This book constitutes the thoroughly refereed post-proceedings of the 8th International Workshop on Applied Parallel Computing, PARA 2006. It covers partial differential equations, parallel scientific computing algorithms, linear algebra, simulation environments, algorithms and applications for blue gene/L, scientific computing tools and applications, parallel search algorithms, peer-to-peer computing, mobility and security, algorithms for single-chip multiprocessors.
Inhalt
Keynote Papers.- The Impact of Multicore on Math Software.- Prospectus for the Next LAPACK and ScaLAPACK Libraries.- Large-Scale Methods in Image Deblurring.- A Case Study in High-Performance Mixed-Language Programming.- Minisymposia Papers.- Stretching Time and Length Scales in Biomolecular Modelling: Minisymposium Abstract.- Averaged Configurations from Molecular Dynamics Simulations.- Atomistic Simulation Studies of Polymers and Water.- A New Monte Carlo Method for the Titration of Molecules and Minerals.- Coarse Graining Biomolecular Systems.- Molecular Dynamics Simulation Studies on the Modulation of Vitamin D Receptor Activity by Agonists and Antagonists.- Sparse Matrix Algebra for Quantum Modeling of Large Systems.- A Highly Efficient Ab Initio Tight-Binding-Like Approximate Density-Functional Quantum Mechanical Method.- Protein Folding Properties from Molecular Dynamics Simulations.- Recent Advances in Dense Linear Algebra: Minisymposium Abstract.- Parallel Variants of the Multishift QZ Algorithm with Advanced Deflation Techniques.- Parallel Algorithms and Condition Estimators for Standard and Generalized Triangular Sylvester-Type Matrix Equations.- LAPACK-Style Codes for Pivoted Cholesky and QR Updating.- Implementing Linear Algebra Routines on Multi-core Processors with Pipelining and a Look Ahead.- Specialized Spectral Division Algorithms for Generalized Eigenproblems Via the Inverse-Free Iteration.- CFD Applications for High Performance Computing: Minisymposium Abstract.- Some Experiences on the Accuracy and Parallel Performance of OpenFOAM for CFD in Water Turbines.- HPC Environments - Visualization and Parallelization Tools: Minisymposium Abstract.- Trusting Floating Point Benchmarks - Are Your Benchmarks Really Data Independent?.- CoMPI - Configuration of Collective Operations in LAM/MPI Using the Scheme Programming Language.- A Load Balancing Strategy for Computations on Large, Read-Only Data Sets.- Automatic and Transparent Optimizations of an Application's MPI Communication.- Parallel Methods for Real-Time Visualization of Snow.- Support for Collaboration, Visualization and Monitoring of Parallel Applications Using Shared Windows.- Tools, Frameworks and Applications for High Performance Computing: Minisymposium Abstract.- Multi-level ?-Finite Element Analysis for Human Bone Structures.- High-Level User Interfaces for the DOE ACTS Collection.- High-Performance Graph Algorithms from Parallel Sparse Matrices.- A Python Module for PDE-Based Numerical Modelling.- COMODI: Architecture for a Component-Based Scientific Computing System.- Workload Characterization Using the TAU Performance System.- Grid Data Management: Minisymposium Abstract.- Supporting SLA Negotiation for QoS-Enabled Simulation Services in a Medical Grid Environment.- A Transparent Grid Filesystem.- Grid Data Integration Based on Schema Mapping.- Simulations in Geophysics and Space Physics: Minisymposium Abstract.- Parallelization of a Public Image Restoration Algorithm.- Visualizing Katrina - Merging Computer Simulations with Observations.- Generation of Microlensing Magnification Patterns with High Performance Computing Techniques.- Phase Space Modulations in Magnetised Plasmas by a Mildly Relativistic Two-Stream Instability.- Implementing a Particle-Fluid Model of Auroral Electrons.- Tools for Parallel Performance Analysis: Minisymposium Abstract.- Automatic Tuning in Computational Grids.- Automated Performance Analysis Using ASL Performance Properties.