Table of Contents

• The Impact of Multicore on Math SoftwareAlfredo Buttari, Jack Dongarra, Jakub Kurzak, Julien Langou, Piotr Luszczek, Stanimire Tomov. 1-10 [doi]
• Prospectus for the Next LAPACK and ScaLAPACK LibrariesJames 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. 11-23 [doi]
• Large-Scale Methods in Image DeblurringPer Christian Hansen, Toke Koldborg Jensen. 24-35 [doi]
• A Case Study in High-Performance Mixed-Language ProgrammingHans Petter Langtangen. 36-49 [doi]
• Stretching Time and Length Scales in Biomolecular Modelling: Minisymposium AbstractAatto Laaksonen. 50 [doi]
• Averaged Configurations from Molecular Dynamics SimulationsK. Gillis, J. Vatamanu, M. S. Gulam Razul, Peter G. Kusalik. 51-58 [doi]
• Atomistic Simulation Studies of Polymers and WaterErik Johansson, Peter Ahlström. 59-65 [doi]
• A New Monte Carlo Method for the Titration of Molecules and MineralsChristophe Labbez, Bo Jönsson. 66-72 [doi]
• Coarse Graining Biomolecular SystemsMikael Lund. 73-81 [doi]
• Molecular Dynamics Simulation Studies on the Modulation of Vitamin D Receptor Activity by Agonists and AntagonistsMikael Peräkylä. 82-89 [doi]
• Sparse Matrix Algebra for Quantum Modeling of Large SystemsEmanuel H. Rubensson, Elias Rudberg, Pawel Salek. 90-99 [doi]
• A Highly Efficient ::::Ab Initio:::: Tight-Binding-Like Approximate Density-Functional Quantum Mechanical MethodYaoquan Tu, Lennart Nilsson, Aatto Laaksonen. 100-108 [doi]
• Protein Folding Properties from Molecular Dynamics SimulationsDavid van der Spoel, Alexandra Patriksson, M. Marvin Seibert. 109-115 [doi]
• Recent Advances in Dense Linear Algebra: Minisymposium AbstractDaniel Kressner, Julien Langou. 116 [doi]
• Parallel Variants of the Multishift QZ Algorithm with Advanced Deflation TechniquesBjörn Adlerborn, Bo Kågström, Daniel Kressner. 117-126 [doi]
• Parallel Algorithms and Condition Estimators for Standard and Generalized Triangular Sylvester-Type Matrix EquationsRobert Granat, Bo Kågström. 127-136 [doi]
• LAPACK-Style Codes for Pivoted Cholesky and ::::QR:::: UpdatingSven Hammarling, Nicholas J. Higham, Craig Lucas. 137-146 [doi]
• Implementing Linear Algebra Routines on Multi-core Processors with Pipelining and a Look AheadJakub Kurzak, Jack Dongarra. 147-156 [doi]
• Specialized Spectral Division Algorithms for Generalized Eigenproblems Via the Inverse-Free IterationMercedes Marqués, Enrique S. Quintana-Ortí, Gregorio Quintana-Ortí. 157-166 [doi]
• CFD Applications for High Performance Computing: Minisymposium AbstractSinisa Krajnovic. 167 [doi]
• Some Experiences on the Accuracy and Parallel Performance of OpenFOAM for CFD in Water TurbinesHåkan Nilsson. 168-176 [doi]
• HPC Environments - Visualization and Parallelization Tools: Minisymposium AbstractAnne C. Elster, Otto J. Anshus. 177 [doi]
• Trusting Floating Point Benchmarks - Are Your Benchmarks Really Data Independent?John Markus Bjørndalen, Otto J. Anshus. 178-188 [doi]
• CoMPI- Configuration of Collective Operations in LAM/MPI Using the Scheme Programming LanguageEspen Skjelnes Johnsen, John Markus Bjørndalen, Otto J. Anshus. 189-197 [doi]
