Accelerating Irregular Computation in Massive Short Reads Mapping on FPGA Co-Processor

doi:10.1109/TPDS.2015.2444393

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	Accelerating Irregular Computation in Massive Short Reads Mapping on FPGA Co-Processor
	Tan, Guangming; Zhang, Chunming; Tang, Wen; Zhang, Peiheng; Sun, Ninghui
刊名	IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS
	2016-05-01
卷号	27 期号:5 页码:1253-1264
关键词	Short read mapping irregular computation FPGA multicore parallelism
ISSN号	1045-9219
DOI	10.1109/TPDS.2015.2444393
英文摘要	Because there is an enormous amount of genomic data, next-generation sequencing (NGS) applications pose significant challenges to current computing systems. In this study, we investigate both algorithmic and architectural strategies to accelerate an NGS data analysis algorithm-short read mapping on commodity multi-core platform and customizable field programmable gate array (FPGA) co-processor architecture, respectively. A workload analysis reveals that conventional memory optimization is limited in its irregular computation of low arithmetic intensity and non-contiguous memory access pattern. To mitigate the inherent irregular computation in mapping, we have developed a FPGA co-processor based on Convey computer, which employs a scatter-gather memory mechanism that exploits both bit-level and word-level parallelism. The customized FPGA co-processor achieves a throughput of 947Gbp per day, about 189 times higher than that of current mapping tools on single CPU core. Moreover, the co-processor's power efficiency is 29 times higher than that of a conventional 64-core multi-processor.
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 ; Engineering
语种	英语
出版者	IEEE COMPUTER SOC
WOS记录号	WOS:000374238100002
内容类型	期刊论文
源URL	[http://119.78.100.204/handle/2XEOYT63/8488]
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; Zhang, Chunming; Tang, Wen; Zhang, Peiheng; Sun, Ninghui
作者单位	Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Tan, Guangming,Zhang, Chunming,Tang, Wen,et al. Accelerating Irregular Computation in Massive Short Reads Mapping on FPGA Co-Processor[J]. IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS,2016,27(5):1253-1264.
APA	Tan, Guangming,Zhang, Chunming,Tang, Wen,Zhang, Peiheng,&Sun, Ninghui.(2016).Accelerating Irregular Computation in Massive Short Reads Mapping on FPGA Co-Processor.IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS,27(5),1253-1264.
MLA	Tan, Guangming,et al."Accelerating Irregular Computation in Massive Short Reads Mapping on FPGA Co-Processor".IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 27.5(2016):1253-1264.