakashita, Tatsuya

en Sakashita, Tatsuya

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Yoshii, Noriyuki

× Yoshii, Noriyuki

en Yoshii, Noriyuki

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Okazaki, Susumu

× Okazaki, Susumu

en Okazaki, Susumu

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アクセス権
アクセス権 open access
アクセス権URI http://purl.org/coar/access_right/c_abf2
権利
言語 en
権利情報 "This is the peer reviewed version of the following article: [Andoh, Y, Ichikawa, S, Sakashita, T, Yoshii, N, Okazaki, S. Algorithm to minimize MPI communications in the parallelized fast multipole method combined with molecular dynamics calculations. J Comput Chem. 2021; 42: 1073– 1087. https://doi.org/10.1002/jcc.26524], which has been published in final form at [https://doi.org/10.1002/jcc.26524]. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."
キーワード
主題Scheme Other
主題 efficient MPI communication
キーワード
主題Scheme Other
主題 exascale supercomputers
キーワード
主題Scheme Other
主題 fast multipole method
キーワード
主題Scheme Other
主題 molecular dynamics calculation
キーワード
主題Scheme Other
主題 MPI parallelization
内容記述
内容記述 In the era of exascale supercomputers, large‐scale, and long‐time molecular dynamics (MD) calculations are expected to make breakthroughs in various fields of science and technology. Here, we propose a new algorithm to improve the parallelization performance of message passing interface (MPI)‐communication in the MPI‐parallelized fast multipole method (FMM) combined with MD calculations under three‐dimensional periodic boundary conditions. Our approach enables a drastic reduction in the amount of communication data, including the atomic coordinates and multipole coefficients, both of which are required to calculate the electrostatic interaction by using the FMM. In communications of multipole coefficients, the reduction rate of communication data in the new algorithm relative to the amount of data in the conventional one increases as both the number of FMM levels and the number of MPI processes increase. The aforementioned rate increase could exceed 50% as the number of MPI processes becomes larger for very large systems. The proposed algorithm, named the minimum‐transferred data (MTD) method, should enable large‐scale and long‐time MD calculations to be calculated efficiently, under the condition of massive MPI‐parallelization on exascale supercomputers.
言語 en
内容記述タイプ Abstract
出版者
言語 en
出版者 Wiley
言語
言語 eng
資源タイプ
資源タイプresource http://purl.org/coar/resource_type/c_6501
タイプ journal article
出版タイプ
出版タイプ AM
出版タイプResource http://purl.org/coar/version/c_ab4af688f83e57aa
関連情報
関連タイプ isVersionOf
識別子タイプ DOI
関連識別子 https://doi.org/10.1002/jcc.26524
収録物識別子
収録物識別子タイプ PISSN
収録物識別子 0192-8651
書誌情報 en : Journal of Computational Chemistry

巻 42, 号 15, p. 1073-1087, 発行日 2021-06-05
ファイル公開日
日付 2022-06-05
日付タイプ Available
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