ACM/IEEE SC 1999 Conference (SC'99)最新文献_第5页

Improved Parallel and Sequential Walking Tree Methods for Biological String Alignments 生物序列比对的改进并行和顺序行走树方法

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331583

P. Cull, Tai Hsu

{"title":"Improved Parallel and Sequential Walking Tree Methods for Biological String Alignments","authors":"P. Cull, Tai Hsu","doi":"10.1145/331532.331583","DOIUrl":"https://doi.org/10.1145/331532.331583","url":null,"abstract":"Approximate string matching is commonly used to align genetic sequences (DNA or RNA) to determine their shared characteristics. Most genetic string matching methods are based on the edit-distance model, which does not provide alignments for inversions and translocations. Recently, a heuristic called the Walking Tree Method [2, 3] has been developed to solve this problem. Unlike other heuristics, it can handle more than one level of inversion, i.e., inversions within inversions. Furthermore, it tends to capture the matched strings' genes while other heuristics fail. There are two versions of the original walking tree heuristics: the score version gives only the alignment score, the alignment version gives both the score and the alignment mapping between the strings. The score version runs in quadratic time and uses linear space while the alignment version uses an extra log factor for time and space. In this paper, we will briefly describe the walking tree method and the original sequential and parallel algorithms. We will explain why different parallel algorithms are needed for a network of workstations rather than the original algorithm which worked well on a symmetric multi-processor. Our improved parallel method also led to a quadratic time sequential algorithm that uses less space. We give an example of our parallel method. We describe several experiments that show speedup linear in the number of processors, but eventual drop off in speedup as the communication network saturates. For big enough strings, we found linear speedup for all processors we had available. These results suggest that our improved parallel method will scale up as both the size of the problem and the number of processors increase. We include two figures that use real biological data and show that the walking tree methods can find translocations and inversions in DNA sequences and also discover unknown genes.","PeriodicalId":354898,"journal":{"name":"ACM/IEEE SC 1999 Conference (SC'99)","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121800440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Scal-Tool: Pinpointing and Quantifying Scalability Bottlenecks in DSM Multiprocessors 尺度工具:精确定位和量化DSM多处理器的可伸缩性瓶颈

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331549

J. Torrellas, Yan Solihin, V. Lam

{"title":"Scal-Tool: Pinpointing and Quantifying Scalability Bottlenecks in DSM Multiprocessors","authors":"J. Torrellas, Yan Solihin, V. Lam","doi":"10.1145/331532.331549","DOIUrl":"https://doi.org/10.1145/331532.331549","url":null,"abstract":"Distributed Shared-Memory (DSM) multiprocessors provide an attractive combination of cost-effective commodity architecture and, thanks to the shared-memory abstraction, relative ease of programming. Unfortunately, it is well known that tuning applications for scalable performance in these machines is time-consuming. To address this problem, programmers use performance monitoring tools. However, these tools are often costly to run, especially if highly-processed information is desired. In addition, they usually cannot be used to experiment with hypothetical architecture organizations. In this paper, we present Scal-Tool, a tool that isolates and quantifies scalability bottlenecks in parallel applications running on DSM machines. The scalability bottlenecks currently quantified include insufficient caching space, load imbalance, and synchronization. The tool is based on an empirical model that uses as inputs measurements from hardware event counters in the processor. A major advantage of the tool is that it is quite inexpensive to run: it only needs the event counter values for the application running with a few different processor counts and data set sizes. In addition, it provides ways to analyze variations of several machine parameters.","PeriodicalId":354898,"journal":{"name":"ACM/IEEE SC 1999 Conference (SC'99)","volume":"84 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127849296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 29

Memory Characteristics of Iterative Methods 迭代方法的记忆特性

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331563

Christian Weiß, Wolfgang Karl, M. Kowarschik, U. Rüde

引用次数: 50

An Efficient Communication Architecture for Commodity Supercomputers 商用超级计算机的高效通信体系结构

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331551

S. Brauss, M. Lienhard, J. Nemecek, A. Gunzinger, M. Naf, M. Frey, M. Heimlicher, A. Huber, Pierre-Alain Muller, R. Paul

引用次数: 3

Adaptive Two-level Thread Management for Fast MPI Execution on Shared Memory Machines 共享内存机器上快速MPI执行的自适应两级线程管理

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331581

Kai Shen, Hong Tang, Tao Yang

引用次数: 21

A Network Performance Tool for Grid Environments 网格环境下的网络性能工具

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331536

Craig A. Lee, J. Stepanek, R. Wolski, C. Kesselman, Ian T Foster

引用次数: 54

Improving Performance of Sparse Matrix-Vector Multiplication 改进稀疏矩阵-向量乘法的性能

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331562

Ali Pinar, M. Heath

引用次数: 118

Scalable Electromagnetic Scattering Calculations on the SGI Origin 2000 基于SGI Origin 2000的可伸缩电磁散射计算

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331586

J. Ottusch, M. Stalzer, J. Visher, S. Wandzura

引用次数: 12

Numerical Simulation and Immersive Visualization of Hairpin Vortices 发夹涡的数值模拟与沉浸式可视化

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331594

H. Tufo, P. Fischer, M. Papka, Kristopher J. Blom

引用次数: 55

MOM: a Matrix SIMD Instruction Set Architecture for Multimedia Applications 多媒体应用的矩阵SIMD指令集体系结构

ACM/IEEE SC 1999 Conference (SC'99) Pub Date : 1900-01-01 DOI: 10.1145/331532.331547

J. Corbal, R. Espasa, M. Valero

引用次数: 30