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Lecture Notes in Computer Science 3911Commenced Publication in 1973Founding and Former Series Editors:Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen
Editorial Board
David HutchisonLancaster University, UK
Takeo KanadeCarnegie Mellon University, Pittsburgh, PA, USA
Josef KittlerUniversity of Surrey, Guildford, UK
Jon M. KleinbergCornell University, Ithaca, NY, USA
Friedemann MatternETH Zurich, Switzerland
John C. MitchellStanford University, CA, USA
Moni NaorWeizmann Institute of Science, Rehovot, Israel
Oscar NierstraszUniversity of Bern, Switzerland
C. Pandu RanganIndian Institute of Technology, Madras, India
Bernhard SteffenUniversity of Dortmund, Germany
Madhu SudanMassachusetts Institute of Technology, MA, USA
Demetri TerzopoulosUniversity of California, Los Angeles, CA, USA
Doug TygarUniversity of California, Berkeley, CA, USA
Moshe Y. VardiRice University, Houston, TX, USA
Gerhard WeikumMax-Planck Institute of Computer Science, Saarbruecken, Germany
Roman Wyrzykowski Jack DongarraNorbert Meyer Jerzy Wasniewski (Eds.)
Parallel ProcessingandApplied Mathematics
6th International Conference, PPAM 2005Poznan, Poland, September 11-14, 2005Revised Selected Papers
13
Volume Editors
Roman WyrzykowskiCzestochowa University of TechnologyDepartment of Computer and Information SciencesDabrowskiego 73, 42-200 Czestochowa, PolandE-mail: [email protected]
Jack DongarraUniversity of TennesseeComputer Science Department1122 Volunteer Blvd., Knoxville, TN 37996-3450, USAE-mail: [email protected]
Norbert MeyerPoznan Supercomputing and Networking CenterNoskowskiego 10, 61-704 Poznan, PolandE-mail: [email protected]
Jerzy WasniewskiTechnical University of DenmarkDepartment of Informatics and Mathematical ModellingRichard Petersens Plads, Building 321, 2800 Kongens Lyngby, DenmarkE-mail: [email protected]
Library of Congress Control Number: 2006925464
CR Subject Classification (1998): D, F.2, G, B.2-3, C.2, J.2
LNCS Sublibrary: SL 1 – Theoretical Computer Science and General Issues
ISSN 0302-9743ISBN-10 3-540-34141-2 Springer Berlin Heidelberg New YorkISBN-13 978-3-540-34141-3 Springer Berlin Heidelberg New York
This work is subject to copyright. All rights are reserved, whether the whole or part of the material isconcerned, specifically the rights of translation, reprinting, re-use of illustrations, recitation, broadcasting,reproduction on microfilms or in any other way, and storage in data banks. Duplication of this publicationor parts thereof is permitted only under the provisions of the German Copyright Law of September 9, 1965,in its current version, and permission for use must always be obtained from Springer. Violations are liableto prosecution under the German Copyright Law.
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Preface
This volume comprises the proceedings of the 6th International Conference onParallel Processing and Applied Mathematics - PPAM 2005, which was heldin Poznań, the industrial, academic and cultural center in the western part ofPoland, during September 11–14, 2005. It was organized by the Department ofComputer and Information Sciences of the Częstochowa University of Technol-ogy, with the help of Poznań Supercomputing and Networking Center. The mainorganizer was Roman Wyrzykowski.PPAM is a biennial conference organized since 1994. Five previous events
have been held in different places in Poland. The proceedings of the last twoconferences were published by Springer in the Lecture Notes in Computer Scienceseries (Nałęczów, 2001, vol.2328; Częstochowa, 2003, vol.3019).The PPAM conferences have become an international forum for exchanging
ideas between researchers involved in parallel and distributed computing, includ-ing theory and applications, as well as applied and computational mathematics.The focus of PPAM 2005 was on grid computing. The main idea behind this de-cision was to foster communication and cooperation between the grid applicationusers, application developers and grid middleware developers, to identify the keyapplication requirements and scenarios on the grid, to gather information abouttools and toolkits, and to broaden the grid community by encouraging new usersto take advantage of grid technologies.This meeting gathered around 200 participants from 33 countries. A strict
refereeing process resulted in acceptance of 130 contributed presentations, whileapproximately 38% of the submissions were rejected. It is worth mentioningthat the conference was visited by both the research community and industryrepresentatives.Regular tracks of the conference covered important fields of parallel/dist-