- A Parallel Trace-Data Interface for Scalable Performance Analysis.- Search of Performance Inefficiencies in Message Passing Applications with KappaPI 2 Tool.- Automatic Monitoring of Memory Hierarchies in Threaded Applications with AMEBA.- Visualization of Repetitive Patterns in Event Traces.- Optimization of Instrumentation in Parallel Performance Evaluation Tools.- GASP! A Standardized Performance Analysis Tool Interface for Global Address Space Programming Models.- Integrated Runtime Measurement Summarisation and Selective Event Tracing for Scalable Parallel Execution Performance Diagnosis.- Grids for Scientific Computing: Minisymposium Abstract.- Roadmap for the ARC Grid Middleware.- Data Management for the World's Largest Machine.- Meta-computations on the CLUSTERIX Grid.- Simulations of Materials: Minisymposium Abstract.- Ab Initio Calculations of the Electronic Structure and Magnetism of Iron Porphyrin-Type Molecules: A Benchmarking Study.- Mechanical Properties of Random Alloys from Quantum Mechanical Simulations.- Novel Data Formats and Algorithms for Dense Linear Algebra Computations: Minisymposium Abstract.- Cache Oblivious Matrix Operations Using Peano Curves.- Recursive Blocked Algorithms for Solving Periodic Triangular Sylvester-Type Matrix Equations.- Minimal Data Copy for Dense Linear Algebra Factorization.- Three Algorithms for Cholesky Factorization on Distributed Memory Using Packed Storage.- In-Place Transposition of Rectangular Matrices.- Rectangular Full Packed Format for LAPACK Algorithms Timings on Several Computers.- Using Non-canonical Array Layouts in Dense Matrix Operations.- New Data Distribution for Solving Triangular Systems on Distributed Memory Machines.- The Design of a New Out-of-Core Multifrontal Solver.- Cholesky Factorization of Band Matrices Using Multithreaded BLAS.- A Master-Worker Type Eigensolver for Molecular Orbital Computations.- Bioinformatics and Computational Biology: Minisymposium Abstract.- Using Parallel Computing and Grid Systems for Genetic Mapping of Quantitative Traits.- Partial Approximation of the Master Equation by the Fokker-Planck Equation.- Design, Construction and Use of the FISH Server.- Scientific Visualization and HPC Applications: Minisymposium Abstract.- Interactive Volume Visualization of Fluid Flow Simulation Data.- Software Tools for Parallel CFD Applications: Minisymposium Abstract.- The Iterative Solver Template Library.- EulFS: A Parallel CFD Code for the Simulation of Euler and Navier-Stokes Problems on Unstructured Grids.- Making Hybrid Tsunami Simulators in a Parallel Software Framework.- HPC-MW: A Problem Solving Environment for Developing Parallel FEM Applications.- SyFi - An Element Matrix Factory.- Life: Overview of a Unified C++ Implementation of the Finite and Spectral Element Methods in 1D, 2D and 3D.- Parallel Program Complex for 3D Unsteady Flow Simulation.- Multi-scale Physics: Minisymposium Abstract.- Simulation of Multiphysics Problems Using Adaptive Finite Elements.- Contributed Papers.- A New Domain Decomposition Approach Suited for Grid Computing.- Parallelization of the Mesh Refinement Algorithm of the FDEM Program Package.- Load Balancing for the Numerical Solution of the Navier-Stokes Equations.- A Method of Adaptive Coarsening for Compressing Scientific Datasets.- A Computational Framework for Topological Operations.- Applications of Grid Computing in Genetics and Proteomics.- Grid Enabling Your Data Resources with OGSA-DAI.- UniGrids Streaming Framework: Enabling Streaming for the New Generation of Grids.- Dynamic Clusters Available Under Clusterix Grid.- Agent-Based Societies for the Sharing, Brokerage and Allocation of Grid Resources.- OpusIB - Grid Enabled Opteron Cluster with InfiniBand Interconnect.- Extending the HPC-ICTM Geographical Categorization Model for Grid Computing.- Distributed SILC: An Easy-to-Use Interface for MPI-Based Parallel Matrix Computation Libraries.- A Study of Real World I/O Performance in Parallel Scienti…