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Development of Enhanced GRAPE library for Quasi general-purpose Computer

Research Project

Project/Area Number 20700031
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Software
Research InstitutionKeio University

Principal Investigator

NARUMI Tetsu  Keio University, 電気通信学部, 准教授 (10342825)

Project Period (FY) 2008 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2009: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000)
Fiscal Year 2008: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords並列処理 / 分散処理 / 分子動力学シミュレーション / GPU / Playstation 3 / PLAYSTATION 3
Research Abstract

I have extended a library program from MDGRAPE special-purpose computer to quasi general-purpose computer (PLAYSTATION 3 and GPU) for molecular dynamics and turbulence simulations with vortex method. First, new MR3 library, which is the library program for MDGRAPE-3, has supported PS3 and GPU. Second, Parallel PS3s further accelerated MD simulations for large number of particles. Third, parallel GPUs further accelerated turbulence simulations with the vortex method.

Report

(3 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • Research Products

    (17 results)

All 2010 2009 2008

All Journal Article (11 results) (of which Peer Reviewed: 11 results) Presentation (6 results)

  • [Journal Article] High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations2009

    • Author(s)
      Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji
    • Journal Title

      PLoS Computational Biology vol.5

      Pages: 10-10

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] JINR CICC in Computational Chemistry and Nanotechnology Problems: DL_POLY Performance for Different Communication Architectures2009

    • Author(s)
      E. Dushanov, Kh. Kholmurodov, G. Aru, V. Korenkov, W. Smith, Y. Ohno, T. Narumi, G. Morimoto, M. Taiji, K. Yasuoka
    • Journal Title

      Physics of Particles and Nuclei Letters ol.6(3)

      Pages: 251-251

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Siegfried Hofinger: Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach2009

    • Author(s)
      Tetsu Narumi, Kenji Yasuoka, Makoto Taiji
    • Journal Title

      Journal of Computational Chemistry vol.30

      Pages: 2351-2351

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] グラフィックカードを用いた水表面張力の高速分子動力学シミュレーション2009

    • Author(s)
      坂牧隆司, 成見哲, 泰岡顕治
    • Journal Title

      情報処理学会論文誌コンピューティングシステム Vol.2,No.2

      Pages: 89-97

    • NAID

      110007990233

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Fast Multipole Methods on a Cluster of GPUs for the Meshless Simulation of Turbulence2009

    • Author(s)
      Yokota, R., Narumi, T., Sakamaki, R., Kameoka, S., Obi, S., Yasuoka, K.
    • Journal Title

      Comput. Phys. Comm. vol.180

      Pages: 2066-2066

    • NAID

      120006581977

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Fast Multipole Methods on a Cluster of GPUs for the Meshless Simulation of Turbulence2009

    • Author(s)
      Yokota, R., Narumi, T., Sakamaki, R., Kameoka, S., Obi, S., Yasuoka, K.
    • Journal Title

      Computer Physics Communication 180

      Pages: 2066-2078

    • NAID

      120006581977

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 42 TFlops Hierarchical N-body Simulations on GPUs with Applications in both Astrophysics and Turbulence2009

    • Author(s)
      Tsuyoshi Hamada, Rio Yokota, Keigo Nitadori, Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Kiyoshi Oguri
    • Journal Title

      Proceedings of International Conference on Supercomputing, SC2009 (USB memory)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-Performance Quasi Double-Precision Method using Single-Pr ecision Hardware for Molecular Dynamics Simulations with GPUs2009

    • Author(s)
      Tetsu Narumi, Tsuyoshi Hamada, Keigo Nitadori, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka
    • Journal Title

      Proceedings of HPC Asia 2009, Kaohsiung, Taiwan

      Pages: 160-167

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach2009

    • Author(s)
      TETSU NARUMI, KENJI YASUOKA, MAKOTO TAIJI, SIEGFRIED H OF TNGER
    • Journal Title

      Journal of Computational Chemistry (掲載確定)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Accelerating Molecular Dynamics Simulations on PLAYSTATION 3 Platform Using Vertual-GRAPE Programming Model2008

    • Author(s)
      Tetsu Narumi, Shun Kameoka, Makoto Taiji, Kenji Yasuoka
    • Journal Title

      SIAM Journal on Scientific Computing vol.30,No.6

      Pages: 108-3125

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Cell Size Dependence of Orientational Order of Uniaxial Liquid2008

    • Author(s)
      Toshiki Mima, Tetsu Narumi, Shun Mameoka, Kenji Yasuoka
    • Journal Title

      Molecular Simulation vol.34

      Pages: 761-773

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Presentation] Achieving Enough Accuracy without Double-Precision Hardware to Accelerate Molecular Dynamics Simulations with GPUs2010

    • Author(s)
      Tetsu Narumi
    • Organizer
      2nd International Workshop on Advances in Computational Mechanics (IWACOM-II)
    • Place of Presentation
      Yokohama, Japan
    • Year and Date
      2010-03-31
    • Related Report
      2009 Final Research Report
  • [Presentation] Achieving Enough Accuracy without Double-Precision Hardware to Accelerate Molecular Dynamics Simulations with GPUs2010

    • Author(s)
      Tetsu Narumi
    • Organizer
      2^<nd> International Workshop on Advances in Computational Mechanics(IWACOM-II)
    • Place of Presentation
      Yokohama, Japan
    • Year and Date
      2010-03-31
    • Related Report
      2009 Annual Research Report
  • [Presentation] 42 TFlops Hierarchical N-body Simulations on GPUs with Applications in both Astrophysics and Turbulence2009

    • Author(s)
      Tsuyoshi Hamada, Rio Yokota, Keigo Nitadori, Tetsu Narumi, Kenji Yasuoka, Makoto Taiji, Kiyoshi Oguri
    • Organizer
      Proceedings of the SC2009
    • Place of Presentation
      Portland, USA
    • Year and Date
      2009-11-18
    • Related Report
      2009 Final Research Report
  • [Presentation] High-Performance Quasi Double-Precision Method using Single-Precision Hardware for Molecular Dynamics Simulations with GPUs2009

    • Author(s)
      Tetsu Narumi, Tsuyoshi Hamada, Keigo Nitadori, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka
    • Organizer
      Proceedings of HPC Asia 2009
    • Place of Presentation
      Kaohsiung, Taiwan
    • Year and Date
      2009-03-03
    • Related Report
      2009 Final Research Report
  • [Presentation] Overheads in Accelerating Molecular Dynamics Simulations with GPUs, Proceedings of the 9th International Conference on Parallel and Distributed Computing2008

    • Author(s)
      Tetsu Narumi, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka
    • Organizer
      Applications, and Technologies (PDCAT ' 08)
    • Place of Presentation
      Dunedin, New Zealand
    • Year and Date
      2008-12-03
    • Related Report
      2009 Final Research Report
  • [Presentation] Using Special-Purpose and Video-Game Computers for Accelerating Molecular Dynamics Simulations2008

    • Author(s)
      Testu Narumi, Ryuji Sakamaki, Shun Kameoka, Kenji Yasuoka
    • Organizer
      International Workshop on Molecular Simulation Studies in Material and Biological Sciences
    • Place of Presentation
      Dubna, Russia
    • Year and Date
      2008-09-12
    • Related Report
      2009 Final Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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