• A Load Balancing Strategy for Computations on Large, Read-Only Data SetsJan Christian Meyer, Anne C. Elster. 198-207 [doi]
• Automatic and Transparent Optimizations of an Application s MPI CommunicationThorvald Natvig, Anne C. Elster. 208-217 [doi]
• Parallel Methods for Real-Time Visualization of SnowIngar Saltvik, Anne C. Elster, Henrik R. Nagel. 218-227 [doi]
• Support for Collaboration, Visualization and Monitoring of Parallel Applications Using Shared WindowsDaniel Stødle, John Markus Bjørndalen, Otto J. Anshus. 228-238 [doi]
• Tools, Frameworks and Applications for High Performance Computing: Minisymposium AbstractOsni Marques. 239 [doi]
• Multi-level ::::mu:::: -Finite Element Analysis for Human Bone StructuresPeter Arbenz, G. Harry van Lenthe, Uche Mennel, Ralph Müller, Marzio Sala. 240-250 [doi]
• High-Level User Interfaces for the DOE ACTS CollectionL. Anthony Drummond, Vicente Galiano Ibarra, Violeta Migallón, José Penadés. 251-259 [doi]
• High-Performance Graph Algorithms from Parallel Sparse MatricesJohn R. Gilbert, Steve Reinhardt, Viral Shah. 260-269 [doi]
• A Python Module for PDE-Based Numerical ModellingLutz Gross, Ben Cumming, Ken Steube, Dion Weatherley. 270-279 [doi]
• COMODI: Architecture for a Component-Based Scientific Computing SystemZsolt I. Lázár, Lehel István Kovács, Zoltán Máthé. 280-288 [doi]
• Workload Characterization Using the TAU Performance SystemSameer Shende, Allen D. Malony, Alan Morris. 289-296 [doi]
• Grid Data Management: Minisymposium AbstractSiegfried Benkner, Heinz Stockinger. 297 [doi]
• Supporting SLA Negotiation for QoS-Enabled Simulation Services in a Medical Grid EnvironmentSiegfried Benkner, Gerhard Engelbrecht, Stuart E. Middleton, Mike Surridge. 298-308 [doi]
• A Transparent Grid FilesystemBrian A. Coghlan, Geoff Quigley, Soha Maad, Gabriele Pierantoni, John Ryan, Eamonn Kenny, David O Callaghan. 309-318 [doi]
• Grid Data Integration Based on Schema MappingCarmela Comito, Domenico Talia. 319-328 [doi]
• Simulations in Geophysics and Space Physics: Minisymposium AbstractMats Holmström, Kjell Rönnmark. 329 [doi]
• Parallelization of a Public Image Restoration AlgorithmFrancisco Almeida, Carlos Delgado, Ramón J. García López, Francisco de Sande. 330-339 [doi]
• Visualizing Katrina - Merging Computer Simulations with ObservationsWerner Benger, Shalini Venkataraman, Amanda Long, Gabrielle Allen, Stephen David Beck, Maciej Brodowicz, Jon MacLaren, Edward Seidel. 340-350 [doi]
• Generation of Microlensing Magnification Patterns with High Performance Computing TechniquesPablo López, Antonio J. Dorta, Evencio Mediavilla, Francisco de Sande. 351-360 [doi]
• Phase Space Modulations in Magnetised Plasmas by a Mildly Relativistic Two-Stream InstabilityMadelene Jeanette Parviainen, Mark Eric Dieckmann, Padma Kant Shukla. 361-370 [doi]
• Implementing a Particle-Fluid Model of Auroral ElectronsJörgen Vedin, Kjell Rönnmark. 371-379 [doi]
• Tools for Parallel Performance Analysis: Minisymposium AbstractFelix Wolf. 380 [doi]
