Fast PhyloCon Algorithm Using OpenMP

Hazrina Yusof Hamdani, N. Rashid, M. F. Wajidi, A. Abdulrazzaq, Rana M. Ghadban
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引用次数: 2

Abstract

This paper is to study and identify suitable algorithm that use in searching regulatory element where PhyloCon algorithm is one of the algorithms. Since PhyloCon has complexity limitation, the time performance is reduced. Therefore, a parallel technique is identified to improve performance of PhyloCon algorithm. The identified parallel technique is implemented on multicore architecture using OpenMP. This technique use multilevel parallelism which consists of outer parallelism and inner parallelism implemented in Phylocon algorithm. In each level, the data decomposition technique is applied to achieve computational load balancing. The implementation result produced maximum speed up until 2.62 on four processors compared to the sequential PhyloCon results.
基于OpenMP的快速PhyloCon算法
本文以PhyloCon算法为主要算法之一,研究并确定适合于搜索规则元素的算法。由于PhyloCon具有复杂度限制,降低了时间性能。因此,提出了一种并行技术来提高PhyloCon算法的性能。利用OpenMP在多核架构上实现了识别的并行技术。该技术采用了由Phylocon算法实现的外部并行和内部并行组成的多级并行。在每一层,应用数据分解技术实现计算负载均衡。与顺序PhyloCon结果相比,实现结果在四个处理器上产生的最大速度达到2.62。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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