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SuperDragon: A Heterogeneous Parallel System for Accelerating 3D Reconstruction of Cryo-Electron Microscopy Images

文献类型：期刊论文

作者Tan, Guangming; Zhang, Chunming; Wang, Wendi; Zhang, Peiheng
刊名ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS
出版日期2015-10-01
卷号8期号:4页码:22
关键词Design Performance Cryo-EM 3D reconstruction heterogeneous FPGA
ISSN号1936-7406
DOI10.1145/2740966
英文摘要The data deluge in medical imaging processing requires faster and more efficient systems. Due to the advance in recent heterogeneous architecture, there has been a resurgence in research aimed at domain-specific accelerators. In this article, we develop an experimental system SuperDragon for evaluating acceleration of a single-particle Cryo-electron microscopy (Cryo-EM) 3D reconstruction package EMAN through a hybrid of CPU, GPU, and FPGA parallel architecture. Based on a comprehensive workload characterization, we exploit multigrained parallelism in the Cryo-EM 3D reconstruction algorithm and investigate a proper computational mapping to the underlying heterogeneous architecture. The package is restructured with task-level (MPI), thread-level (OpenMP), and data-level (GPU and FPGA) parallelism. Especially, the proposed FPGA accelerator is a stream architecture that emphasizes the importance of optimizing computing dominated data access patterns. Besides, the configurable computing streams are constructed by arranging the hardware modules and bypassing channels to form a linear deep pipeline. Compared to the multicore (six-core) program, the GPU and FPGA implementations achieve speedups of 8.4 and 2.25 times in execution time while improving power efficiency by factors of 7.2 and 14.2, respectively.
资助项目National Natural Science Foundation of China[61272134] ; National Natural Science Foundation of China[31327901] ; National Natural Science Foundation of China[91430218] ; National Natural Science Foundation of China[60921002] ; National Natural Science Foundation of China[60925009] ; National Natural Science Foundation of China[61472395] ; National 863 Program[2009AA01A129] ; 973 Program[2012CB316502] ; 973 Program[2011CB302502]
WOS研究方向Computer Science
语种英语
WOS记录号WOS:000363659000005
出版者ASSOC COMPUTING MACHINERY
源URL[http://119.78.100.204/handle/2XEOYT63/9242]  
专题中国科学院计算技术研究所期刊论文_英文
通讯作者Tan, Guangming
作者单位Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing 100864, Peoples R China
推荐引用方式
GB/T 7714		 Tan, Guangming,Zhang, Chunming,Wang, Wendi,et al. SuperDragon: A Heterogeneous Parallel System for Accelerating 3D Reconstruction of Cryo-Electron Microscopy Images[J]. ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS,2015,8(4):22.
APA Tan, Guangming,Zhang, Chunming,Wang, Wendi,&Zhang, Peiheng.(2015).SuperDragon: A Heterogeneous Parallel System for Accelerating 3D Reconstruction of Cryo-Electron Microscopy Images.ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS,8(4),22.
MLA Tan, Guangming,et al."SuperDragon: A Heterogeneous Parallel System for Accelerating 3D Reconstruction of Cryo-Electron Microscopy Images".ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS 8.4(2015):22.

入库方式： OAI收割

来源：计算技术研究所

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