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학술지 Toward High Utilization of Heterogeneous Computing Resources in SNP Detection
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저자
임명은, 김민호, 정호열, 김대희, 최재훈, 최완, 이규철
발행일
201504
출처
ETRI Journal, v.37 no.2, pp.212-221
ISSN
1225-6463
출판사
한국전자통신연구원 (ETRI)
DOI
https://dx.doi.org/10.4218/etrij.15.2314.0144
협약과제
14MS1400, 유전체 분석용 슈퍼컴퓨팅 시스템 개발, 최완
초록
As the amount of re-sequencing genome data grows, minimizing the execution time of an analysis is required. For this purpose, recent computing systems have been adopting both high-performance coprocessors and host processors. However, there are few applications that efficiently utilize these heterogeneous computing resources. This problem equally refers to the work of single nucleotide polymorphism (SNP) detection, which is one of the bottlenecks in genome data processing. In this paper, we propose a method for speeding up an SNP detection by enhancing the utilization of heterogeneous computing resources often used in recent high-performance computing systems. Through the measurement of workload in the detection procedure, we divide the SNP detection into several task groups suitable for each computing resource. These task groups are scheduled using a window overlapping method. As a result, we improved upon the speedup achieved by previous open source applications by a magnitude of 10.
키워드
CPU-GPU overlapping, Heterogeneous computing resources, Multithreading, Overlapped window, SNP detection
KSP 제안 키워드
CPU-GPU, Computing resources, Data processing, Detection procedure, Heterogeneous computing, High-performance computing systems, Open source, Single nucleotide polymorphism (SNP) detection, execution time, task groups