Development of Enhanced GRAPE library for Quasi general-purpose Computer

2009 Fiscal Year Final Research Report

• Project/Area Number: 20700031
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Software
• Research Institution: Keio University
• Principal Investigator: NARUMI Tetsu Keio University, 電気通信学部, 准教授 (10342825)
• Project Period (FY): 2008 – 2009
• Keywords: 並列処理 / 分散処理

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.

Research Products

• [Journal Article] High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations (2009)
  • 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
  • Peer Reviewed
• [Journal Article] JINR CICC in Computational Chemistry and Nanotechnology Problems: DL_POLY Performance for Different Communication Architectures (2009)
  • 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
  • Peer Reviewed
• [Journal Article] Siegfried Hofinger: Current Performance Gains from Utilizing the GPU or the ASIC MDGRAPE-3 within an Enhanced Poisson Boltzmann Approach (2009)
  • Author(s): Tetsu Narumi, Kenji Yasuoka, Makoto Taiji
  • Journal Title: Journal of Computational Chemistry vol.30 Pages: 2351
  • 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
  • Peer Reviewed
• [Journal Article] Fast Multipole Methods on a Cluster of GPUs for the Meshless Simulation of Turbulence (2009)
  • Author(s): Yokota, R., Narumi, T., Sakamaki, R., Kameoka, S., Obi, S., Yasuoka, K.
  • Journal Title: Comput. Phys. Comm. vol.180 Pages: 2066
  • Peer Reviewed
• [Journal Article] Accelerating Molecular Dynamics Simulations on PLAYSTATION 3 Platform Using Vertual-GRAPE Programming Model (2008)
  • Author(s): Tetsu Narumi, Shun Kameoka, Makoto Taiji, Kenji Yasuoka
  • Journal Title: SIAM Journal on Scientific Computing vol.30,No.6 Pages: 108-3125
  • Peer Reviewed
• [Journal Article] Cell Size Dependence of Orientational Order of Uniaxial Liquid (2008)
  • Author(s): Toshiki Mima, Tetsu Narumi, Shun Mameoka, Kenji Yasuoka
  • Journal Title: Molecular Simulation vol.34 Pages: 761-773
  • Peer Reviewed
• [Presentation] Achieving Enough Accuracy without Double-Precision Hardware to Accelerate Molecular Dynamics Simulations with GPUs (2010)
  • 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
• [Presentation] 42 TFlops Hierarchical N-body Simulations on GPUs with Applications in both Astrophysics and Turbulence (2009)
  • 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
• [Presentation] High-Performance Quasi Double-Precision Method using Single-Precision Hardware for Molecular Dynamics Simulations with GPUs (2009)
  • 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
• [Presentation] Overheads in Accelerating Molecular Dynamics Simulations with GPUs, Proceedings of the 9th International Conference on Parallel and Distributed Computing (2008)
  • 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
• [Presentation] Using Special-Purpose and Video-Game Computers for Accelerating Molecular Dynamics Simulations (2008)
  • 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