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JINR CICC in computational chemistry and nanotechnology problems: DL_POLY performance for different communication architectures

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Abstract

This report compares the performance of the DL_POLY general-purpose molecular dynamics simulation package on the LIT JINR computing cluster CICC with various communication systems. The comparison involved two cluster architectures: Gigabit Ethernet and InfiniBand technologies, respectively. The code performance tests include some comparison of the CICC cluster with the special-purpose computer MDGRAPE-3 developed at RIKEN for a high-speed acceleration of the MD (molecular dynamics) without a fixed cutoff. The DL_POLY benchmark covers a set of typical MD system simulations detailed below.

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Authors and Affiliations

  1. Joint Institute for Nuclear Research, Dubna, Russia

    E. Dushanov, Kh. Kholmurodov, G. Aru & V. Korenkov

  2. Institute of Nuclear Physics, Tashkent, Uzbekistan

    E. Dushanov

  3. Daresbury Laboratory, Warrington, UK

    W. Smith

  4. High-Performance Computing Team, Integrated Simulation of Living Matter Group, Computational Science Research Program, RIKEN (The Institute of Physical and Chemical Research), Yokohama, Kanagawa, Japan

    Y. Ohno, T. Narumi, G. Morimoto & M. Taiji

  5. Keio University, Yokohama, Japan

    K. Yasuoka

Authors
  1. E. Dushanov
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  2. Kh. Kholmurodov
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  3. G. Aru
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  4. V. Korenkov
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  5. W. Smith
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  6. Y. Ohno
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  7. T. Narumi
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  8. G. Morimoto
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  9. M. Taiji
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  10. K. Yasuoka
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Dushanov, E., Kholmurodov, K., Aru, G. et al. JINR CICC in computational chemistry and nanotechnology problems: DL_POLY performance for different communication architectures. Phys. Part. Nuclei Lett. 6, 251–259 (2009). https://doi.org/10.1134/S154747710903011X

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  • DOI: https://doi.org/10.1134/S154747710903011X

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