PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm

doi:10.1007/s11390-020-0825-3

	PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm
	Li, Xue-Qi 1; Tan, Guang-Ming ; Sun, Ning-Hui
刊名	JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY
	2021
卷号	36 期号:1 页码:56-70
关键词	accelerator design genomic sequence alignment near-memory computing
ISSN号	1000-9000
DOI	10.1007/s11390-020-0825-3
英文摘要	Genomic sequence alignment is the most critical and time-consuming step in genomic analysis. Alignment algorithms generally follow a seed-and-extend model. Acceleration of the extension phase for sequence alignment has been well explored in computing-centric architectures on field-programmable gate array (FPGA), application-specific integrated circuit (ASIC), and graphics processing unit (GPU) (e.g., the Smith-Waterman algorithm). Compared with the extension phase, the seeding phase is more critical and essential. However, the seeding phase is bounded by memory, i.e., fine-grained random memory access and limited parallelism on conventional system. In this paper, we argue that the processing-in-memory (PIM) concept could be a viable solution to address these problems. This paper describes "PIM-Align"-application-driven near-data processing architecture for sequence alignment. In order to achieve memory-capacity proportional performance by taking advantage of 3D-stacked dynamic random access memory (DRAM) technology, we propose a lightweight message mechanism between different memory partitions, and a specialized hardware prefetcher for memory access patterns of sequence alignment. Our evaluation shows that the proposed architecture can achieve 20x and 1 820x speedup when compared with the best available ASIC implementation and the software running on 32-thread CPU, respectively.
资助项目	National Key Research and Development Program of China[2018YFB0204400] ; National Key Research and Development Program of China[2016YFB0201305] ; National Key Research and Development Program of China[2016YFB0200803] ; National Key Research and Development Program of China[2016YFB0200300] ; National Key Research and Development Program of China[XDC01030000] ; National Natural Science Foundation of China[6197237] ; National Natural Science Foundation of China[61702483] ; CAS[QYZDJ-SSW-JSC035]
WOS研究方向	Computer Science
语种	英语
出版者	SCIENCE PRESS
WOS记录号	WOS:000615566300005
内容类型	期刊论文
源URL	[http://119.78.100.204/handle/2XEOYT63/16162]
专题	中国科学院计算技术研究所
通讯作者	Li, Xue-Qi
作者单位	1.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
推荐引用方式 GB/T 7714	Li, Xue-Qi,Tan, Guang-Ming,Sun, Ning-Hui. PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm[J]. JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,2021,36(1):56-70.
APA	Li, Xue-Qi,Tan, Guang-Ming,&Sun, Ning-Hui.(2021).PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm.JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY,36(1),56-70.
MLA	Li, Xue-Qi,et al."PIM-Align: A Processing-in-Memory Architecture for FM-Index Search Algorithm".JOURNAL OF COMPUTER SCIENCE AND TECHNOLOGY 36.1(2021):56-70.