8. PARA 2006: Umeå, Sweden
Bo Kågström, Erik Elmroth, Jack Dongarra, Jerzy Wasniewski (Eds.): Applied Parallel Computing. State of the Art in Scientific Computing, 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers. Springer 2007 Lecture Notes in Computer Science ISBN 978-3-540-75754-2
Keynote Papers
- Alfredo Buttari, Jack Dongarra, Jakub Kurzak, Julien Langou, Piotr Luszczek, Stanimire Tomov: The Impact of Multicore on Math Software. 1-10
- James Demmel, Jack Dongarra, Beresford N. Parlett, William Kahan, Ming Gu, David Bindel, Yozo Hida, Xiaoye S. Li, Osni Marques, E. Jason Riedy, Christof Vömel, Julien Langou, Piotr Luszczek, Jakub Kurzak, Alfredo Buttari, Julie Langou, Stanimire Tomov: Prospectus for the Next LAPACK and ScaLAPACK Libraries. 11-23
- Hans Petter Langtangen: A Case Study in High-Performance Mixed-Language Programming. 36-49
Minisymposia Papers
Stretching Time and Length Scales in Biomolecular Modelling
- Aatto Laaksonen: Stretching Time and Length Scales in Biomolecular Modelling: Minisymposium Abstract. 50
- K. Gillis, J. Vatamanu, M. S. Gulam Razul, Peter G. Kusalik: Averaged Configurations from Molecular Dynamics Simulations. 51-58
- Christophe Labbez, Bo Jönsson: A New Monte Carlo Method for the Titration of Molecules and Minerals. 66-72
- Mikael Lund: Coarse Graining Biomolecular Systems. 73-81
- Mikael Peräkylä: Molecular Dynamics Simulation Studies on the Modulation of Vitamin D Receptor Activity by Agonists and Antagonists. 82-89
- Emanuel H. Rubensson, Elias Rudberg, Pawel Salek: Sparse Matrix Algebra for Quantum Modeling of Large Systems. 90-99
- Yaoquan Tu, Lennart Nilsson, Aatto Laaksonen: A Highly Efficient Ab Initio Tight-Binding-Like Approximate Density-Functional Quantum Mechanical Method. 100-108
- David van der Spoel, Alexandra Patriksson, M. Marvin Seibert: Protein Folding Properties from Molecular Dynamics Simulations. 109-115
Recent Advances in Dense Linear Algebra
- Daniel Kressner, Julien Langou: Recent Advances in Dense Linear Algebra: Minisymposium Abstract. 116
- Björn Adlerborn, Bo Kågström, Daniel Kressner: Parallel Variants of the Multishift QZ Algorithm with Advanced Deflation Techniques. 117-126
- Robert Granat, Bo Kågström: Parallel Algorithms and Condition Estimators for Standard and Generalized Triangular Sylvester-Type Matrix Equations. 127-136
- Sven Hammarling, Nicholas J. Higham, Craig Lucas: LAPACK-Style Codes for Pivoted Cholesky and QR Updating. 137-146
- Jakub Kurzak, Jack Dongarra: Implementing Linear Algebra Routines on Multi-core Processors with Pipelining and a Look Ahead. 147-156
- Mercedes Marqués, Enrique S. Quintana-Ortí, Gregorio Quintana-Ortí: Specialized Spectral Division Algorithms for Generalized Eigenproblems Via the Inverse-Free Iteration. 157-166
CFD Applications for High Performance Computing
- Sinisa Krajnovic: CFD Applications for High Performance Computing: Minisymposium Abstract. 167
- Håkan Nilsson: Some Experiences on the Accuracy and Parallel Performance of OpenFOAM for CFD in Water Turbines. 168-176
HPC Environments: Visualization and Parallelization Tools
- Anne C. Elster, Otto J. Anshus: HPC Environments - Visualization and Parallelization Tools: Minisymposium Abstract. 177
- John Markus Bjørndalen, Otto J. Anshus: Trusting Floating Point Benchmarks - Are Your Benchmarks Really Data Independent? 178-188
- Espen Skjelnes Johnsen, John Markus Bjørndalen, Otto J. Anshus: CoMPI- Configuration of Collective Operations in LAM/MPI Using the Scheme Programming Language. 189-197
- Jan Christian Meyer, Anne C. Elster: A Load Balancing Strategy for Computations on Large, Read-Only Data Sets. 198-207
- Thorvald Natvig, Anne C. Elster: Automatic and Transparent Optimizations of an Application's MPI Communication. 208-217
