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Journal Article
Toward High Utilization of Heterogeneous Computing Resources in SNP Detection
- Authors
- Myungeun Lim, Minho Kim, Ho-Youl Jung, Dae-Hee Kim, Jae-Hun Choi, Wan Choi, Kyu-Chul Lee
- Issue Date
- 2015-04
- Citation
- ETRI Journal, v.37, no.2, pp.212-221
- ISSN
- 1225-6463
- Publisher
- 한국전자통신연구원 (ETRI)
- Language
- English
- Type
- Journal Article
- Abstract
- 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.
- KSP Keywords
- Computing resources, Data processing, Detection procedure, Heterogeneous computing, High-performance computing systems, Open source, Single nucleotide polymorphism (SNP) detection, execution time, task groups