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RScaLAPACK: High-Performance parallel Statistical computing with R and ScaLAPACK 18

RScaLAPACK: High-Performance Parallel Statistical Computing ...

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Yoginath, Srikanth Samatova, Nagiza F. Bauer, David Kora, Guruprasad Fann, George Geist, Al Computer Science and Mathematics Division Oak Ridge National Laboratory Oak RidgeTN37831 United States

ISBN: (纸本)9781604234565

With the growing popularity of parallel computation, researchers are looking for various means to reduce the problem solving time by performing the computations in parallel. While benefiting from parallel computation, they do not want to deal with the parallel programming complexities. In this paper, through RScaLAPACK we demonstrate a means that enables the user to carryout parallel computation without dealing with the intricacies of parallel programming. RScaLAPACK is built on top of two Open source software packages: R and ScaLAPACK. the former provides an environment and a language for statistical computing and graphics. the latter is a library of high-performance parallel linear algebra routines using PVM and/or MPI. through RScaLAPACK the user can setup the parallel environment, distribute data and carry out the required parallel computation using a single R function call. While the interface maintains look and feel of the R system, RScaLAPACK allows carrying out analyses with a performance that scales well with both the problem size and the number of processors. RScaLAPACK is made available as an Open Source package and can be found at http://***/parallel-R or on R’s CRAN web site http://***. In this paper we discuss the design, working and performance characteristics of RScaLAPACK. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： parallel programming

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distributed Protein Sequence Alignment 18

Distributed Protein Sequence Alignment

引用

18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Michael Meehan, J. Young, Heidi Hearne, James Nelson, Philip A. Computers Science Department Western Washington University BellinghamWA98225 United States

ISBN: (纸本)9781604234565

Given the explosive growth of biological sequence databases and the computational complexity of aligning large sequences over extremely large databases most researchers have opted for utilizing the BLAST algorithm. While BLAST is completely appropriate for some purposes, the more rigorous and more computationally expensive Smith-Waterman algorithm is preferred for certain purposes. this work presents an implementation of the mathematically optimal Smith-Waterman protein sequence alignment algorithm using a collection of distributed computers. We also present the use of the Unicon programming language as an alternative for writing biological search algorithms and other applications in bioinformatics rather than the most commonly found C or Perl approaches. the system has fault tolerant capabilities and can dynamically add and remove nodes to deal with worker node failure. the system currently operates on up to 87 P4 3.0 GHz machines. the system is called UDPS for Unicon distributed Protein Searcher © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： Bioinformatics

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A Feasible Baseline Architecture for Building and Evaluating distributed systems 18

A Feasible Baseline Architecture for Building and Evaluating...

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Chen, Kevin F. Liu, Meilin Sha, Edwin H.-M. Department of Computer Science University of Texas at Dallas RichardsonTX75083 United States

ISBN: (纸本)9781604234565

Although distributed networks and systems are widely deployed, an effective overall benchmark architecture is still lacking. Recently we defined and studied the fat-stack network architecture and found that it is both efficient and scalable to distributed systems of various scales. In precedent work, we theoretically proved that the fat-stack is universal by measure of routing efficiency with a low 1.5-powered logarithmic overhead. Universality implies that the fat-stack of a given size is nearly the best routing network of that size. the fat-stack is also the minimal universal network in terms of number of links and nodes used. In this paper, we add more analytical proof and report our simulation results. Simulations show that the fat-stack outperforms a mesh-based distributed network of comparable hardware usage. We show how the fat-stack can be an effective benchmark architecture and how to scale the network from a VLSI graph layout to a large-scale distributed topology. Our work helps explain why some deployed networks function in the way they do in terms of routing. It also provides an exemplary network of proven efficiency and scalability for building new distributed systems. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： Network architecture

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Performance Sensitivity of Adaptive Space Sharing to parallel Job Structure and I/O Models 18

Performance Sensitivity of Adaptive Space Sharing to Paralle...

