在EARTH多线程架构上实现并行hmm-pfam

Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003 Pub Date : 2003-08-11 DOI:10.1109/CSB.2003.1227404

Weirong Zhu, Yanwei Niu, Jizhu Lu, G. Gao

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引用次数: 14

摘要

Hmmpfam是一个广泛使用的计算密集型生物信息学软件，用于序列分类。这张海报描述了hmpfam在EARTH上的一种新的并行实现，它是一种事件驱动的细粒度多线程编程执行模型。原始的PVM实现和我们的实现的比较结果显示在绝对加速和可伸缩性方面有显著的改进。在128个双cpu节点的集群上，代表性测试台架的执行时间从15.9小时减少到4.3分钟。

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Implementing parallel hmm-pfam on the EARTH multithreaded architecture

Hmmpfam is a widely used computation-intensive bioinformatics software for sequence classification. This poster describes a new parallel implementation of hmmpfam on EARTH, which is an event-driven fine-grain multithreaded programming execution model. The comparison results of the original PVM implementation and our implementation shows notable improvements on absolute speedup and scalability. On a cluster of 128 dual-CPU nodes, the execution time of a representative testbench is reduced from 15.9 hours to 4.3 minutes.

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Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003

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