- Ingar Saltvik, Anne C. Elster, Henrik R. Nagel: Parallel Methods for Real-Time Visualization of Snow. 218-227
- Daniel Stødle, John Markus Bjørndalen, Otto J. Anshus: Support for Collaboration, Visualization and Monitoring of Parallel Applications Using Shared Windows. 228-238
Tools, Frameworks and Applications for High Performance Computing
- Osni Marques: Tools, Frameworks and Applications for High Performance Computing: Minisymposium Abstract. 239
- Peter Arbenz, G. Harry van Lenthe, Uche Mennel, Ralph Müller, Marzio Sala: Multi-level mu -Finite Element Analysis for Human Bone Structures. 240-250
- L. Anthony Drummond, Vicente Galiano Ibarra, Violeta Migallón, José Penadés: High-Level User Interfaces for the DOE ACTS Collection. 251-259
- John R. Gilbert, Steve Reinhardt, Viral Shah: High-Performance Graph Algorithms from Parallel Sparse Matrices. 260-269
- Lutz Gross, Ben Cumming, Ken Steube, Dion Weatherley: A Python Module for PDE-Based Numerical Modelling. 270-279
- Zsolt I. Lázár, Lehel István Kovács, Zoltán Máthé: COMODI: Architecture for a Component-Based Scientific Computing System. 280-288
- Sameer Shende, Allen D. Malony, Alan Morris: Workload Characterization Using the TAU Performance System. 289-296
Grid Data Management
- Siegfried Benkner, Gerhard Engelbrecht, Stuart E. Middleton, Mike Surridge: Supporting SLA Negotiation for QoS-Enabled Simulation Services in a Medical Grid Environment. 298-308
- Brian A. Coghlan, Geoff Quigley, Soha Maad, Gabriele Pierantoni, John Ryan, Eamonn Kenny, David O'Callaghan: A Transparent Grid Filesystem. 309-318
Simulations in Geophysics and Space Physics
- Mats Holmström, Kjell Rönnmark: Simulations in Geophysics and Space Physics: Minisymposium Abstract. 329
- Francisco Almeida, Carlos Delgado, Ramón J. García López, Francisco de Sande: Parallelization of a Public Image Restoration Algorithm. 330-339
- Werner Benger, Shalini Venkataraman, Amanda Long, Gabrielle Allen, Stephen David Beck, Maciej Brodowicz, Jon MacLaren, Edward Seidel: Visualizing Katrina - Merging Computer Simulations with Observations. 340-350
- Pablo López, Antonio J. Dorta, Evencio Mediavilla, Francisco de Sande: Generation of Microlensing Magnification Patterns with High Performance Computing Techniques. 351-360
- Madelene Jeanette Parviainen, Mark Eric Dieckmann, Padma Kant Shukla: Phase Space Modulations in Magnetised Plasmas by a Mildly Relativistic Two-Stream Instability. 361-370
Tools for Parallel Performance Analysis
- Felix Wolf: Tools for Parallel Performance Analysis: Minisymposium Abstract. 380
- Genaro Costa, Anna Morajko, Tomàs Margalef, Emilio Luque: Automatic Tuning in Computational Grids. 381-389
- Karl Fürlinger, Michael Gerndt: Automated Performance Analysis Using ASL Performance Properties. 390-397
- Markus Geimer, Felix Wolf, Andreas Knüpfer, Bernd Mohr, Brian J. N. Wylie: A Parallel Trace-Data Interface for Scalable Performance Analysis. 398-408
- Josep Jorba, Tomàs Margalef, Emilio Luque: Search of Performance Inefficiencies in Message Passing Applications with KappaPI 2 Tool. 409-419
- Edmond Kereku, Michael Gerndt: Automatic Monitoring of Memory Hierarchies in Threaded Applications with AMEBA. 420-429
- Andreas Knüpfer, Bernhard Voigt, Wolfgang E. Nagel, Hartmut Mix: Visualization of Repetitive Patterns in Event Traces. 430-439
- Sameer Shende, Allen D. Malony, Alan Morris: Optimization of Instrumentation in Parallel Performance Evaluation Tools. 440-449
- Hung-Hsun Su, Dan Bonachea, Adam Leko, Hans Sherburne, Max Billingsley, Alan D. George: GASP! A Standardized Performance Analysis Tool Interface for Global Address Space Programming Models. 450-459
- Brian J. N. Wylie, Felix Wolf, Bernd Mohr, Markus Geimer: Integrated Runtime Measurement Summarisation and Selective Event Tracing for Scalable Parallel Execution Performance Diagnosis. 460-469
