High Performance Computing for Computational Science - VECPAR 2004: 6th International Conference, Valencia, Spain, June 28-30, 2004, Revised Selected and Invited Papers

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Michel Daydé, Jack Dongarra, Vincente Hernández, José M.L.M. Palma
Springer Science & Business Media, Apr 28, 2005 - Computers - 732 pages
VECPAR is a series of international conferences dedicated to the promotion and advancement of all aspects of high-performance computing for computational science, as an industrial technique and academic discipline, extending the fr- tier of both the state of the art and the state of practice. The audience for and participants in VECPAR are seen as researchers in academic departments, g- ernment laboratories and industrial organizations. There is now a permanent website for the series, http://vecpar.fe.up.pt, where the history of the conf- ences is described. ThesixtheditionofVECPARwasthe?rsttimetheconferencewascelebrated outside Porto – at the Universitad Politecnica de Valencia (Spain), June 28–30, 2004. The whole conference programme consisted of 6 invited talks, 61 papers and26posters,outof130contributionsthatwereinitiallysubmitted.Themajor themes were divided into large-scale numerical and non-numerical simulations, parallel and grid computing, biosciences, numerical algorithms, data mining and visualization. This postconference book includes the best 48 papers and 5 invited talks presented during the three days of the conference. The book is organized into 6 chapters, with a prominent position reserved for the invited talks and the Best Student Paper. As a whole it appeals to a wide research community, from those involved in the engineering applications to those interested in the actual details of the hardware or software implementations, in line with what, in these days, tends to be considered as computational science and engineering (CSE).
 

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Contents

Large Scale Simulations
1
Development and Integration of Parallel Multidisciplinary Computational Software for Modeling a Modern Manufacturing Process
10
Automatically Tuned FFTs for BlueGeneLs Double FPU
23
A Survey of HighQuality Computational Libraries and Their Impact in Science and Engineering Applications
37
A Performance Evaluation of the Cray X1 for Scientific Applications
51
Modelling Overhead of Tuple Spaces with Design of Experiments
66
Analysis of the Interaction of Electromagnetic Signals with ThinWires Structures Multiprocessing Issues for an Iterative Method
78
A Performance Prediction Model for Tomographic Reconstruction in Structural Biology
90
Parallel Resolution of the TwoGroup Time Dependent Neutron Diffusion Equation with Public Domain ODE Codes
368
FPGA Implementations of the RNR Cellular Automata to Model Electrostatic Field
382
A WhatIf Prediction Tool for Tuning Message Passing Programs
396
Maintaining Cache Coherency for B+ Tree Indexes in a Shared Disks Cluster
410
Message StripMining Heuristics for High Speed Networks
424
Analysis of the Abortion Rate on Lazy Replication Protocols
438
A UserLevel RAID Emulator for Fast Prototyping in Fibre Channel SAN Environment
454
Parallel Computational Model with Dynamic Load Balancing in PC Clusters
468

Data Management in LargeScale P2P Systems
104
A High Performance System for Processing Queries on Distributed Geospatial Data Sets
119
Parallel Implementation of Information Retrieval Clustering Models
129
Distributed Processing of Large BioMedical 3D Images
142
Developing Distributed Data Mining Applications in the KNOWLEDGE GRID Framework
156
Scaling Up the Preventive Replication of Autonomous Databases in Cluster Systems
170
Parallel Implementation of a Fuzzy Rule Based Classifier
184
The EGEE European Grid Infrastructure Project
194
Grid Technology for Biomedical Applications
204
ThreeDimensional Cardiac Electrical Activity Simulation on Cluster and Grid Platforms
219
Migrating a LargeScale Numerical Mathematical Application to a Grid Environment
233
Design of an OGSACompliant Grid Information Service Using NET Technologies
247
A WebBased Application Service Provision Architecture for Enabling HighPerformance Image Processing
260
Influence of Grid Economic Factors on Scheduling and Migration
274
Specification and Solution
288
Three Case Studies
302
Security Mechanism for Medical Image Information on PACS Using Invisible Watermark
315
Parallel Generalized Finite Element Method for Magnetic Multiparticle Problems
325
Parallel Model Reduction of Large Linear Descriptor Systems via Balanced Truncation
340
A Parallel Algorithm for Automatic Particle Identification in Electron Micrographs
354
Dynamically Adaptive Binomial Trees for Broadcasting in Heterogeneous Networks of Workstations
480
Parallel Simulation of Multicomponent Systems Invited Talk
496
A Portable 3D Elastostatic Implementation for Shared Memory Systems
514
On Dependence Analysis for SIMD Enhanced Processors
527
A Preliminary NestedParallel Framework to Efficiently Implement Scientific Applications
541
DWT as a Case Study
556
Domain Decomposition Methods for PDE Constrained Optimization Problems
569
Parallelism in Bioinformatics Workflows
583
Recursivity Versus Multithreading
598
Probabilistic Program Analysis for Parallelizing Compilers
610
Parallel Acceleration of Krylov Solvers by Factorized Approximate Inverse Preconditioners
623
Krylov and Polynomial Iterative Solvers Combined with Partial Spectral Factorization for SPD Linear Systems
637
Three Parallel Algorithms for Solving Nonlinear Systems and Optimization Problems
657
A High Performance Computing Approach
671
An Efficient and Stable Parallel Solution for Nonsymmetric Toeplitz Linear Systems
685
Partial Spectral Information from Linear Systems to SpeedUp Numerical Simulations in Computational Fluid Dynamics
699
Parallel Newton Iterative Methods Based on Incomplete LU Factorizations for Solving Nonlinear Systems
716
Author Index
730
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