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Design and implementation of a windows-based parallel computing environment for large scale optimization

ADVANCES IN ENGINEERING SOFTWARE 2004年第8-9期35卷 577-584页

作者： Wei, LY Wei, RY Tang, TB Univ Queensland Adv Computat Modlling Ctr St Lucia Qld 4072 Australia Guangxi Univ Sch Comp & Informat Engn Nanning 530004 Peoples R China Jiao Tong Univ State Key Lab Vibrat Shock & Noise Shanghai 200030 Peoples R China

A parallel computing environment to support optimization of large-scale engineering systems is designed and implemented on Windows-based personal computer networks, using the master-worker model and the parallel Virtual Machine (PVM). It is involved in decomposition of a large engineering system into a number of smaller subsystems optimized in parallel on worker nodes and coordination of subsystem optimization results on the master node. The environment consists of six functional modules, i.e. the master control, the optimization model generator, the optimizer, the data manager, the monitor, and the post processor. Object-oriented design of these modules is presented. The environment supports steps from the generation of optimization models to the solution and the visualization on networks of computers. User-friendly graphical interfaces make it easy to define the problem, and monitor and steer the optimization process. It has been verified by an example of a large space truss optimization. (C) 2004 Elsevier Ltd. All rights reserved.

关键词： optimization parallel and distributed computing problem solving environment object-oriented design windows

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The AxML program family for maximum likelihood-based phylogenetic tree inference

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CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 2004年第9期16卷 975-988页

作者： Stamatakis, AP Ludwig, T Meier, H Tech Univ Munich Lehrstuhl Rechnertech & Rechnerorgan 110 D-85748 Munich Germany Heidelberg Univ Inst Informat D-69120 Heidelberg Germany

Inference of phylogenetic (evolutionary) trees comprising hundreds or thousands of organisms based on the maximum likelihood criterion is a computationally extremely intensive task. This paper describes the evolution of the AxML program family which provides novel algorithmic as well as technical solutions for the maximum likelihood-based inference of huge phylogenetic trees. Algorithmic optimizations and a new tree building algorithm yield runtime improvements of a factor greater than 4 compared with fastDNAml and parallel fastDNAml, returning equally good trees at the same time. Various parallel, distributed, and Grid-based implementations of AxML give the program the capability to acquire the large amount of required computational resources for the inference of huge high-quality trees. Copyright (C) 2004 John Wiley Sons, Ltd.

关键词： phylogenetic trees maximum likelihood parallel and distributed computing

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Development and implementation of a parallel algorithm for the fast design of oligonucleotide probe sets for diagnostic DNA microarrays

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CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 2004年第9期16卷 873-893页

作者： Meier, H Krause, A Kräutner, M Bode, A Tech Univ Munich Inst Informat LRR TUM D-85748 Garching Germany

We describe an accurate method for the automatic parallel generation of oligonucleotide probe sets for DNA microarrays. This approach includes a component for high-performance specificity evaluation of designed probes in large data sets. The three main algorithmic components of the method, namely probe preselection, hybridization prediction and probe selection are explained in detail. We introduce new combinatorial techniques for the efficient selection of probe sets of high differentiation capability even from sequence databases of conserved homologous genes. These techniques include the automatic generation of group specific probes as well as the design of excluding probes. A basic prototype has been implemented including a shared memory parallelization. Test runs have been performed on a multiprocessor personal computer with subsets of a small subunit ribosomal ribonucleic acid database, containing very conserved sequence data. The applicability of our program is pointed out by designing a set of oligonucleotide probes that shall allow a comprehensive parallel identification and differentiation of several groups of extremophilic prokaryotes by DNA microarray. The probe set is accessible via the Internet. On applying the parallel version on a dual processor system an efficiency of 80% was achieved. Copyright (C) 2004 John Wiley Sons, Ltd.

关键词： DNA microarray bioinformatic algorithm molecular sequence analysis parallel and distributed computing oligonucleotide probe combinatorial DNA chip

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A peer to peer computing framework: Design and performance evaluation of YML

A peer to peer computing framework: Design and performance e...

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3rd International Symposium on parallel and distributed computing (ISPDC 2004)/3rd International Workshop on Algorithms, Models and Tools for parallel computing on Heterogeneous Networks (HeteroPar 04)

作者： Delannoy, O Petiton, S Univ Versailles St Quentin PRiSM Versailles France

ISBN: (纸本)0769522106

Peer to peer and grid systems provide attractive middlewares to solve large numerical problems. The development, deployment and execution of applications using those middlewares suffer from the lack of well-adapted advanced tools. There is not any available solution to use the same application on two distinct middlewares. Our article presents the YML Framework which provides supporting tools to design and execute portable parallel applications over large scale peel, to peer and grid middlewares. The YML Framework defines a new parallel programming language called YvetteML which is composed of a graph language and a component model. We evaluate the performance of our framework with a simple numerical application using XtremWeb as a middleware.

