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Development of a Parallel Programming Environment based on Distributed Shared Arrays with Application-Specific Resource Management

Research Project

Project/Area Number 13680396
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeSingle-year Grants
Section一般
Research Field 計算機科学
Research InstitutionThe University of Tokyo

Principal Investigator

SHIMIZU Kentaro  The University of Tokyo, Graduate School of Agriculture and Life Sciences, Professor, 大学院・農学生命科学研究科, 教授 (80178970)

Project Period (FY) 2001 – 2003
Project Status Completed (Fiscal Year 2003)
Budget Amount *help
¥4,100,000 (Direct Cost: ¥4,100,000)
Fiscal Year 2003: ¥700,000 (Direct Cost: ¥700,000)
Fiscal Year 2002: ¥1,800,000 (Direct Cost: ¥1,800,000)
Fiscal Year 2001: ¥1,600,000 (Direct Cost: ¥1,600,000)
KeywordsParallel programming environment / distributed shared memory / scientific computing / bioinformatics / data consistency protocol / MPI / grid computing / バイオインフォマティクス / データー貫性制御 / 分子動力学法
Research Abstract

We have developed a parallel programming environment called "Distributed Shared Array (DSA)," which provides a shared global array abstract across different machines connected by a network. In DSA, users can define and use global arrays that can be accessed uniformly from any machines in the network. Explicit management of array area allocation, replication, and migration is achieved by explicit calls for array manipulation defining array regions, reading and writing array regions, synchronization, and control of replication and migration. The DSA is integrated with Grid (Globus) services. We also develop the bioinformatics applications such as gene cluster analysis, multiple sequence alignment, and molecular dynamics simulation. In these applications, global arrays are used for storing the distance matrix, alignment matrix and atom coordinates, respectively. Large array areas, which cannot be stored in the memory of individual machines, will be made available by this system. Scalable performance of DSA was obtained compared to that of conventional parallel programs written in MPI.

Report

(4 results)
  • 2003 Annual Research Report   Final Research Report Summary
  • 2002 Annual Research Report
  • 2001 Annual Research Report
  • Research Products

    (31 results)

All Other

All Publications (31 results)

  • [Publications] 野本 享: "Application-specific data consistency in the DSA parallel programming environment"Proceedings of the 2004 Symposium on Applications & the Internet. 630-636 (2004)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] 金子 済: "Design and implementation of a parallel programming environment based on distributed shared arrays"Proceedings of the fifth International Symposium on High Performance Computing, Lecture Notes in Computer Science. LNCS 2858. 402-411 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] 野本 享: "Distributed shared arrays : Portable shared-memory programming interface for multiple computer systems"Cluster Computing. 7. 65-72 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] 渡辺 恭男: "Parallel programming environment based on distributed shared arrays : Design and applications to molecular biology"Proceedings of the Third International Conference on Parallel and Distributed Computing, Applications and Technologies. 44-51 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] 清水 謙多郎: "分子動力学シミュレーション並列計算方式"化学フロンティア. 8. 50-62 (2002)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] 坂村 健: "大人のための「情報」教科書"数研出版. 278 (2003)

    • Description
      「研究成果報告書概要(和文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Akira Nomoto, Yasuo Watanabe, Wataru Kaneko, Tohru Terada, Shugo Nakamura, Kentaro Shimizu: "The application-specific data consistency in the DSA parallel programming environment"Proceedings of the 2004 Symposium on Applications & the Internet. 630-636 (2004)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Wataru Kaneko, Alcira Nomoto, Yasuo Watanabe, Kentaro Shimizu, Shugo Nakamura: "Design and implementation of a parallel programming environment based on distributed shared arrays"Proceedings of the fifth International Symposium on High Performance Computing, Lecture Notesin Computer Scinece. LNCS-2858. 402-411 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Akira Nomoto, Yasuo Watanabe, Wataru Kaneko, Shugo Nakamura, Kentaro Shimizu: "Distributed shared arrays : Portable shared-memory programming interface for multiple computer system"Cluster Computing. 7. 65-72 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Yasuo Watanabe, Shugo Nakamura, Kentaro Shimizu: "Parallel programming environment based on distributed shared arrays Design and applications to molecular biology"Proceedings of the Third International Conference on Parallel and Distributed Computing, Applications and Technologies. 44-51 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Kentaro Shimizu, Shugo Nakamura: "Parallel molecular dynamics simulation"The Frontier of Chemistry Parallel molecular dynamics simulation 2004. 8. 50-62 (2002)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] Takeshi Sakamura, Kentaro Shimizu, Mamoru Koshiduka: "Otonanotameno Ijouhoui kyoukashon"Suukenshuppan. 278 (2003)

