Ebook: Applied Parallel Computing. State of the Art in Scientific Computing: 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers

This book constitutes the thoroughly refereed post-proceedings of the 8th International Workshop on Applied Parallel Computing, PARA 2006, held in Umeå, Sweden, June 2006.

This volume contains four keynote lectures and 86 revised papers of 15 invited minisymposia arranged on the following topics: recent advances in dense linear algebra, CFD applications for high performance computing, HPC environments: visualization and parallelization tools, tools, grid data management, grids for scientific computing, simulations of materials, novel data formats and algorithms for dense linear algebra computations, bioinformatics and computational biology, software tools for parallel CFD applications, and multi-scale physics.

The 45 revised full papers of the main track are organized in topical sections on partial differential equations, grid computing, parallel scientific computing algorithms, linear algebra, simulation environments, algorithms and applications for blue gene/L, scientific computing applications, scientific computing tools, parallel search algorithms, peer-to-peer computing, mobility and security, algorithms for single-chip multiprocessors.

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This book constitutes the thoroughly refereed post-proceedings of the 8th International Workshop on Applied Parallel Computing, PARA 2006, held in Ume?, Sweden, June 2006.

This volume contains four keynote lectures and 86 revised papers of 15 invited minisymposia arranged on the following topics: recent advances in dense linear algebra, CFD applications for high performance computing, HPC environments: visualization and parallelization tools, tools, grid data management, grids for scientific computing, simulations of materials, novel data formats and algorithms for dense linear algebra computations, bioinformatics and computational biology, software tools for parallel CFD applications, and multi-scale physics.

The 45 revised full papers of the main track are organized in topical sections on partial differential equations, grid computing, parallel scientific computing algorithms, linear algebra, simulation environments, algorithms and applications for blue gene/L, scientific computing applications, scientific computing tools, parallel search algorithms, peer-to-peer computing, mobility and security, algorithms for single-chip multiprocessors.

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This book constitutes the thoroughly refereed post-proceedings of the 8th International Workshop on Applied Parallel Computing, PARA 2006, held in Ume?, Sweden, June 2006.

This volume contains four keynote lectures and 86 revised papers of 15 invited minisymposia arranged on the following topics: recent advances in dense linear algebra, CFD applications for high performance computing, HPC environments: visualization and parallelization tools, tools, grid data management, grids for scientific computing, simulations of materials, novel data formats and algorithms for dense linear algebra computations, bioinformatics and computational biology, software tools for parallel CFD applications, and multi-scale physics.

The 45 revised full papers of the main track are organized in topical sections on partial differential equations, grid computing, parallel scientific computing algorithms, linear algebra, simulation environments, algorithms and applications for blue gene/L, scientific computing applications, scientific computing tools, parallel search algorithms, peer-to-peer computing, mobility and security, algorithms for single-chip multiprocessors.