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Wang, Liuhong Dandamudi, Sivarama School of Computer Science Carleton University 1125 Colonel By Drive OttawaONK1S 5B6 Canada

ISBN: (纸本)9781604234565

We study the performance of an adaptive space sharing policy for parallel systems when the application involves I/O operations. We consider four types of I/O models in this paper: NO, NOP, O1 and O2 models. In the NO and NOP models, jobs can either perform an I/O operation or a computation. In the O1 and O2 models, I/O operations overlap with computation. In the O1 model, I/O operations are done at the beginning and end of each task. In contrast, in the O2 model, I/O operations and computation are interleaved. these I/O models are studied in combination with three parallel job structures: Fork-and-Join, Divide- and-Conquer, and Guassian elimination. these three parallel structures cover a spectrum of variable parallelism job structures. the fork-and-join program exhibits a constant parallelism. the parallelism of the divide-and-conquer program increases initially to a maximum and then decreases progressively. In the GE job program, a job starts with its maximum parallelism and progressively decreases to 1. We present simulation results on the performance sensitivity of adaptive space sharing to parallel job structure and I/O model. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： distributed computer systems

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Towards a Simple Service Class for distributed Multimedia Applications in Next Generation IP Networks 18

Towards a Simple Service Class for Distributed Multimedia Ap...

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Usha, M. Wahida Banu, R.S.D. Salem636 005 India Dept. of Computer Science and Engineering Govt. College of Engineering Anna University Salem636 011 India

ISBN: (纸本)9781604234565

the Internet carries all types of traffic and provides end-to-end Quality of Service. But high-demanding audio and video applications that operate in distributed environments are very sensitive to transmission delay and jitter. the best-effort unpredictable nature of the Internet is unfriendly to stream traffic generated by voice and video. this paper suggests a ‘Better than Best Effort’ treatment to such flows. An important contribution is that a simple classification at the router identifying these ‘favored’ UDP flows simplifies the entire service model. A simple AQM (Active Queue Management) scheme is proposed. the flows belonging to certain multimedia applications are given preference, yet giving fair chance to other flows. the AQM algorithm is a modified version of the de facto standard RED (random Early Detection). RED favors only TCP and TCP-friendly flows in congestion avoidance. this work aims at providing a service class to these normally victimized non-TCP friendly flows. Simulation results show that fairness can also be maintained with other flows. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： Quality of service

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ON REARRANGEABILITY of CASCADED BANYAN-TYPE NETWORKS 18

ON REARRANGEABILITY of CASCADED BANYAN-TYPE NETWORKS

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Tan, Xuesong Robert Li, Shuo-Yen Department of Information Engineering The Chinese University of Hong Kong Room 735 SHB CUHK Shatin N.T. Hong Kong Hong Kong

ISBN: (纸本)9781604234565

the cascade of two baseline networks in tandem is a rearrangeable network. the cascade of two omega networks through a certain interconnection pattern is also rearrangeable. these belong to the general problem: for what banyan-type network (i.e., bit-permuting unique-routing network) is the tandem cascade a rearrangeable network? We relate the problem to the trace and guide of banyan-type networks. When the trace and guide of a 2n×2n banyan-type network are represented by the permutations τ and γ on integers 1 to n, respectively, rearrangeability of the tandem cascade of the network is solely determined by τγ–1. Such a permutation is said to be tandem rearrangeable when the tandem cascade is indeed rearrangeable. We identify a few tandem rearrangeable permutations, each implying the rearrangeability of the tandem cascade of a wide class of banyan-type networks. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： distributed computer systems

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Multi-level Loop Fusion with Mimimal Code Size 18

Multi-level Loop Fusion with Mimimal Code Size

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Liu, Meilin Shao, Zili Xue, Chun Chen, Kevin F. Sha, Edwin H.-M. Department of Computer Science University of Texas at Dallas RichardsonTX75083 United States

ISBN: (纸本)9781604234565

Loop fusion is one of the most effective and common techniques to increase the performance of programs with multiple loops. the code size of the fused loop after loop fusion legalization might be increased due to the generation of the extra prologue and epilogue. Code size should be considered and minimized for embedded system designs. In this paper, we develop the Select_LF technique, which is to select one of the possible dimensions to legalize loop fusion such that the resultant code size of the fused loop is minimized. We propose a theoretical foundation to determine which dimensions are possible to be retimed to legalize loop fusion for any "J + K" model loop with a J-level outer loop and multiple K-level inner loops. the experimental results show that the execution time of the fused loops by our Select_LF technique is reduced by 55.4% on average compared to the original loops, and the code size of the fused loops is reduced by 7.8% on average compared to the previously reported Max_LF algorithm. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： distributed computer systems

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Automated Implementation of Complex distributed Algorithms Specified in the IOA Language 18

Automated Implementation of Complex Distributed Algorithms S...