• Automatic Tuning in Computational GridsGenaro Costa, Anna Morajko, Tomàs Margalef, Emilio Luque. 381-389 [doi]
• Automated Performance Analysis Using ASL Performance PropertiesKarl Fürlinger, Michael Gerndt. 390-397 [doi]
• A Parallel Trace-Data Interface for Scalable Performance AnalysisMarkus Geimer, Felix Wolf, Andreas Knüpfer, Bernd Mohr, Brian J. N. Wylie. 398-408 [doi]
• Search of Performance Inefficiencies in Message Passing Applications with KappaPI 2 ToolJosep Jorba, Tomàs Margalef, Emilio Luque. 409-419 [doi]
• Automatic Monitoring of Memory Hierarchies in Threaded Applications with AMEBAEdmond Kereku, Michael Gerndt. 420-429 [doi]
• Visualization of Repetitive Patterns in Event TracesAndreas Knüpfer, Bernhard Voigt, Wolfgang E. Nagel, Hartmut Mix. 430-439 [doi]
• Optimization of Instrumentation in Parallel Performance Evaluation ToolsSameer Shende, Allen D. Malony, Alan Morris. 440-449 [doi]
• GASP! A Standardized Performance Analysis Tool Interface for Global Address Space Programming ModelsHung-Hsun Su, Dan Bonachea, Adam Leko, Hans Sherburne, Max Billingsley, Alan D. George. 450-459 [doi]
• Integrated Runtime Measurement Summarisation and Selective Event Tracing for Scalable Parallel Execution Performance DiagnosisBrian J. N. Wylie, Felix Wolf, Bernd Mohr, Markus Geimer. 460-469 [doi]
• Grids for Scientific Computing: Minisymposium AbstractOxana Smirnova. 470 [doi]
• Roadmap for the ARC Grid MiddlewarePaula 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. 471-479 [doi]
• Data Management for the World s Largest MachineSigve Haug, Farid Ould-Saada, Katarina Pajchel, Alexander L. Read. 480-488 [doi]
• Meta-computations on the CLUSTERIX GridRoman Wyrzykowski, Norbert Meyer, Tomasz Olas, Lukasz Kuczynski, Bogdan Ludwiczak, Cezary Czaplewski, Stanislaw Oldziej. 489-500 [doi]
• Simulations of Materials: Minisymposium AbstractLars Nordström. 501 [doi]
• ::::Ab Initio:::: Calculations of the Electronic Structure and Magnetism of Iron Porphyrin-Type Molecules: A Benchmarking StudyPooja M. Panchmatia, Biplab Sanyal, Peter M. Oppeneer. 502-509 [doi]
• Mechanical Properties of Random Alloys from Quantum Mechanical SimulationsLevente Vitos, Börje Johansson. 510-519 [doi]
• Novel Data Formats and Algorithms for Dense Linear Algebra Computations: Minisymposium AbstractFred G. Gustavson, Jerzy Wasniewski. 520 [doi]
• Cache Oblivious Matrix Operations Using Peano CurvesMichael Bader, Christian Mayer. 521-530 [doi]
• Recursive Blocked Algorithms for Solving Periodic Triangular Sylvester-Type Matrix EquationsRobert Granat, Isak Jonsson, Bo Kågström. 531-539 [doi]
• Minimal Data Copy for Dense Linear Algebra FactorizationFred G. Gustavson, John A. Gunnels, James C. Sexton. 540-549 [doi]
• Three Algorithms for Cholesky Factorization on Distributed Memory Using Packed StorageFred G. Gustavson, Lars Karlsson, Bo Kågström. 550-559 [doi]
• In-Place Transposition of Rectangular MatricesFred G. Gustavson, Tadeusz Swirszcz. 560-569 [doi]
• Rectangular Full Packed Format for LAPACK Algorithms Timings on Several ComputersFred G. Gustavson, Jerzy Wasniewski. 570-579 [doi]