Grids for Scientific Computing
- Oxana Smirnova: Grids for Scientific Computing: Minisymposium Abstract. 470
- Paula Eerola, Tord Ekelöf, Mattias Ellert, Michael Grønager, John Renner Hansen, Sigve Haug, Josva Kleist, Aleksandr Konstantinov, Balázs Kónya, Farid Ould-Saada, Oxana Smirnova, Ferenc Szalai, Anders Wäänänen: Roadmap for the ARC Grid Middleware. 471-479
- Sigve Haug, Farid Ould-Saada, Katarina Pajchel, Alexander L. Read: Data Management for the World's Largest Machine. 480-488
- Roman Wyrzykowski, Norbert Meyer, Tomasz Olas, Lukasz Kuczynski, Bogdan Ludwiczak, Cezary Czaplewski, Stanislaw Oldziej: Meta-computations on the CLUSTERIX Grid. 489-500
Simulations of Materials
- Lars Nordström: Simulations of Materials: Minisymposium Abstract. 501
- Pooja M. Panchmatia, Biplab Sanyal, Peter M. Oppeneer: Ab Initio Calculations of the Electronic Structure and Magnetism of Iron Porphyrin-Type Molecules: A Benchmarking Study. 502-509
- Levente Vitos, Börje Johansson: Mechanical Properties of Random Alloys from Quantum Mechanical Simulations. 510-519
Novel Data Formats and Algorithms for Dense Linear Algebra Computations
- Fred G. Gustavson, Jerzy Wasniewski: Novel Data Formats and Algorithms for Dense Linear Algebra Computations: Minisymposium Abstract. 520
- Robert Granat, Isak Jonsson, Bo Kågström: Recursive Blocked Algorithms for Solving Periodic Triangular Sylvester-Type Matrix Equations. 531-539
- Fred G. Gustavson, John A. Gunnels, James C. Sexton: Minimal Data Copy for Dense Linear Algebra Factorization. 540-549
- Fred G. Gustavson, Lars Karlsson, Bo Kågström: Three Algorithms for Cholesky Factorization on Distributed Memory Using Packed Storage. 550-559
- Fred G. Gustavson, Jerzy Wasniewski: Rectangular Full Packed Format for LAPACK Algorithms Timings on Several Computers. 570-579
- José R. Herrero, Juan J. Navarro: Using Non-canonical Array Layouts in Dense Matrix Operations. 580-588
- Przemyslaw Stpiczynski: New Data Distribution for Solving Triangular Systems on Distributed Memory Machines. 589-597
- Alfredo Remón, Enrique S. Quintana-Ortí, Gregorio Quintana-Ortí: Cholesky Factorization of Band Matrices Using Multithreaded BLAS. 608-616
- Tetsuya Sakurai, Yoshihisa Kodaki, Hiroto Tadano, Hiroaki Umeda, Yuichi Inadomi, Toshio Watanabe, Umpei Nagashima: A Master-Worker Type Eigensolver for Molecular Orbital Computations. 617-625
Bioinformatics and Computational Biology
- Ann-Charlotte Berglund Sonnhammer, Sverker Holmgren: Bioinformatics and Computational Biology: Minisymposium Abstract. 626
- Mahen Jayawardena, Kajsa Ljungberg, Sverker Holmgren: Using Parallel Computing and Grid Systems for Genetic Mapping of Quantitative Traits. 627-636
- Paul Sjöberg: Partial Approximation of the Master Equation by the Fokker-Planck Equation. 637-646
- Jeanette Tångrot, Lixiao Wang, Bo Kågström, Uwe H. Sauer: Design, Construction and Use of the FISH Server. 647-657
Scientific Visualization and HPC Applications
- Matthew D. Cooper, Anders Ynnerman: Scientific Visualization and HPC Applications: Minisymposium Abstract. 658
- Paul R. Woodward, David H. Porter, James B. S. G. Greensky, Alex J. Larson, Michael R. Knox, James Hanson, Niranjay Ravindran, Tyler Fuchs: Interactive Volume Visualization of Fluid Flow Simulation Data. 659-664
Software Tools for Parallel CFD Applications
- Xing Cai, Hans Petter Langtangen: Software Tools for Parallel CFD Applications: Minisymposium Abstract. 665
- Aldo Bonfiglioli, Bruno Carpentieri, Masha Sosonkina: EulFS : A Parallel CFD Code for the Simulation of Euler and Navier-Stokes Problems on Unstructured Grids. 676-685
- Xing Cai, Hans Petter Langtangen: Making Hybrid Tsunami Simulators in a Parallel Software Framework. 686-693
