PRAM和LARPBS模型上的近似串匹配并行算法  

Parallel Algorithms for Approximate String Matching on PRAM and LARPBS

作　　者：钟诚[1] 陈国良[2] 

机构地区：[1]中国科学技术大学计算机科学与技术系,安徽合肥230027 [2]国家高性能计算中心,安徽合肥230027

出　　处：《软件学报》2004年第2期159-169,共11页Journal of Software

基　　金：国家重点基础研究发展规划(973)No.G1998030403;国家高技术研究发展计划(863)No.2001AA111041~~

摘　　要：近似串匹配技术在网络信息搜索、数字图书馆、模式识别、文本挖掘、IP路由查找、网络入侵检测、生物信息学、音乐研究计算等领域具有广泛的应用.基于CREW-PRAM(parallel random access machine with concurrent read and exclusive write)模型,采用波前式并行推进的方法直接计算编辑距离矩阵D,设计了一个允许k-差别的近似串匹配动态规划并行算法,该算法使用(m+1)个处理器,时间复杂度为O(n),算法理论上达到线性加速;采取水平和斜向双并行计算编辑距离矩阵D的方法,设计了一个使用a(m+1)个处理器和O(n/a+m)时间的、可伸缩的、允许k-差别的近似串匹配动态规划并行算法,+<11mna.基于分治策略,通过灵活拆分总线和合并子总线动态重构光总线系统,并充分利用光总线的消息播送技术和并行计算前缀和的方法,实现了汉明距离的并行计算,设计了两个基于LARPBS(linear arrays with reconfigurable pipelined bus system)模型的通信高效、可扩放的允许k-误配的近似串匹配并行算法,其中一个算法使用n个处理器,时间为O(m);另一个为常数时间算法,使用mn个处理器.Approximate string matching technique has been widely applied to many fields such as network information retrieval, digital library, pattern recognition, text mining, IP routing searching, network intrusion detection, bioinformatics, and computing in musicology. The two concise parallel dynamic programming algorithms for approximate string matching with k-differences on CREW-PRAM (parallel random access machine with concurrent read and exclusive write) are presented by parallel computing the edition distance matrix D in the wave-front approach and by parallel computing the edition distance matrix D along the diagonal and horizontal directions, respectively. The first algorithm requires O(n) time and obtains a linear speedup by (m+1) processors. The second algorithm needs O(n/a+m) time in use of a(m+1) processors, where 1<a+1mn. The simulation experiment shows that both of the algorithms achieve a good speedup. Based on the divide-and-conquer strategy and split-merge approach, the two communication-efficient and scalable parallel algorithms for approximate string matching with k-mismatches on linear arrays with reconfigurable pipelined bus system (LARPBS) are presented by reconfiguring dynamically the optical bus system, applying neatly the optical message-passing technique, and computing in parallel the prefix sums. The first algorithm requires O(m) time by n processors and the second one has O(1) time in use of nm processors.

关 键 词：近似串匹配 并行算法 CREW-PRAM(parallel random access machine with concurrent read and EXCLUSIVE write) 可重构光总线系统 编辑距离 汉明距离 

分 类 号：TP301[自动化与计算机技术—计算机系统结构]