## High Performance Computing for Computational Science - VECPAR 2004: 6th International Conference, Valencia, Spain, June 28-30, 2004, Revised Selected and Invited PapersMichel Daydé, Jack Dongarra, Vincente Hernández, José M.L.M. Palma 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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### Common terms and phrases

analysis applications approach architecture B+ tree bioinformatics block BlueGene/L cache cells cluster communication components convergence cost database dataset decomposition deﬁned deﬁnition developed DICOM diﬀerent disk distributed DRESOL Earth Simulator eﬀect eﬃcient EGEE eigenvalues elements environment equation execution factorization ﬁle ﬁltering ﬁrst ﬂow function global Grid Grid Computing High Performance interface iterations JavaSpaces LAPACK linear systems loop Lyapunov equation matrix memory mesh method module node number of nodes number of processors obtained operations optimization parallel algorithm Parallel Computing parallel implementation parameters particles partitioning Power4 preconditioner prediction problem Proc projection query RAID reduce replication routines scalability ScaLAPACK scientiﬁc sequential server SIMD simulation solution solve solver speciﬁc speedup step structure swap synchronous Table techniques tion transactions Tsol update values variables VECPAR vector voxels workflow