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

doi:10.1145/2740966

	SuperDragon: A Heterogeneous Parallel System for Accelerating 3D Reconstruction of Cryo-Electron Microscopy Images
	Tan, Guangming; Zhang, Chunming; Wang, Wendi; Zhang, Peiheng
	2015-10-01
发表期刊	ACM TRANSACTIONS ON RECONFIGURABLE TECHNOLOGY AND SYSTEMS
ISSN	1936-7406
卷号	8 期号:4 页码:22
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.
关键词	Design Performance Cryo-EM 3D reconstruction heterogeneous FPGA
DOI	10.1145/2740966
收录类别	SCI
语种	英语
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
WOS类目	Computer Science, Hardware & Architecture
WOS记录号	WOS:000363659000005
出版者	ASSOC COMPUTING MACHINERY
引用统计	被引频次：3[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/9243
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.