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

开发基于分布式共享数组和特定应用资源管理的并行编程环境

• 批准号: 13680396
• 负责人: SHIMIZU Kentaro
• 金额: $ 2.62万
• 依托单位: The University of Tokyo
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2001
• 资助国家: 日本
• 起止时间: 2001 至 2003
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-13680396/
• 关键词: Parallel 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

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.

我们开发了一个名为“分布式共享数组（DSA）”的并行编程环境，它提供了通过网络连接的不同机器之间的共享全局数组抽象。在DSA中，用户可以定义和使用可以从网络中的任何机器统一访问的全局数组。阵列区域分配、复制和迁移的显式管理是通过显式调用定义阵列区域的阵列操作、读取和写入阵列区域、同步以及复制和迁移的控制来实现的。 DSA 与网格 (Globus) 服务集成。我们还开发生物信息学应用，例如基因簇分析、多序列比对和分子动力学模拟。在这些应用中，全局数组分别用于存储距离矩阵、对齐矩阵和原子坐标。该系统将提供无法存储在单个机器内存中的大型阵列区域。与用 MPI 编写的传统并行程序相比，DSA 获得了可扩展的性能。

项目成果

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)

Masakazu Sekijima：“Parsley 并行编程环境中调度策略的自动改进”并行和分布式计算与系统论文集 2002。 380-385 (2002)

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, App

Yasuo Watanabe、Shugo Nakamura、Kentaro Shimizu：《基于分布式共享数组的并行编程环境设计及其在分子生物学中的应用》第三届并行与分布式计算国际会议论文集、App

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)

Mitsunori Ikeguchi：“尿素水溶液中疏水效应的分子动力学研究”美国化学会杂志 123,4 (2001)。

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)

清水健太郎：“分子动力学模拟并行计算方法”化学前沿 8. 50-62 (2002)。

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 (2

Akira Nomoto、Yasuo Watanabe、Wataru Kaneko、Tohru Terada、Shugo Nakamura、Kentaro Shimizu：“DSA 并行编程环境中特定于应用程序的数据一致性”2004 年应用研讨会论文集