## High Performance Computing for Computational Science - VECPAR 2006: 7th International Conference, Rio de Janeiro, Brazil, June 10-13, 2006, Revised Selected and Invited PapersMichel Daydé, José M.L.M. Palma, Álvaro L.G.A. Couthino, Esther Pacitti, João Correia Lopes This book constitutes the thoroughly refereed post-proceedings of the 7th International Conference on High Performance Computing for Computational Science, VECPAR 2006, held in Rio de Janeiro, Brazil, in June 2006. The 44 revised full papers presented together with one invited paper and 12 revised workshop papers cover Grid computing, cluster computing, numerical methods, large-scale simulations in Physics, and computing in Biosciences. |

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### Contents

An Opportunistic Algorithm for Scheduling Workflows on Grids | 1 |

Computational Grids | 13 |

Scalable Desktop Grid System | 27 |

Analyzing Overheads and Scalability Characteristics of OpenMP Applications | 39 |

Parallel Fuzzy cMeans Cluster Analysis | 52 |

A Scalable Architecture | 66 |

A Programming and Execution Environment for Asynchronous Iterative Computations on Volatile Nodes | 79 |

Aspect Oriented Pluggable Support for Parallel Computing | 93 |

Multiresolution Simulations Using Particles | 391 |

Evaluation of Several Variants of Explicitly Restarted Lanczos Eigensolvers and Their Parallel Implementations | 403 |

A HighLevel Framework for Fast Development of High Performance Applications | 417 |

Sequential and Parallel Resolution of the TwoGroup Transient Neutron Diffusion Equation Using SecondDegree Iterative Methods | 426 |

Enhancing the Performance of Multigrid Smoothers in Simultaneous Multithreading Architectures | 439 |

Block Iterative Algorithms for the Solution of Parabolic Optimal Control Problems | 452 |

Evaluation of Linear Solvers for Astrophysics Transfer Problems | 466 |

Scalable Cosmological Simulations on Parallel Machines | 476 |

Model for Simulation of Heterogeneous HighPerformance Computing Environments | 107 |

On Evaluating Decentralized Parallel IO Scheduling Strategies for Parallel File Systems | 120 |

Distributed Security Constrained Optimal Power Flow Integrated to a DSM Based Energy Management System for Real Time Power Systems Security... | 131 |

Metaserver Locality and Scalability in a Distributed NFS | 145 |

Topk Query Processing in the APPA P2P System | 158 |

Posterior Task Scheduling Algorithms for Heterogeneous Computing Systems | 172 |

Design and Implementation of an Environment for ComponentBased Parallel Programming | 184 |

A Programming Environment for Cluster Computing | 198 |

A Tool for Mining Frequent Item Sets Efficiently in Data Warehouses | 212 |

A Parallel Implementation of the K Nearest Neighbours Classiﬁer in Three Levels Threads MPI Processes and the Grid | 225 |

On the Use of the MMC Language to Utilize SIMD Instruction Set | 236 |

for Encryption and Decryption Using Advanced Encryption Standard | 249 |

The Enabling Power of Discrete Algorithms in Computational Science | 260 |

Improving the Numerical Simulation of an Airﬂow Problem with the BlockCGSI Algorithm | 281 |

A Parallel Vertex and Node Reordering Package for Optimizing EdgeBased Computations in Unstructured Grids | 292 |

Parallel Processing of Matrix Multiplication in a CPU and GPU Heterogeneous Environment | 305 |

Robust TwoLevel LowerOrder Preconditioners for a HigherOrder Stokes Discretization with Highly Discontinuous Viscosities | 319 |

The Impact of Parallel Programming Models on the Performance of Iterative Linear Solvers for Finite Element Applications | 334 |

Efficient Parallel Algorithm for Constructing a Unit Triangular Matrix with Prescribed Singular Values | 349 |

A Rewriting System for the Vectorization of Signal Transforms | 363 |

High Order FourierSpectral Solutions to Self Adjoint Elliptic Equations | 378 |

Performance Evaluation of Scientiﬁc Applications on Modern Parallel Vector Systems | 490 |

Numerical Simulation of ThreePhase Flow in Heterogeneous Porous Media | 504 |

Simulation of Laser Propagation in a Plasma with a Frequency Wave Equation | 518 |

A Particle Gradient Evolutionary Algorithm Based on Statistical Mechanics and Convergence Analysis | 530 |

A Computational Framework for Cardiac Modeling Based on Distributed Computing and Web Applications | 544 |

Triangular Clique Based Multilevel Approaches to Identify Protein Functional Modules | 556 |

A Portal for Deployment of Bioinformatics Applications on Cluster and Grid Environments | 566 |

Adaptive Distributed Metamodeling | 579 |

Distributed General Logging Architecture for Grid Environments | 589 |

Interoperability Between UNICORE and ITBL | 601 |

Using Failure Injection Mechanisms to Experiment and Evaluate a Grid Failure Detector | 610 |

SemanticBased Service Trading Application to Linear Algebra | 622 |

Management of Services Based on a Semantic Description Within the GRIDTLSE Project | 634 |

Extending the Services and Sites of Production Grids by the Support of Advanced Portals | 644 |

PSOGrid Data Replication Service | 656 |

Execution Management of Scientific Models on Computational Grids | 670 |

Replica Refresh Strategies in a Database Cluster | 679 |

A Practical Evaluation of a Data Consistency Protocol for Efﬁcient Visualization in Grid Applications | 692 |

Experiencing Data Grids | 707 |

719 | |

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### Common terms and phrases

algorithm analysis application approach architecture Berlin Heidelberg 2007 bioinformatics BOINC cache Charm++ client cluster coeﬃcient component Computer Science computing nodes conﬁguration convergence database deﬁned desktop grid diﬀerent distributed dynamic Earth Simulator eﬀective eﬃcient eigenvalues equations evaluation execution failure ﬁle system ﬁrst ﬂow function global graph Grid Computing Grid environments Grid service I/O scheduling IEEE implementation input interface ITBL iterative Lanczos linear system matrix memory messages method middleware nodes number of processors OpenMP operation Opteron optimal orthogonality overhead Parallel Computing parallel programming parameters particles partition peers PETSc pointcut portal Power5 preconditioner problem production Grid proposed query replication scalability ScaLAPACK scheduling scientiﬁc server simulation solution solve solvers sparse speciﬁc speedup SPGEA strategy structure SZTAKI Desktop Grid task techniques threads tool UNICORE values VECPAR vector workflow