• Using Non-canonical Array Layouts in Dense Matrix OperationsJosé R. Herrero, Juan J. Navarro. 580-588 [doi]
• New Data Distribution for Solving Triangular Systems on Distributed Memory MachinesPrzemyslaw Stpiczynski. 589-597 [doi]
• The Design of a New Out-of-Core Multifrontal SolverJohn K. Reid, Jennifer A. Scott. 598-607 [doi]
• Cholesky Factorization of Band Matrices Using Multithreaded BLASAlfredo Remón, Enrique S. Quintana-Ortí, Gregorio Quintana-Ortí. 608-616 [doi]
• A Master-Worker Type Eigensolver for Molecular Orbital ComputationsTetsuya Sakurai, Yoshihisa Kodaki, Hiroto Tadano, Hiroaki Umeda, Yuichi Inadomi, Toshio Watanabe, Umpei Nagashima. 617-625 [doi]
• Bioinformatics and Computational Biology: Minisymposium AbstractAnn-Charlotte Berglund Sonnhammer, Sverker Holmgren. 626 [doi]
• Using Parallel Computing and Grid Systems for Genetic Mapping of Quantitative TraitsMahen Jayawardena, Kajsa Ljungberg, Sverker Holmgren. 627-636 [doi]
• Partial Approximation of the Master Equation by the Fokker-Planck EquationPaul Sjöberg. 637-646 [doi]
• Design, Construction and Use of the FISH ServerJeanette Tångrot, Lixiao Wang, Bo Kågström, Uwe H. Sauer. 647-657 [doi]
• Scientific Visualization and HPC Applications: Minisymposium AbstractMatthew D. Cooper, Anders Ynnerman. 658 [doi]
• Interactive Volume Visualization of Fluid Flow Simulation DataPaul R. Woodward, David H. Porter, James B. S. G. Greensky, Alex J. Larson, Michael R. Knox, James Hanson, Niranjay Ravindran, Tyler Fuchs. 659-664 [doi]
• Software Tools for Parallel CFD Applications: Minisymposium AbstractXing Cai, Hans Petter Langtangen. 665 [doi]
• The Iterative Solver Template LibraryMarkus Blatt, Peter Bastian. 666-675 [doi]
• ::::EulFS:::: : A Parallel CFD Code for the Simulation of Euler and Navier-Stokes Problems on Unstructured GridsAldo Bonfiglioli, Bruno Carpentieri, Masha Sosonkina. 676-685 [doi]
• Making Hybrid Tsunami Simulators in a Parallel Software FrameworkXing Cai, Hans Petter Langtangen. 686-693 [doi]
• HPC-MW: A Problem Solving Environment for Developing Parallel FEM ApplicationsSatoshi Ito, Hiroshi Okuda. 694-702 [doi]
• SyFi - An Element Matrix FactoryKent-Andre Mardal. 703-711 [doi]
• Life: Overview of a Unified C++ Implementation of the Finite and Spectral Element Methods in 1D, 2D and 3DChristophe Prud homme. 712-721 [doi]
• Parallel Program Complex for 3D Unsteady Flow SimulationEugene V. Shilnikov. 722-731 [doi]
• Multi-scale Physics: Minisymposium AbstractMats G. Larson. 732 [doi]
• Simulation of Multiphysics Problems Using Adaptive Finite ElementsFredrik Bengzon, August Johansson, Mats G. Larson, Robert Söderlund. 733-743 [doi]
• A New Domain Decomposition Approach Suited for Grid ComputingJuan A. Acebrón, Raúl Durán, Rafael Rico, Renato Spigler. 744-753 [doi]
• Parallelization of the Mesh Refinement Algorithm of the FDEM Program PackageTorsten Adolph, Willi Schönauer. 754-763 [doi]
• Load Balancing for the Numerical Solution of the Navier-Stokes EquationsGregory Karagiorgos, Petros Katsafados, Andreas Kontarinis, Nikolaos M. Missirlis, Filippos Tzaferis. 764-773 [doi]
