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DOI:
Journal of Software:2004.15(2):170-178

基因序列分析软件Hmmpfam的可扩展并行性能优化
陈军,赵文辉,莫则尧,李晓梅
(应用物理与计算数学研究所,高性能计算中心,北京,100088;国防科学技术大学,计算机学院,湖南,长沙,410073;总装备部指挥技术学院,北京,101416)
Scalable Parallel Performance Optimization of the Gene Sequence Analyzing Software Hmmpfam
CHEN Jun,ZHAO Wen-Hui,MO Ze-Yao,LI Xiao-Mei
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Received:March 24, 2003    Revised:May 27, 2003
> 中文摘要: 基于MPI(message passing interface)平台实现了HMMER软件包核心程序之一Hmmpfam的大规模并行计算.该版本针对原PVM(parallel virtual machine)并行版本在并行规模扩大后,master易成为通信瓶颈的问题,对通信结构进行了优化,提出了一种新的三层通信结构,在序列和HMM模型的两个层次上实现了并行化,并分别提供了有效的负载平衡策略,同时优化了I/O性能,在700多台处理机上达到95%的效率.
中文关键词: 并行计算  基因序列分析  HMMER
Abstract:A scalable parallel MPI (message passing interface) version of the popular protein structure prediction tool Hmmpfam is presented, which is one of the kernel programs in the HMMER package. The master process in the previous PVM (parallel virtual machine) version is a communication bottleneck, and the speedup will decrease rapidly when running on large scale parallel systems. A novel three-level communication structure is presented, by which the parallel processing at sequence level and HMM model level is obtained in both. Meanwhile, the load-balance strategies to sequence level and HMM model level distribution are provided separately. Since disk access for getting HMM model costs very much, a so-called once load strategy is provided to reduce the cost. By all these optimization methods, 95% in parallel efficiency is achieved when running on a parallel computer containing more than 700 processors.
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基金项目:Supported by the National Grand Fundamental Research 973 Program of China under Grant No.G199508032805(国家重点基础研究发展规划(973));the National High-Tech Research and Development Plan of China under Grant No.863-2002AA104570(国家高技术研究发展计划(863)) Supported by the National Grand Fundamental Research 973 Program of China under Grant No.G199508032805(国家重点基础研究发展规划(973));the National High-Tech Research and Development Plan of China under Grant No.863-2002AA104570(国家高技术研究发展计划(863))
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陈军,赵文辉,莫则尧,李晓梅.基因序列分析软件Hmmpfam的可扩展并行性能优化.软件学报,2004,15(2):170-178

CHEN Jun,ZHAO Wen-Hui,MO Ze-Yao,LI Xiao-Mei.Scalable Parallel Performance Optimization of the Gene Sequence Analyzing Software Hmmpfam.Journal of Software,2004,15(2):170-178