关键词： parallel and distributed computing peer to peer matrix computation

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Adaptive computing on the grid using AppLeS

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IEEE TRANSACTIONS ON parallel AND distributed SYSTEMS 2003年第4期14卷 369-382页

作者： Berman, F Wolski, R Casanova, H Cirne, W Dail, H Faerman, M Figueira, S Hayes, J Obertelli, G Schopf, J Shao, G Smallen, S Spring, N Su, A Zagorodnov, D San Diego Supercomp Ctr La Jolla CA 92093 USA Univ Calif Santa Barbara Dept Comp Sci Santa Barbara CA 93106 USA Univ Calif San Diego Dept Comp Sci & Engn La Jolla CA 92093 USA Dept Sistemas & Comp BR-58109970 Campina Grande PB Brazil Santa Clara Univ Dept Comp Engn Santa Clara CA 95053 USA Argonne Natl Lab Math & Comp Sci Div Distributed Syst Lab Argonne IL 60439 USA Univ Washington Seattle WA 98195 USA

Ensembles of distributed, heterogeneous resources, also known as Computational Grids, have emerged as critical platforms for high-performance and resource-intensive applications. Such platforms provide the potential for applications to aggregate enormous bandwidth, computational power, memory, secondary storage, and other resources during a single execution. However, achieving this performance potential in dynamic, heterogeneous environments is challenging. Recent experience with distributed, applications indicates that adaptivity is fundamental to achieving application performance in dynamic grid environments. The AppLeS (Application Level Scheduling) project provides a methodology, application software, and software environments for adaptively scheduling and deploying applications in heterogeneous, multiuser grid environments. In this article, we discuss the AppLeS project and outline our findings.

关键词： scheduling parallel and distributed computing heterogeneous computing grid computing

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Engineering high-performance legacy codes as CORBA components for problem-solving environments

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JOURNAL OF parallel and distributed computing 2003年第11期63卷 1152-1163页

作者： Li, M Walker, DW Rana, OF Huang, Y Williams, PT Ward, RC Brunel Univ Dept Elect & Comp Engn Uxbridge UB8 3PH Middx England Cardiff Univ Sch Comp Sci Cardiff CF24 3XF S Glam Wales Oak Ridge Natl Lab Computat Sci & Engn Div Oak Ridge TN 37831 USA

This paper describes techniques used to leverage high-performance legacy codes as CORBA components to a distributed problem-solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high-performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element-based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high-performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user's desktop computing environment can be extended to a high-performance computing environment using a cluster of workstations or a parallel computer. (C) 2003 Elsevier Inc. All rights reserved.

关键词： problem-solving environments high-performance legacy codes CORBA components wrapper generator parallel and distributed computing

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A distributed object infrastructure for interaction and steering

A distributed object infrastructure for interaction and stee...

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7th European Conference on parallel computing

作者： Muralidhar, R Parashar, M Rutgers State Univ Dept Elect & Comp Engn Appl Software Syst Lab Piscataway NJ 08854 USA

This paper presents the design, implementation and experimental evaluation of DIOS (distributed Interactive Object Substrate), an interactive object infrastructure to enable the runtime monitoring, interaction and computational steering of parallel and distributed applications. DIOS enables application objects (data structures, algorithms) to be enhanced with sensors and actuators so that they can be interrogated and controlled. Application objects may be distributed (spanning many processors) and dynamic (be created, deleted, changed or migrated). Furthermore, DIOS provides a control network that interconnects the interactive objects in a parallel/distributed application and enables external discovery, interrogation, monitoring and manipulation of these objects at runtime. DIOS is currently being used to enable interactive visualization, monitoring and steering of a wide range of scientific applications, including oil reservoir, compressible turbulence and numerical relativity simulations. Copyright (C) 2003 John Wiley Sons, Ltd.

关键词： distributed and dynamic objects computational interaction and steering sensors and actuators computational collaboratory scientific applications parallel and distributed computing

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Dynamic load partitioning strategies for managing data of space and time heterogeneity in parallel SAMR applications

Dynamic load partitioning strategies for managing data of sp...

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9th International Euro-Par Conference on parallel Processing

作者： Li, XL Parashar, M Rutgers State Univ Dept Elect & Comp Engn Appl Software Syst Lab Piscataway NJ 08854 USA

ISBN: (纸本)354040788X

This paper presents the design and experimental evaluation of two dynamic load partitioning and balancing strategies for parallel Structured Adaptive Mesh Refinement (SAMR) applications: the Level-based Partitioning Algorithm (LPA) and the Hierarchical Partitioning Algorithm (HPA). These techniques specifically address the computational and communication heterogeneity across refinement levels of the adaptive grid hierarchy underlying these methods. An experimental evaluation of the partitioning schemes is also presented.

关键词： dynamic load balancing parallel and distributed computing structured adaptive mesh refinement scientific computing

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A distributed object infrastructure for interaction and steering

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CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 2003年第10期15卷 957-977页

作者： Muralidhar, R Parashar, M Rutgers State Univ Dept Elect & Comp Engn Appl Software Syst Lab Piscataway NJ 08854 USA

关键词： distributed and dynamic objects computational interaction and steering sensors and actuators computational collaboratory scientific applications parallel and distributed computing

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A parallel procedure for nonlinear analysis of reinforced concrete three-dimensional frames

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COMPUTERS & STRUCTURES 2002年第16-17期80卷 1337-1350页

作者： Romero, ML Miguel, PF Cano, JJ Univ Jaume 1 Dept Technol Castellon de La Plana 12071 Spain Univ Politecn Valencia Dept Civil Engn Valencia Spain

The paper discusses the parallelisation of complex three-dimensional software for nonlinear analysis of R/C buildings structures. It presents a comparative study for handling the nonlinear response in different parallel architectures. The nonlinear finite element model adopts a fiber decomposition approach for the cross-section of beam elements to capture nonlinear behavior of concrete. The parallelisation strategy is designed regarding three items: the numerical stability of the nonlinear procedure, the parallel sparse equation solver and the application on heterogeneous hardware: dedicated shared memory machines or clusters of networked personal computers. (C) 2002 Published by Elsevier Science Ltd.

关键词： nonlinear analysis reinforced concrete parallel and distributed computing cluster of personal computers

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