- Satoshi Ito, Hiroshi Okuda: HPC-MW: A Problem Solving Environment for Developing Parallel FEM Applications. 694-702
- Kent-André Mardal: SyFi - An Element Matrix Factory. 703-711
- Christophe Prud'homme: Life: Overview of a Unified C++ Implementation of the Finite and Spectral Element Methods in 1D, 2D and 3D. 712-721
- Eugene V. Shilnikov: Parallel Program Complex for 3D Unsteady Flow Simulation. 722-731
Multi-scale Physics
- Mats G. Larson: Multi-scale Physics: Minisymposium Abstract. 732
- Fredrik Bengzon, August Johansson, Mats G. Larson, Robert Söderlund: Simulation of Multiphysics Problems Using Adaptive Finite Elements. 733-743
Contributed Papers
Partial Differential Equations
- Juan A. Acebrón, Raúl Durán, Rafael Rico, Renato Spigler: A New Domain Decomposition Approach Suited for Grid Computing. 744-753
- Torsten Adolph, Willi Schönauer: Parallelization of the Mesh Refinement Algorithm of the FDEM Program Package. 754-763
- Gregory Karagiorgos, Petros Katsafados, Andreas Kontarinis, Nikolaos M. Missirlis, Filippos Tzaferis: Load Balancing for the Numerical Solution of the Navier-Stokes Equations. 764-773
- Tallat M. Shafaat, Scott B. Baden: A Method of Adaptive Coarsening for Compressing Scientific Datasets. 774-780
- Michael Spevak, René Heinzl, Philipp Schwaha, Siegfried Selberherr: A Computational Framework for Topological Operations. 781-790
Grid Computing
- Jorge Andrade, Malin C. Andersen, Lisa Berglund, Jacob Odeberg: Applications of Grid Computing in Genetics and Proteomics. 791-798
- Mario Antonioletti, Malcolm P. Atkinson, Neil P. Chue Hong, Bartosz Dobrzelecki, Alastair C. Hume, Mike Jackson, Konstantinos Karasavvas, Amy Krause, Jennifer M. Schopf, Tom Sugden, Elias Theocharopoulos: Grid Enabling Your Data Resources with OGSA-DAI. 799-808
- Krzysztof Benedyczak, Aleksander Nowinski, Krzysztof Nowinski, Piotr Bala: UniGrids Streaming Framework: Enabling Streaming for the New Generation of Grids. 809-818
- Jan Kwiatkowski, Marcin Pawlik, Gerard Frankowski, Kazimierz Balos, Roman Wyrzykowski, Konrad Karczewski: Dynamic Clusters Available Under Clusterix Grid. 819-829
- Gabriele Pierantoni, Brian A. Coghlan, Eamonn Kenny: Agent-Based Societies for the Sharing, Brokerage and Allocation of Grid Resources. 830-839
- Olaf Schneider, Frank Schmitz, Ivan Kondov, Thomas Brandel: OpusIB - Grid Enabled Opteron Cluster with InfiniBand Interconnect. 840-849
- Rafael K. S. Silva, Marilton S. de Aguiar, César A. F. De Rose, Graçaliz Pereira Dimuro: Extending the HPC-ICTM Geographical Categorization Model for Grid Computing. 850-859
Parallel Scientific Computing Algorithms
- Tamito Kajiyama, Akira Nukada, Reiji Suda, Hidehiko Hasegawa, Akira Nishida: Distributed SILC: An Easy-to-Use Interface for MPI-Based Parallel Matrix Computation Libraries. 860-870
- Dries Kimpe, Andrea Lani, Tiago Quintino, Stefan Vandewalle, Stefaan Poedts, Herman Deconinck: A Study of Real World I/O Performance in Parallel Scientific Computing. 871-881
- Carmen B. Navarrete, Susana Holgado, Eloy Anguiano: Epitaxial Surface Growth with Local Interaction, Parallel and Non-parallel Simulations. 882-889
- Gerhard W. Zumbusch: Data Dependence Analysis for the Parallelization of Numerical Tree Codes. 890-899
Linear Algebra
- Mats Aspnäs, Artur Signell, Jan Westerholm: Efficient Assembly of Sparse Matrices Using Hashing. 900-907
- Ali Cevahir, Cevdet Aykanat, Ata Turk, Berkant Barla Cambazoglu: A Web-Site-Based Partitioning Technique for Reducing Preprocessing Overhead of Parallel PageRank Computation. 908-918
- John A. Gunnels, Fred G. Gustavson, Keshav Pingali, Kamen Yotov: Is Cache-Oblivious DGEMM Viable? 919-928
- Pascal Hénon, Pierre Ramet, Jean Roman: Partitioning and Blocking Issues for a Parallel Incomplete Factorization. 929-937