ributed/grid computing and applied mathematics such as:
– Parallel and distributed architectures– Parallel and distributed non-numerical algorithms– Performance analysis, prediction and optimization– Grid programming– Tools and environments for clusters and grids– Numerical and non-numerical applications of parallel/distributed/grid com-puting– Evolutionary computing– Parallel data mining– Parallel numerics– Mathematical and computing methods
VI Preface
The plenary and invited talks were presented by:
– Ben Bennett from Intel (USA)– Jack Dongarra from the University of Tennessee and Oak Ridge NationalLaboratory (USA)– Geoffrey Fox from Indiana University (USA)– Jacek Gondzio from the University of Edinburgh, Scotland (UK)– Rich L. Graham from Los Alamos National Laboratory (USA)– Kate Keahey from Argonne National Laboratory (USA)– Eric Kronstadt from IBM T.J. Watson Research Center (USA)– Bolesław Szymański from Rensselaer Polytechnic Institute (USA)– Ziga Turk from the University of Ljubljana (Slovenia)– Jerzy Waśniewski from the Technical University of Denmark (Denmark)
Important and integral parts of the PPAM 2005 conference were the work-shops:
– The Second Grid Application and Middleware Workshop - GAMW 2005organized by Ewa Deelman from the USC Information Sciences Institute(USA) and Norbert Meyer from the Poznań Supercomputing and NetworkingCenter (Poland)– The Second Grid Resource Management Workshop - GRMW 2005 orga-nized by Jarek Nabrzyski from the Poznań Supercomputing and NetworkingCenter (Poland) and Ramin Yahyapour from the University of Dortmund(Germany)– Workshop on Large Scale Computations on Grids organized by Przemys-law Stpiczyński from Marie Curie-Skłodowska University in Lublin (Poland),Dana Petcu from the Western University of Timisoara(Romania), andMarcinPaprzycki from SWPS in Warsaw (Poland)– Workshop on Scheduling for Parallel Computing organized by Maciej Droz-dowski from the Poznań University of Technology (Poland)– Workshop on Language-Based Parallel Programming Models organized byAmi Marowka from the Hebrew University (Israel)– Workshop on Dependability of the Distributed Systems organized by JanKwiatkowski and Piotr Karwaczyński from the Wroclaw University of Tech-nology (Poland)– Workshop on HPC Linear Algebra Libraries for Computers with MultilevelMemories organized by Jerzy Waśniewski from the Technical University ofDenmark (Denmark)– Workshop on Parallel Bio-Computing organized by David A. Bader from theGeorgia Institute of Technology in Atlanta (USA) and Denis Trystram fromID-IMAG in Grenoble (France)
The PPAM 2005 meeting began with four half-day tutorials:
– Using CLUSTERIX: National Cluster of Linux Systems, by the CLUS-TERIX Team from Czestochowa University of Technology, Poznań Super-computing and Networking Center, Gdańsk University of Technology, andBiałystok Technical University (Poland)
Preface VII
– Enterprise GRID Solutions: Eliminating Isolated Technology Islands withInfiniBand, by CISCO– Scientific Programming for Heterogeneous Systems, by Alexey Lastovetskyfrom the University College Dublin (Ireland) and Alexey Kalinov from theInstitute for System Programming in Moscow (Russia)– Upgrading Cluster Performance with InfiniBand and the Intel MPI Library,by Tom Lehmann from Intel (USA)
The organizers are indebted to the PPAM 2005 sponsors, whose support wasvital to the success of the conference. The main sponsor was Intel Corporation.The other sponsors were: IBM Corporation, Optimus S.A., Cisco Systems, andAPC Corporation. We thank all members of the International Program Com-mittee, Workshop Program Comittees and additional reviewers for their dili-gent work in refereeing the submitted papers. Finally, we thank all of the localorganizers from the Częstochowa University of Technology and Poznań Super-computing and Networking Center, who helped us run the event very smoothly.We are especially indebted to Grażyna Kołakowska, Urszula Kroczewska, Kon-rad Karczewski, Jarosław Żola, from the Częstochowa University of Technol-ogy, and Maciej Stroiński, Sławomir Niwiński from Poznań Supercomputing andNetworking Center.We hope that this volume will be useful to you. We would like to invite
everyone who reads it to the next conference, PPAM 2007, which will be heldon the Baltic Coast in Gdańsk/Sopot (Poland) on September 9-12, 2007(http://ppam.pcz.pl).