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Georgiou, Chryssis Lynch, Nancy Mavrommatis, Panayiotis Tauber, Joshua A. Dept. of Computer Science University of Cyprus Nicosia Cyprus MIT CSAIL CambridgeMA02139 United States

ISBN: (纸本)9781604234565

IOA is a formal language for describing Input/Output automata that serves both as a formal specification language and as a programming language [14]. the IOA compiler automatically translates IOA specifications into Java code that runs on a set of workstations communicating via the Message Passing Interface. this paper describes the process of compiling IOA specifications and our experiences running several distributed algorithms. We focus on our implementation of the algorithm of Gallager, Humblet and Spira (GHS) for minimum-weight spanning tree formation in an arbitrary graph [13]. Our IOA code for GHS is derived from the Input/Output automaton description of the algorithm proved correct by Welch, Lamport, and Lynch [33]. the successful implementation of such a complicated algorithm is significant for two reasons: (a) it is an indication of the capabilities of the IOA compiler and of its advanced state of development, and (b) to the best of our knowledge, this is the first complex, distributed algorithm implemented in an automated way that has been formally and rigorously proved correct. thus, this work shows that it is possible to formally specify, prove correct, and implement complex distributed algorithms using a common formal methodology. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： Trees (mathematics)

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Efficient VSM-based parallel Text Retrieval on a PC-Cluster Environment using MPI 18

Efficient VSM-based Parallel Text Retrieval on a PC-Cluster ...

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Kehagias, Dimitris Mamalis, Basilis Pantziou, Grammati Technological Educational Institution of Athens Dept. of Informatics Agiou Spyridonos Str. Aigaleo Athens12210 Greece

ISBN: (纸本)9781604234565

the design, implementation and experimental study of an efficient VSM-based parallel text retrieval method oriented to PC-Cluster environments are presented in this paper. Our approach is based on direct VSM-based indexing, distribution and retrieval methods and efficiently handles the two main problems met in this case: (a) even distribution of the computational load over the multiple processors and (b) efficient parallelization of the necessary global ranking sub-procedure, in order to gain both low response times and high speed-up values. Both the above aspects have been proved to lead to significant overheads in all the related parallel approaches in the bibliography till today. With regard to (a) we present an appropriate data sharing and balancing scheme based on ‘document clustering’, which finally leads to quite significant speed-up improvements, whereas with regard to (b) we have appropriately applied and evaluated tree-based merge-sort as well as other comparison-based sorting algorithms in order to achieve acceptably high efficiency. Additionally, our system is appropriately designed to operate both with and without the use of its built-in ‘clustering-based search mechanism’, in order to be able to perform efficient parallel selective retrieval over very large document collections. the corresponding implementation and experimental evaluation have been performed over a low/medium-cost PC-Cluster parallel environment with the use of MPI and they clearly validate the high efficiency of the suggested techniques. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： Cluster computing

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A Cache-Aware parallel Implementation of the Push-Relabel Network Flow Algorithm and Experimental Evaluation of the Gap Relabeling Heuristic 18

A Cache-Aware Parallel Implementation of the Push-Relabel Ne...

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18th international conference on parallel and distributed computing systems, PDCS 2005

作者： Bader, David A. Sachdeva, Vipin College of Computing Georgia Institute of Technology AtlantaGA30332 United States Electrical and Computer Engineering Department University of New Mexico AlbuquerqueNM87106 United States

ISBN: (纸本)9781604234565

the maximum flow problem is a combinatorial problem of significant importance in a wide variety of research and commercial applications. It has been extensively studied and implemented over the past 40 years. the push-relabel method has been shown to be superior to other methods, both in theoretical bounds and in experimental implementations. Our study discusses the implementation of the push-relabel network flow algorithm on present-day symmetric multiprocessors (SMP’s) with large shared memories. the maximum flow problem is an irregular graph problem and requires frequent fine-grained locking of edges and vertices. Over a decade ago, Anderson and Setubal implemented Goldberg’s push-relabel algorithm for shared memory parallel computers;however, modern systems differ significantly from those targeted by their implementation in that SMP’s today have deep memory hierarchies and different performance costs for synchronization and fine-grained locking. Besides our new cache-aware implementation of Goldberg’s parallel algorithm for modern shared-memory parallel computers, our main new contribution is the first parallel implementation and analysis of the gap relabeling heuristic that runs from 2.1 to 4.3 times faster for sparse graphs. © 2005 18th ISCA international conference on parallel and distributed computing systems 2005, PDCS 2005. All rights reserved.

关键词： Memory architecture

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