| 冷冻电镜三维重构在CPU-GPU系统中的并行性 |
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| 引用本文： | 李兴建,李临川,谭光明,张佩珩.冷冻电镜三维重构在CPU-GPU系统中的并行性[J].华中科技大学学报(自然科学版),2011,39(Z1):115-119. |
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| 作者姓名： | 李兴建 李临川 谭光明 张佩珩 |
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| 作者单位： | 1. 中国科学院计算技术研究所计算机系统结构重点实验室，北京100190;中国科学院研究生院，北京100049
2. 中国科学院计算技术研究所计算机系统结构重点实验室,北京,100190 |
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| 基金项目： | 国家重大研究发展计划资助项目(2009AA01A129); 中国科学院知识创新工程重大项目(KGGX1-YW-13); 国家自然科学基金资助项目(60803030) |
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| 摘 要： | 为了有效地发掘和利用异构系统在应用和体系结构上的并行性,以冷冻电镜三维重构为例展示如何利用应用程序潜在的并行性.通过分析重构计算所有的并行性,实现了将动态自适应的划分算法用于任务在异构系统上高效的分发.在曙光星云系统的部分节点系统(32节点)上评估并行化的程序性能.实验证明:多层次的并行化是CPU与GPU异构系统上开发并行性的有效模式;CPU-GPU混合程序在给定问题规模上相对单纯CPU程序获得2.4倍加速比.
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| 关 键 词： | 任务级并行 数据级并行 高性能计算 统一计算设备架构(CUDA) 冷冻电镜 |
Parallelism for cryo-EM 3D reconstruction on CPU-GPU heterogeneous system |
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| Li Xingjian,Li Linchuan,Tan Guangming,Zhang Peiheng.Parallelism for cryo-EM 3D reconstruction on CPU-GPU heterogeneous system[J].JOURNAL OF HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY.NATURE SCIENCE,2011,39(Z1):115-119. |
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| Authors: | Li Xingjian Li Linchuan Tan Guangming Zhang Peiheng |
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| Institution: | Li Xingjian1,2 Li Linchuan1,2 Tan Guangming1 Zhang Peiheng1(1 Key Laboratory of Computer System and Architecture,Institute of Computing Technology Chinese Academy of Sciences,Beijing 100190 China,2 Graduate University of Chinese Academy of Sciences,Beijing 100049,China) |
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| Abstract: | It is a challenge to efficiently utilize massive parallelism on both applications and architectures for heterogeneous systems.A practice of accelerating a cryo-EM 3D program was presented on how to exploit and orchestrate parallelism of applications to take advantage of the underlying parallelism exposed at the architecture level.All possible parallelism in cryo-EM 3D was exploited,and a self-adaptive dynamic scheduling algorithm was leveraged to efficiently implement parallelism mapping between the applica... |
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| Keywords: | task parallelism data parallelism high performance computing compute unified device architecture(CUDA) cryo-electron microscopy |
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