• A Method of Adaptive Coarsening for Compressing Scientific DatasetsTallat M. Shafaat, Scott B. Baden. 774-780 [doi]
• A Computational Framework for Topological OperationsMichael Spevak, René Heinzl, Philipp Schwaha, Siegfried Selberherr. 781-790 [doi]
• Applications of Grid Computing in Genetics and ProteomicsJorge Andrade, Malin Andersen, Lisa Berglund, Jacob Odeberg. 791-798 [doi]
• Grid Enabling Your Data Resources with OGSA-DAIMario Antonioletti, Malcolm P. Atkinson, Neil P. Chue Hong, Bartosz Dobrzelecki, Alastair C. Hume, Mike Jackson 0003, Kostas Karasavvas, Amy Krause, Jennifer M. Schopf, Tom Sugden, Elias Theocharopoulos. 799-808 [doi]
• UniGrids Streaming Framework: Enabling Streaming for the New Generation of GridsKrzysztof Benedyczak, Aleksander Nowinski, Krzysztof Nowinski, Piotr Bala. 809-818 [doi]
• Dynamic Clusters Available Under Clusterix GridJan Kwiatkowski, Marcin Pawlik, Gerard Frankowski, Kazimierz Balos, Roman Wyrzykowski, Konrad Karczewski. 819-829 [doi]
• Agent-Based Societies for the Sharing, Brokerage and Allocation of Grid ResourcesGabriele Pierantoni, Brian A. Coghlan, Eamonn Kenny. 830-839 [doi]
• Opus:::IB::: - Grid Enabled Opteron Cluster with InfiniBand InterconnectOlaf Schneider, Frank Schmitz, Ivan Kondov, Thomas Brandel. 840-849 [doi]
• Extending the HPC-ICTM Geographical Categorization Model for Grid ComputingRafael K. S. Silva, Marilton S. de Aguiar, César A. F. De Rose, Graçaliz Pereira Dimuro. 850-859 [doi]
• Distributed SILC: An Easy-to-Use Interface for MPI-Based Parallel Matrix Computation LibrariesTamito Kajiyama, Akira Nukada, Reiji Suda, Hidehiko Hasegawa, Akira Nishida. 860-870 [doi]
• A Study of Real World I/O Performance in Parallel Scientific ComputingDries Kimpe, Andrea Lani, Tiago Quintino, Stefan Vandewalle, Stefaan Poedts, Herman Deconinck. 871-881 [doi]
• Epitaxial Surface Growth with Local Interaction, Parallel and Non-parallel SimulationsCarmen B. Navarrete, Susana Holgado, Eloy Anguiano. 882-889 [doi]
• Data Dependence Analysis for the Parallelization of Numerical Tree CodesGerhard W. Zumbusch. 890-899 [doi]
• Efficient Assembly of Sparse Matrices Using HashingMats Aspnäs, Artur Signell, Jan Westerholm. 900-907 [doi]
• A Web-Site-Based Partitioning Technique for Reducing Preprocessing Overhead of Parallel PageRank ComputationAli Cevahir, Cevdet Aykanat, Ata Turk, Berkant Barla Cambazoglu. 908-918 [doi]
• Is Cache-Oblivious DGEMM Viable?John A. Gunnels, Fred G. Gustavson, Keshav Pingali, Kamen Yotov. 919-928 [doi]
• Partitioning and Blocking Issues for a Parallel Incomplete FactorizationPascal Hénon, Pierre Ramet, Jean Roman. 929-937 [doi]
• Automatic Performance Tuning for the Multi-section with Multiple Eigenvalues Method for Symmetric Tridiagonal EigenproblemsTakahiro Katagiri, Christof Vömel, James Demmel. 938-948 [doi]
• Optimizing a Parallel Self-verified Method for Solving Linear SystemsMariana Luderitz Kolberg, Lucas Baldo, Pedro Velho, Luiz Gustavo Fernandes, Dalcidio Moraes Claudio. 949-955 [doi]
• A Parallel Block Iterative Method for Interactive Contacting Rigid Multibody Simulations on Multicore PCsClaude Lacoursière. 956-965 [doi]
