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

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
HPC Environments – Visualization and Parallelization Tools: Minisymposium Abstract....Pages 177-177
Trusting Floating Point Benchmarks – Are Your Benchmarks Really Data Independent?....Pages 178-188
 CoMPI – Configuration of Collective Operations in LAM/MPI Using the Scheme Programming Language....Pages 189-197
A Load Balancing Strategy for Computations on Large, Read-Only Data Sets....Pages 198-207
Automatic and Transparent Optimizations of an Application’s MPI Communication....Pages 208-217
Parallel Methods for Real-Time Visualization of Snow....Pages 218-227
Support for Collaboration, Visualization and Monitoring of Parallel Applications Using Shared Windows....Pages 228-238
Tools, Frameworks and Applications for High Performance Computing: Minisymposium Abstract....Pages 239-239
Multi-level μ -Finite Element Analysis for Human Bone Structures....Pages 240-250
High-Level User Interfaces for the DOE ACTS Collection....Pages 251-259
High-Performance Graph Algorithms from Parallel Sparse Matrices....Pages 260-269
A Python Module for PDE-Based Numerical Modelling....Pages 270-279
COMODI: Architecture for a Component-Based Scientific Computing System....Pages 280-288
Workload Characterization Using the TAU Performance System....Pages 289-296
Grid Data Management: Minisymposium Abstract....Pages 297-297
Supporting SLA Negotiation for QoS-Enabled Simulation Services in a Medical Grid Environment....Pages 298-308
A Transparent Grid Filesystem....Pages 309-318
Grid Data Integration Based on Schema Mapping....Pages 319-328
Simulations in Geophysics and Space Physics: Minisymposium Abstract....Pages 329-329
Some Experiences on the Accuracy and Parallel Performance of OpenFOAM for CFD in Water Turbines....Pages 168-176
Parallelization of a Public Image Restoration Algorithm....Pages 330-339
Visualizing Katrina - Merging Computer Simulations with Observations....Pages 340-350
Generation of Microlensing Magnification Patterns with High Performance Computing Techniques....Pages 351-360
Phase Space Modulations in Magnetised Plasmas by a Mildly Relativistic Two-Stream Instability....Pages 361-370
Implementing a Particle-Fluid Model of Auroral Electrons....Pages 371-379
Tools for Parallel Performance Analysis: Minisymposium Abstract....Pages 380-380
Automatic Tuning in Computational Grids....Pages 381-389
Automated Performance Analysis Using ASL Performance Properties....Pages 390-397
A Parallel Trace-Data Interface for Scalable Performance Analysis....Pages 398-408
Search of Performance Inefficiencies in Message Passing Applications with KappaPI 2 Tool....Pages 409-419
Automatic Monitoring of Memory Hierarchies in Threaded Applications with AMEBA....Pages 420-429
Visualization of Repetitive Patterns in Event Traces....Pages 430-439
Optimization of Instrumentation in Parallel Performance Evaluation Tools....Pages 440-449
GASP! A Standardized Performance Analysis Tool Interface for Global Address Space Programming Models....Pages 450-459
Integrated Runtime Measurement Summarisation and Selective Event Tracing for Scalable Parallel Execution Performance Diagnosis....Pages 460-469
Grids for Scientific Computing: Minisymposium Abstract....Pages 470-470
Roadmap for the ARC Grid Middleware....Pages 471-479
Data Management for the World’s Largest Machine....Pages 480-488
Meta-computations on the CLUSTERIX Grid....Pages 489-500
Simulations of Materials: Minisymposium Abstract....Pages 501-501
 Ab Initio Calculations of the Electronic Structure and Magnetism of Iron Porphyrin-Type Molecules: A Benchmarking Study....Pages 502-509
Mechanical Properties of Random Alloys from Quantum Mechanical Simulations....Pages 510-519
Novel Data Formats and Algorithms for Dense Linear Algebra Computations: Minisymposium Abstract....Pages 520-520
Cache Oblivious Matrix Operations Using Peano Curves....Pages 521-530
Recursive Blocked Algorithms for Solving Periodic Triangular Sylvester-Type Matrix Equations....Pages 531-539
Minimal Data Copy for Dense Linear Algebra Factorization....Pages 540-549
Three Algorithms for Cholesky Factorization on Distributed Memory Using Packed Storage....Pages 550-559
In-Place Transposition of Rectangular Matrices....Pages 560-569
Rectangular Full Packed Format for LAPACK Algorithms Timings on Several Computers....Pages 570-579
Using Non-canonical Array Layouts in Dense Matrix Operations....Pages 580-588
New Data Distribution for Solving Triangular Systems on Distributed Memory Machines....Pages 589-597
The Design of a New Out-of-Core Multifrontal Solver....Pages 598-607
Cholesky Factorization of Band Matrices Using Multithreaded BLAS....Pages 608-616
A Master-Worker Type Eigensolver for Molecular Orbital Computations....Pages 617-625
Bioinformatics and Computational Biology: Minisymposium Abstract....Pages 626-626
Using Parallel Computing and Grid Systems for Genetic Mapping of Quantitative Traits....Pages 627-636
Partial Approximation of the Master Equation by the Fokker-Planck Equation....Pages 637-646
