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High-performance simulation cloud for development of large-scale general biophysical model

Research Project

Project/Area Number 26730035
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Software
Research InstitutionOsaka University

Principal Investigator

Okita Masao  大阪大学, 情報科学研究科, 助教 (50563988)

Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2016: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2015: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
Fiscal Year 2014: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Keywords並列・分散処理 / 生体シミュレーション / 自動並列化 / クラウドサービス
Outline of Final Research Achievements

We improved the efficiency of Flint and Flint K3, a parallel general biophysical simulator and a cloud service powered by Flint respectively, and accomplished a practical simulation of large-scale biophysical model.
Our contributions are three auto-parallelization refinement techniques: improving parallel efficiency based on two-layers graph structure, load balancing, and optimizing calculation order and data layout.
For a simulation of a 2D visual cortex neuron model that consists of more than 28 million ODEs, our method achieved 98.7% of parallel efficiency and 27.4 times speed-up.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (8 results)

All 2016 2015 2014 Other

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 1 results,  Acknowledgement Compliant: 1 results) Presentation (4 results) Remarks (2 results)

  • [Journal Article] Accelerating ODE-based Simulation of General and Heterogeneous Biophysical Models using a GPU2014

    • Author(s)
      Tomohiro Okuyama, Masao Okita, Takeshi Abe, Yoshiyuki Asai, Hiroaki Kitano, Taishin Nomura, and Kenichi Hagihara
    • Journal Title

      IEEE Transactions on Parallel and Distributed Systems

      Volume: 201(印刷中) Issue: 8 Pages: 1966-1975

    • DOI

      10.1109/tpds.2013.198

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] A Versatile Platform for Multilevel Modeling of Physiological Systems: SBML-PHML Hybrid Modeling and Simulation2014

    • Author(s)
      Asai Y, Abe T, Oka H, Okita M, Hagihara K, Ghosh S, Matsuoka Y, Kurachi Y, Nomura T, Kitano H
    • Journal Title

      Advanced Biomedical Engineering

      Volume: 3 Issue: 0 Pages: 50-58

    • DOI

      10.14326/abe.3.50

    • NAID

      130005001705

    • ISSN
      2187-5219
    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] 数式の依存グラフを仕様とするOpenMPプログラムのメモリ参照効率向上2016

    • Author(s)
      角田優貴, 置田真生, 萩原兼一
    • Organizer
      報処理学会研究報告, 2016-HPC-155
    • Place of Presentation
      松本市
    • Year and Date
      2016-08-08
    • Related Report
      2016 Annual Research Report
  • [Presentation] 並列分散処理基盤 Apache Spark における系譜つき中間データに対する効果的なメモリ内キャッシュ指示の検討2016

    • Author(s)
      米尾謙史, 置田真生, 萩原兼一
    • Organizer
      第16回ハイパフォーマンスコンピューティングと計算科学シンポジウム
    • Place of Presentation
      仙台市
    • Year and Date
      2016-06-06
    • Related Report
      2016 Annual Research Report
  • [Presentation] 生体シミュレーションサービスFlint K3における高性能計算に向けて2015

    • Author(s)
      永井美穂, 置田真生, 安部武志, 浅井義之, 北野宏明, 萩原兼一
    • Organizer
      情報処理学会第77回全国大会,
    • Place of Presentation
      京都大学吉田キャンパス,京都府京都市左京区
    • Year and Date
      2015-03-17 – 2015-03-19
    • Related Report
      2014 Research-status Report
  • [Presentation] 大規模生体モデルを対象とする Flint シミュレーションコードの並列生成2014

    • Author(s)
      中村亜希, 吉川禎, 置田真生, 萩原兼一
    • Organizer
      平成26年度情報処理学会関西支部支部大会
    • Place of Presentation
      大阪大学中之島センター,大阪府大阪市北区
    • Year and Date
      2014-09-17
    • Related Report
      2014 Research-status Report
  • [Remarks] FLINT K3

    • URL

      https://flintk3.unit.oist.jp

    • Related Report
      2016 Annual Research Report
  • [Remarks] Flint K3

    • URL

      https://flintk3.unit.oist.jp

    • Related Report
      2015 Research-status Report

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Published: 2014-04-04   Modified: 2018-03-22  

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