• PyTrilinos: High-Performance Distributed-Memory Solvers for PythonMarzio Sala, William F. Spotz, Michael A. Heroux. 966-975 [doi]
• Amesos: A Set of General Interfaces to Sparse Direct Solver LibrariesMarzio Sala, Kendall S. Stanley, Michael A. Heroux. 976-985 [doi]
• ::::d-Spline:::: Based Incremental Parameter Estimation in Automatic Performance TuningTeruo Tanaka, Takahiro Katagiri, Toshitsugu Yuba. 986-995 [doi]
• A High Performance Generic Scientific Simulation EnvironmentRené Heinzl, Michael Spevak, Philipp Schwaha, Siegfried Selberherr. 996-1005 [doi]
• NestStepModelica - Mathematical Modeling and Bulk-Synchronous Parallel SimulationChristoph W. Kessler, Peter Fritzson, Mattias V. Eriksson. 1006-1015 [doi]
• Flecs, a Flexible Coupling Shell Application to Fluid-Structure InteractionMargreet Nool, Erik Jan Lingen, Aukje de Boer, Hester Bijl. 1016-1025 [doi]
• New Scalability Frontiers in ::::Ab Initio:::: Electronic Structure Calculations Using the BG/L SupercomputerConstantine Bekas, Alessandro Curioni, Wanda Andreoni. 1026-1035 [doi]
• A PAPI Implementation for BlueGeneNils Smeds. 1036-1044 [doi]
• Numerical Simulation of 3D Acoustic LoggingVictor I. Kostin, Dmitry V. Pissarenko, Galina V. Reshetova, Vladimir A. Tcheverda. 1045-1054 [doi]
• An Improved Interval Global Optimization Method and Its Application to Price Management ProblemBartlomiej Jacek Kubica, Ewa Niewiadomska-Szynkiewicz. 1055-1064 [doi]
• Optimizing Neural Network Classifiers with ROOT on a Rocks Linux ClusterTomas Lindén, Francisco García, Aatos Heikkinen, Sami Lehti. 1065-1073 [doi]
• A Model of Small-Scale Turbulence for Use in the PPM Gas Dynamics SchemePaul R. Woodward, David H. Porter. 1074-1083 [doi]
• Mapping in Heterogeneous Systems with Heuristic MethodsJuan-Pedro Martínez-Gallar, Francisco Almeida, Domingo Giménez. 1084-1093 [doi]
• The parXXL Environment: Scalable Fine Grained Development for Large Coarse Grained PlatformsJens Gustedt, Stéphane Vialle, Amelia De Vivo. 1094-1104 [doi]
• Performance Analysis of Two Parallel Game-Tree Search ApplicationsYurong Chen, Ying Tan, Yimin Zhang, Carole Dulong. 1105-1114 [doi]
• Implementation of a Black-Box Global Optimization Algorithm with a Parallel Branch and Bound TemplateRaimondas Ciegis, Milda Baravykaite. 1115-1125 [doi]
• Parallelization Techniques for Tabu SearchJacek Dabrowski. 1126-1135 [doi]
• ::::TreeP::::: A Self-reconfigurable Topology for Unstructured P2P SystemsEuloge Edi, Tahar Kechadi, Ronan McNulty. 1136-1146 [doi]
• A Middleware for Job Distribution in Peer-to-Peer NetworksThomas Fischer, Stephan Fudeus, Peter Merz. 1147-1157 [doi]
• Mobile Agents Self-optimization with MAWeSEmilio Pasquale Mancini, Massimiliano Rak, Salvatore Venticinque, Umberto Villano. 1158-1167 [doi]
• Performance Impact of Resource Conflicts on Chip Multi-processor ServersMyungho Lee, Yeonseung Ryu, Sugwon Hong, Chungki Lee. 1168-1177 [doi]
• An Implementation of Parallel 1-D FFT Using SSE3 Instructions on Dual-Core ProcessorsDaisuke Takahashi. 1178-1187 [doi]