Design, Construction and Use of the FISH Server....Pages 647-657
Scientific Visualization and HPC Applications: Minisymposium Abstract....Pages 658-658
Interactive Volume Visualization of Fluid Flow Simulation Data....Pages 659-664
Software Tools for Parallel CFD Applications: Minisymposium Abstract....Pages 665-665
The Iterative Solver Template Library....Pages 666-675
 EulFS : A Parallel CFD Code for the Simulation of Euler and Navier-Stokes Problems on Unstructured Grids....Pages 676-685
Making Hybrid Tsunami Simulators in a Parallel Software Framework....Pages 686-693
HPC-MW: A Problem Solving Environment for Developing Parallel FEM Applications....Pages 694-702
SyFi - An Element Matrix Factory....Pages 703-711
Life: Overview of a Unified C++ Implementation of the Finite and Spectral Element Methods in 1D, 2D and 3D....Pages 712-721
Parallel Program Complex for 3D Unsteady Flow Simulation....Pages 722-731
Multi-scale Physics: Minisymposium Abstract....Pages 732-732
Simulation of Multiphysics Problems Using Adaptive Finite Elements....Pages 733-743
A New Domain Decomposition Approach Suited for Grid Computing....Pages 744-753
Parallelization of the Mesh Refinement Algorithm of the FDEM Program Package....Pages 754-763
Load Balancing for the Numerical Solution of the Navier-Stokes Equations....Pages 764-773
A Method of Adaptive Coarsening for Compressing Scientific Datasets....Pages 774-780
A Computational Framework for Topological Operations....Pages 781-790
Applications of Grid Computing in Genetics and Proteomics....Pages 791-798
Grid Enabling Your Data Resources with OGSA-DAI....Pages 799-808
UniGrids Streaming Framework: Enabling Streaming for the New Generation of Grids....Pages 809-818
Dynamic Clusters Available Under Clusterix Grid....Pages 819-829
Agent-Based Societies for the Sharing, Brokerage and Allocation of Grid Resources....Pages 830-839
Efficient Assembly of Sparse Matrices Using Hashing....Pages 900-907
A Web-Site-Based Partitioning Technique for Reducing Preprocessing Overhead of Parallel PageRank Computation....Pages 908-918
Is Cache-Oblivious DGEMM Viable?....Pages 919-928
Partitioning and Blocking Issues for a Parallel Incomplete Factorization....Pages 929-937
Automatic Performance Tuning for the Multi-section with Multiple Eigenvalues Method for Symmetric Tridiagonal Eigenproblems....Pages 938-948
Optimizing a Parallel Self-verified Method for Solving Linear Systems....Pages 949-955
A Parallel Block Iterative Method for Interactive Contacting Rigid Multibody Simulations on Multicore PCs....Pages 956-965
 PyTrilinos : High-Performance Distributed-Memory Solvers for Python....Pages 966-975
 Amesos : A Set of General Interfaces to Sparse Direct Solver Libraries....Pages 976-985
 d-Spline Based Incremental Parameter Estimation in Automatic Performance Tuning....Pages 986-995
New Scalability Frontiers in Ab Initio Electronic Structure Calculations Using the BG/L Supercomputer....Pages 1026-1035
Opus IB – Grid Enabled Opteron Cluster with InfiniBand Interconnect....Pages 840-849
Extending the HPC-ICTM Geographical Categorization Model for Grid Computing....Pages 850-859
A High Performance Generic Scientific Simulation Environment....Pages 996-1005
NestStepModelica – Mathematical Modeling and Bulk-Synchronous Parallel Simulation....Pages 1006-1015
Flecs, a Flexible Coupling Shell Application to Fluid-Structure Interaction....Pages 1016-1025
Distributed SILC: An Easy-to-Use Interface for MPI-Based Parallel Matrix Computation Libraries....Pages 860-870
A Study of Real World I/O Performance in Parallel Scientific Computing....Pages 871-881
Epitaxial Surface Growth with Local Interaction, Parallel and Non-parallel Simulations....Pages 882-889
Data Dependence Analysis for the Parallelization of Numerical Tree Codes....Pages 890-899
Mapping in Heterogeneous Systems with Heuristic Methods....Pages 1084-1093
The parXXL Environment: Scalable Fine Grained Development for Large Coarse Grained Platforms....Pages 1094-1104
Numerical Simulation of 3D Acoustic Logging....Pages 1045-1054
An Improved Interval Global Optimization Method and Its Application to Price Management Problem....Pages 1055-1064
Optimizing Neural Network Classifiers with ROOT on a Rocks Linux Cluster....Pages 1065-1073
A Model of Small-Scale Turbulence for Use in the PPM Gas Dynamics Scheme....Pages 1074-1083
Mobile Agents Self-optimization with MAWeS....Pages 1158-1167
Performance Analysis of Two Parallel Game-Tree Search Applications....Pages 1105-1114
Implementation of a Black-Box Global Optimization Algorithm with a Parallel Branch and Bound Template....Pages 1115-1125
Parallelization Techniques for Tabu Search....Pages 1126-1135
A PAPI Implementation for BlueGene....Pages 1036-1044
 TreeP : A Self-reconfigurable Topology for Unstructured P2P Systems....Pages 1136-1146
A Middleware for Job Distribution in Peer-to-Peer Networks....Pages 1147-1157
Performance Impact of Resource Conflicts on Chip Multi-processor Servers....Pages 1168-1177
An Implementation of Parallel 1-D FFT Using SSE3 Instructions on Dual-Core Processors....Pages 1178-1187
Back Matter....Pages -