Content:
Front Matter....Pages -
The Impact of Multicore on Math Software....Pages 1-10
Prospectus for the Next LAPACK and ScaLAPACK Libraries....Pages 11-23
Large-Scale Methods in Image Deblurring....Pages 24-35
A Case Study in High-Performance Mixed-Language Programming....Pages 36-49
Stretching Time and Length Scales in Biomolecular Modelling: Minisymposium Abstract....Pages 50-50
Averaged Configurations from Molecular Dynamics Simulations....Pages 51-58
Atomistic Simulation Studies of Polymers and Water....Pages 59-65
A New Monte Carlo Method for the Titration of Molecules and Minerals....Pages 66-72
Coarse Graining Biomolecular Systems....Pages 73-81
Molecular Dynamics Simulation Studies on the Modulation of Vitamin D Receptor Activity by Agonists and Antagonists....Pages 82-89
Sparse Matrix Algebra for Quantum Modeling of Large Systems....Pages 90-99
A Highly Efficient Ab Initio Tight-Binding-Like Approximate Density-Functional Quantum Mechanical Method....Pages 100-108
Protein Folding Properties from Molecular Dynamics Simulations....Pages 109-115
Recent Advances in Dense Linear Algebra: Minisymposium Abstract....Pages 116-116
Parallel Variants of the Multishift QZ Algorithm with Advanced Deflation Techniques....Pages 117-126
Parallel Algorithms and Condition Estimators for Standard and Generalized Triangular Sylvester-Type Matrix Equations....Pages 127-136
LAPACK-Style Codes for Pivoted Cholesky and QR Updating....Pages 137-146
Implementing Linear Algebra Routines on Multi-core Processors with Pipelining and a Look Ahead....Pages 147-156
Specialized Spectral Division Algorithms for Generalized Eigenproblems Via the Inverse-Free Iteration....Pages 157-166
CFD Applications for High Performance Computing: Minisymposium Abstract....Pages 167-167
Some Experiences on the Accuracy and Parallel Performance of OpenFOAM for CFD in Water Turbines....Pages 168-176
HPC Environments – Visualization and Parallelization Tools: Minisymposium Abstract....Pages 177-177
Trusting Floating Point Benchmarks – Are Your Benchmarks Really Data Independent?....Pages 178-188
A Load Balancing Strategy for Computations on Large, Read-Only Data Sets....Pages 189-197
Automatic and Transparent Optimizations of an Application’s MPI Communication....Pages 198-207
Parallel Methods for Real-Time Visualization of Snow....Pages 208-217
Support for Collaboration, Visualization and Monitoring of Parallel Applications Using Shared Windows....Pages 218-227
Tools, Frameworks and Applications for High Performance Computing: Minisymposium Abstract....Pages 228-238
Multi-level ?-Finite Element Analysis for Human Bone Structures....Pages 239-239
High-Level User Interfaces for the DOE ACTS Collection....Pages 240-250
High-Performance Graph Algorithms from Parallel Sparse Matrices....Pages 251-259
A Python Module for PDE-Based Numerical Modelling....Pages 260-269
COMODI: Architecture for a Component-Based Scientific Computing System....Pages 270-279
Workload Characterization Using the TAU Performance System....Pages 280-288
Grid Data Management: Minisymposium Abstract....Pages 289-296
Supporting SLA Negotiation for QoS-Enabled Simulation Services in a Medical Grid Environment....Pages 297-297
A Transparent Grid Filesystem....Pages 298-308
Grid Data Integration Based on Schema Mapping....Pages 309-318
Simulations in Geophysics and Space Physics: Minisymposium Abstract....Pages 319-328
Parallelization of a Public Image Restoration Algorithm....Pages 329-329
Visualizing Katrina - Merging Computer Simulations with Observations....Pages 330-339
Generation of Microlensing Magnification Patterns with High Performance Computing Techniques....Pages 340-350
Phase Space Modulations in Magnetised Plasmas by a Mildly Relativistic Two-Stream Instability....Pages 351-360
Implementing a Particle-Fluid Model of Auroral Electrons....Pages 361-370
Tools for Parallel Performance Analysis: Minisymposium Abstract....Pages 371-379
Automatic Tuning in Computational Grids....Pages 380-380
Automated Performance Analysis Using ASL Performance Properties....Pages 381-389
A Parallel Trace-Data Interface for Scalable Performance Analysis....Pages 390-397
Search of Performance Inefficiencies in Message Passing Applications with KappaPI 2 Tool....Pages 398-408
Automatic Monitoring of Memory Hierarchies in Threaded Applications with AMEBA....Pages 409-419
Visualization of Repetitive Patterns in Event Traces....Pages 420-429
Optimization of Instrumentation in Parallel Performance Evaluation Tools....Pages 430-439
GASP! A Standardized Performance Analysis Tool Interface for Global Address Space Programming Models....Pages 440-449
Integrated Runtime Measurement Summarisation and Selective Event Tracing for Scalable Parallel Execution Performance Diagnosis....Pages 450-459
Grids for Scientific Computing: Minisymposium Abstract....Pages 460-469
Roadmap for the ARC Grid Middleware....Pages 470-470
Data Management for the World’s Largest Machine....Pages 471-479
Meta-computations on the CLUSTERIX Grid....Pages 480-488
Simulations of Materials: Minisymposium Abstract....Pages 489-500
Mechanical Properties of Random Alloys from Quantum Mechanical Simulations....Pages 501-501
Novel Data Formats and Algorithms for Dense Linear Algebra Computations: Minisymposium Abstract....Pages 502-509
Cache Oblivious Matrix Operations Using Peano Curves....Pages 510-519
Recursive Blocked Algorithms for Solving Periodic Triangular Sylvester-Type Matrix Equations....Pages 520-520
Minimal Data Copy for Dense Linear Algebra Factorization....Pages 521-530