    • Description
      「研究成果報告書概要(欧文)」より
    • Related Report
      2003 Final Research Report Summary
  • [Publications] 野本 享: "Distributed shared arrays : Portable shared memory programming interface for multiple computer systems"Proceedings of the 2004 Symposium on Applications & the Internet. 630-636 (2004)

    • Related Report
      2003 Annual Research Report
  • [Publications] 石田 貴士: "Development of an ab initio protein structure prediction system ABLE"Proceedings of the 14th International Conference on Genome Informatics (GIW 2003). 228-237 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 金子 済: "Design and implementation of a parallel programming environment based on distributed shared arrays"Proceedings of the fifth International Symposium on High Performance Computing, Lecture Notes in Computer Science. LNCS 2858. 402-411 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 河野 健二: "資源濫用攻撃に耐性のある資源管理方式"情報処理学会ACS論文誌. 74. 818-828 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 塚本 弘毅: "SAM1 semiempirical calculations on the catalytic cycle of nitric oxide reductase from Fusarium oxysporum"Journal of Molecular Structure : THEOCHEM. 624. 309-322 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 野本 享: "Distributed shared arrays : Portable shared-memory programming interface for multiple computer systems"Journal of Computer Software and Communications. 7. 65-72 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 坂村 健: "大人のための「情報」教科書"数研出版. 278 (2003)

    • Related Report
      2003 Annual Research Report
  • [Publications] 野本享: "Distributed shared arrays : Portable shared-memory programming interface for multiple computer systems"International Journal of Computer Systems, Science and Engineering. (印刷中). (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] 金子済: "Preemptive resource management : Defending against resource monopolizing DoS"Proceedings of IASTED International Conference on Parallel Computing and Networks. 318-327 (2003)

    • Related Report
      2002 Annual Research Report
  • [Publications] 関嶋政和: "Automatic improvement of scheduling policies in Parsley parallel programming environment"Proceedings of the Parallel and Distributed Computing and Systems 2002. 380-385 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 渡辺恭男: "Parallel programming environment based on distributed shared arrays : Design and applications to molecular biology"Proceedings of the Third International Conference on Parallel and Distributed Computing, Applications and Technologies. 44-51 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 中村周吾: "New method for parallel computation of Hessian matrix of conformational energy function in internal coordinates"Journal of Computational Chemistry. 23,4. 463-469 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 清水謙多郎: "分子動力学シミュレーションの並列計算"化学フロンティア. 50-62 (2002)

    • Related Report
      2002 Annual Research Report
  • [Publications] 門田幸司: "Preprocessing implementation for microarray(PRIM):an efficient method for processing cDNA microarray data"Phisiological Genomics. 4, 3. 183-188 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 池口満徳: "Molecular dynamics study on hydrophobic effects in aqueous urea solutions"Journal of the American Chemical Society. 123,4. 677-682 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 繁田聡一: "Access route control by extended key/lock scheme"International Journal of Computer Systems, Science and Engineering. 16,5. 319-325 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 繁田聡一: "キー/ロック方式の拡張によるアクセスルートコントロール"情報処理学会論文誌. 42,6. 1545-1556 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 中村周吾: "A new method for parallel computation of Hessian matrix of conformational energy function in internal coordinates"Journal of Computational Chemistry. 23,4. 463-469 (2001)

    • Related Report
      2001 Annual Research Report
  • [Publications] 清水謙太郎: "コンピュータを用いたタンパク質の立体構造予測"日本農芸化学会シンポジウム「ポストゲノム時代の植物科学」予稿集. 36-38 (2001)

    • Related Report
      2001 Annual Research Report

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Published: 2001-04-01   Modified: 2016-04-21  

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