- Takahiro Katagiri, Christof Vömel, James Demmel: Automatic Performance Tuning for the Multi-section with Multiple Eigenvalues Method for Symmetric Tridiagonal Eigenproblems. 938-948
- Mariana Luderitz Kolberg, Lucas Baldo, Pedro Velho, Luiz Gustavo Fernandes, Dalcidio Moraes Claudio: Optimizing a Parallel Self-verified Method for Solving Linear Systems. 949-955
- Claude Lacoursière: A Parallel Block Iterative Method for Interactive Contacting Rigid Multibody Simulations on Multicore PCs. 956-965
- Marzio Sala, William F. Spotz, Michael A. Heroux: PyTrilinos: High-Performance Distributed-Memory Solvers for Python. 966-975
- Marzio Sala, Kendall S. Stanley, Michael A. Heroux: Amesos: A Set of General Interfaces to Sparse Direct Solver Libraries. 976-985
- Teruo Tanaka, Takahiro Katagiri, Toshitsugu Yuba: d-Spline Based Incremental Parameter Estimation in Automatic Performance Tuning. 986-995
Simulation Environments
- René Heinzl, Michael Spevak, Philipp Schwaha, Siegfried Selberherr: A High Performance Generic Scientific Simulation Environment. 996-1005
- Christoph W. Kessler, Peter Fritzson, Mattias V. Eriksson: NestStepModelica - Mathematical Modeling and Bulk-Synchronous Parallel Simulation. 1006-1015
- Margreet Nool, Erik Jan Lingen, Aukje de Boer, Hester Bijl: Flecs, a Flexible Coupling Shell Application to Fluid-Structure Interaction. 1016-1025
Algorithms and Applications for Blue Gene/L
- Constantine Bekas, Alessandro Curioni, Wanda Andreoni: New Scalability Frontiers in Ab Initio Electronic Structure Calculations Using the BG/L Supercomputer. 1026-1035
- Nils Smeds: A PAPI Implementation for BlueGene. 1036-1044
Scientific Computing Applications
- Victor I. Kostin, Dmitry V. Pissarenko, Galina V. Reshetova, Vladimir A. Tcheverda: Numerical Simulation of 3D Acoustic Logging. 1045-1054
- Bartlomiej Jacek Kubica, Ewa Niewiadomska-Szynkiewicz: An Improved Interval Global Optimization Method and Its Application to Price Management Problem. 1055-1064
- Tomas Lindén, Francisco García, Aatos Heikkinen, Sami Lehti: Optimizing Neural Network Classifiers with ROOT on a Rocks Linux Cluster. 1065-1073
- Paul R. Woodward, David H. Porter: A Model of Small-Scale Turbulence for Use in the PPM Gas Dynamics Scheme. 1074-1083
Scientific Computing Tools
- Juan-Pedro Martínez-Gallar, Francisco Almeida, Domingo Giménez: Mapping in Heterogeneous Systems with Heuristic Methods. 1084-1093
- Jens Gustedt, Stéphane Vialle, Amelia De Vivo: The parXXL Environment: Scalable Fine Grained Development for Large Coarse Grained Platforms. 1094-1104
Parallel Search Algorithms
- Yurong Chen, Ying Tan, Yimin Zhang, Carole Dulong: Performance Analysis of Two Parallel Game-Tree Search Applications. 1105-1114
- Raimondas Ciegis, Milda Baravykaite: Implementation of a Black-Box Global Optimization Algorithm with a Parallel Branch and Bound Template. 1115-1125
- Jacek Dabrowski: Parallelization Techniques for Tabu Search. 1126-1135
Peer-to-Peer Computing
- Euloge Edi, M. Tahar Kechadi, Ronan McNulty: TreeP: A Self-reconfigurable Topology for Unstructured P2P Systems. 1136-1146
- Thomas Fischer, Stephan Fudeus, Peter Merz: A Middleware for Job Distribution in Peer-to-Peer Networks. 1147-1157
Mobility and Security
- Emilio Pasquale Mancini, Massimiliano Rak, Salvatore Venticinque, Umberto Villano: Mobile Agents Self-optimization with MAWeS. 1158-1167
Algorithms for Single-Chip Multiprocessors
- Myungho Lee, Yeonseung Ryu, Sugwon Hong, Chungki Lee: Performance Impact of Resource Conflicts on Chip Multi-processor Servers. 1168-1177
- Daisuke Takahashi: An Implementation of Parallel 1-D FFT Using SSE3 Instructions on Dual-Core Processors. 1178-1187
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