Three Algorithms for Cholesky Factorization on Distributed Memory Using Packed Storage....Pages 531-539
In-Place Transposition of Rectangular Matrices....Pages 540-549
Rectangular Full Packed Format for LAPACK Algorithms Timings on Several Computers....Pages 550-559
Using Non-canonical Array Layouts in Dense Matrix Operations....Pages 560-569
New Data Distribution for Solving Triangular Systems on Distributed Memory Machines....Pages 570-579
The Design of a New Out-of-Core Multifrontal Solver....Pages 580-588
Cholesky Factorization of Band Matrices Using Multithreaded BLAS....Pages 589-597
A Master-Worker Type Eigensolver for Molecular Orbital Computations....Pages 598-607
Bioinformatics and Computational Biology: Minisymposium Abstract....Pages 608-616
Using Parallel Computing and Grid Systems for Genetic Mapping of Quantitative Traits....Pages 617-625
Partial Approximation of the Master Equation by the Fokker-Planck Equation....Pages 626-626
Design, Construction and Use of the FISH Server....Pages 627-636
Scientific Visualization and HPC Applications: Minisymposium Abstract....Pages 637-646
Interactive Volume Visualization of Fluid Flow Simulation Data....Pages 647-657
Software Tools for Parallel CFD Applications: Minisymposium Abstract....Pages 658-658
The Iterative Solver Template Library....Pages 659-664
Making Hybrid Tsunami Simulators in a Parallel Software Framework....Pages 665-665
HPC-MW: A Problem Solving Environment for Developing Parallel FEM Applications....Pages 666-675
SyFi - An Element Matrix Factory....Pages 676-685
Life: Overview of a Unified C++ Implementation of the Finite and Spectral Element Methods in 1D, 2D and 3D....Pages 686-693
Parallel Program Complex for 3D Unsteady Flow Simulation....Pages 694-702
Multi-scale Physics: Minisymposium Abstract....Pages 703-711
Simulation of Multiphysics Problems Using Adaptive Finite Elements....Pages 712-721
A New Domain Decomposition Approach Suited for Grid Computing....Pages 722-731
Parallelization of the Mesh Refinement Algorithm of the FDEM Program Package....Pages 732-732
Load Balancing for the Numerical Solution of the Navier-Stokes Equations....Pages 733-743
A Method of Adaptive Coarsening for Compressing Scientific Datasets....Pages 744-753
A Computational Framework for Topological Operations....Pages 754-763
Applications of Grid Computing in Genetics and Proteomics....Pages 764-773
Grid Enabling Your Data Resources with OGSA-DAI....Pages 774-780
UniGrids Streaming Framework: Enabling Streaming for the New Generation of Grids....Pages 781-790
Dynamic Clusters Available Under Clusterix Grid....Pages 791-798
Agent-Based Societies for the Sharing, Brokerage and Allocation of Grid Resources....Pages 799-808
OpusIB – Grid Enabled Opteron Cluster with InfiniBand Interconnect....Pages 809-818
Extending the HPC-ICTM Geographical Categorization Model for Grid Computing....Pages 819-829
Distributed SILC: An Easy-to-Use Interface for MPI-Based Parallel Matrix Computation Libraries....Pages 830-839
A Study of Real World I/O Performance in Parallel Scientific Computing....Pages 840-849
Epitaxial Surface Growth with Local Interaction, Parallel and Non-parallel Simulations....Pages 850-859
Data Dependence Analysis for the Parallelization of Numerical Tree Codes....Pages 860-870
Efficient Assembly of Sparse Matrices Using Hashing....Pages 871-881
A Web-Site-Based Partitioning Technique for Reducing Preprocessing Overhead of Parallel PageRank Computation....Pages 882-889
Is Cache-Oblivious DGEMM Viable?....Pages 890-899
Partitioning and Blocking Issues for a Parallel Incomplete Factorization....Pages 900-907
Automatic Performance Tuning for the Multi-section with Multiple Eigenvalues Method for Symmetric Tridiagonal Eigenproblems....Pages 908-918
Optimizing a Parallel Self-verified Method for Solving Linear Systems....Pages 919-928
A Parallel Block Iterative Method for Interactive Contacting Rigid Multibody Simulations on Multicore PCs....Pages 929-937
A High Performance Generic Scientific Simulation Environment....Pages 938-948
NestStepModelica – Mathematical Modeling and Bulk-Synchronous Parallel Simulation....Pages 949-955
Flecs, a Flexible Coupling Shell Application to Fluid-Structure Interaction ....Pages 956-965
New Scalability Frontiers in Ab Initio Electronic Structure Calculations Using the BG/L Supercomputer....Pages 966-975
A PAPI Implementation for BlueGene....Pages 976-985
Numerical Simulation of 3D Acoustic Logging....Pages 986-995
An Improved Interval Global Optimization Method and Its Application to Price Management Problem....Pages 996-1005
Optimizing Neural Network Classifiers with ROOT on a Rocks Linux Cluster....Pages 1006-1015
A Model of Small-Scale Turbulence for Use in the PPM Gas Dynamics Scheme....Pages 1016-1025
Mapping in Heterogeneous Systems with Heuristic Methods....Pages 1026-1035
The parXXL Environment: Scalable Fine Grained Development for Large Coarse Grained Platforms....Pages 1036-1044
Performance Analysis of Two Parallel Game-Tree Search Applications....Pages 1045-1054
Implementation of a Black-Box Global Optimization Algorithm with a Parallel Branch and Bound Template....Pages 1055-1064
Parallelization Techniques for Tabu Search....Pages 1065-1073
A Middleware for Job Distribution in Peer-to-Peer Networks....Pages 1074-1083
Mobile Agents Self-optimization with MAWeS....Pages 1084-1093
Performance Impact of Resource Conflicts on Chip Multi-processor Servers....Pages 1094-1104
An Implementation of Parallel 1-D FFT Using SSE3 Instructions on Dual-Core Processors....Pages 1105-1114
Back Matter....Pages 1115-1125
....Pages 1126-1135