February 2006 Roman WyrzykowskiJack DongarraNorbert MeyerJerzy Waśniewski
Organization
Program Committee
Jan Węglarz Poznań University of Technology, PolandHonorary Chair
Roman Wyrzykowski Częstochowa University of Technology, PolandChair of Program Committee
Bolesław Szymański Rensselaer Polytechnic Institute, USAVice-Chair of Program Committee
Peter Arbenz Swiss Federal Institute of Technology, SwitzerlandPiotr Bała N. Copernicus University, PolandRadim Blaheta Institute of Geonics, Czech Academy of Sciences,
Czech RepublicJacek Blażewicz Poznań University of Technology, PolandTadeusz Burczyński Silesia University of Technology, PolandPeter Brezany University of Vienna, AustriaJerzy Brzeziński Poznań University of Technology, PolandMarian Bubak Institute of Computer Science, AGH, PolandRaimondas Ciegis Vilnius Gediminas Technical University, LithuaniaBogdan Chlebus University of Colorado at Denver, USAZbigniew Czech Silesia University of Technology, PolandSergei Gorlatch University of Muenster, GermanyJack Dongarra University of Tennessee and ORNL, USAMaciej Drozdowski Poznań University of Technology, PolandAndrzej Gościński Deakin University, AustraliaFrederic Guinand Universite du Havre, FranceThomas Fahringer University of Innsbruck, AustriaMarta Fairen Universitat Polit. de Catalunya, Barcelona, SpainLadislav Hluchy Slovak Academy of Sciences, BratislavaAlexey Kalinov Institute for System Programming, RussiaAyse Kiper Middle East Technical University, TurkeyJacek Kitowski Institute of Computer Science, AGH, PolandErricos Kontoghiorghes Universite de Neuchatel, SwitzerlandJozef Korbicz University of Zielona Góra, PolandStanislaw Kozielski Silesia University of Technology, PolandDieter Kranzlmueller Johannes Kepler University Linz, AustriaHenryk Krawczyk Gdańsk University of Technology, PolandPiotr Krzyżanowski University of Warsaw, PolandJan Kwiatkowski Wrocław University of Technology, PolandAlexey Lastovetsky University College Dublin, Ireland
X Organization
Vyacheslav Maksimov Ural Branch, Russian Academy of Sciences,Russia
Tomas Margalef Universitat Autonoma de Barcelona, SpainAmi Marowka Hebrew University, IsraelNorbert Meyer PSNC, Poznań, PolandJarek Nabrzyski PSNC, Poznań, PolandMarcin Paprzycki SWPS, Warsaw, PolandDana Petcu Western University of Timisoara, RomaniaEdwige Pissaloux Universite de Rouen, FranceJacek Rokicki Warsaw University of Technology, PolandLeszek Rutkowski Częstochowa University of Technology, PolandYousef Saad University of Minnesota, USAFranciszek Seredyński Polish Academy of Sciences, Warsaw, PolandRobert Schaefer Institute of Computer Science, AGH, PolandNorbert Sczygiol Częstochowa University of Technology, PolandJurij Silc Jozef Stefan Institute, SloveniaPeter M.A. Sloot University of Amsterdam, The NetherlandsPrzemyslaw Stpiczyński UMCS, Lublin, PolandDomenico Talia University of Calabria, ItalyAndrei Tchernykh CICESE, Ensenada, MexicoSivan Toledo Tel-Aviv University, IsraelRoman Trobec Jozef Stefan Institute, SloveniaDenis Trystram ID-IMAG, Grenoble, FranceMarek Tudruj Polish Academy of Sciences, Warsaw, PolandPavel Tvrdik Czech Technical University, Prague,
Czech RepublicJens Volkert Johannes Kepler University Linz, AustriaJerzy Waśniewski Technical University of Denmark, DenmarkBogdan Wiszniewski Gdańsk University of Technology, PolandKrzysztof Zieliński Institute of Computer Science, AGH, PolandJianping Zhu University of Akron, USA
Table of Contents
Parallel and Distributed Architectures
Multi-version Coherence Protocol for Replicated Shared ObjectsJerzy Brzezinski, Jacek Kobusinski, Dariusz Wawrzyniak . . . . . . . . . . . . 1
Checkpointing Speculative Distributed Shared MemoryArkadiusz Danilecki, Anna Kobusinska, Michal Szychowiak . . . . . . . . . . 9
Evaluation of the Acknowledgment Reduction in a Software-DSMSystem
Kenji Kise, Takahiro Katagiri, Hiroki Honda, Toshitsugu Yuba . . . . . . 17
Taking Advantage of the SHECS-Based Critical Sections in the SharedMemory Parallel Architectures
Tomasz Madajczak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Dynamic SMP Clusters in SoC Technology – Towards MassivelyParallel Fine Grain Numerics
Marek Tudruj, Lukasz Masko . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34
Paralel and Distributed Non-numerical Algorithms
Frequency of Co-operation of Parallel Simulated Annealing ProcessesZbigniew J. Czech, Bozena Wieczorek . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Maximal Group Membership in Ad Hoc NetworksMamoun Filali, Valerie Issarny, Philippe Mauran, Gerard Padiou,Philippe Queinnec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
Multi-thread Processing of Long Aggregates ListsMarcin Gorawski, Rafal Malczok . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
A New Algorithm for Generation of Exactly M–Block Set Partitions inAssociative Model
Zbigniew Kokosinski . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
A Self-stabilizing Algorithm for Finding a Spanning Tree in aPolynomial Number of Moves
Adrian Kosowski, �Lukasz Kuszner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
XII Table of Contents
Massive Concurrent Deletion of Keys in B*-TreeS. Arash Ostadzadeh, M. Amir Moulavi, Zeinab Zeinalpour . . . . . . . . . 83
The Distributed Stigmergic Algorithm for Multi-parameterOptimization
Jurij Silc, Peter Korosec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
Performance Analysis, Prediction and Optimization
Total Exchange Performance Modelling Under Network ContentionLuiz Angelo Barchet-Steffenel, Gregory Mounie . . . . . . . . . . . . . . . . . . . . 100
Towards the Performance Visualization of Web-Service BasedApplications
Marian Bubak, Wlodzimierz Funika, Marcin Koch, Dominik Dziok,Allen D. Malony, Marcin Smetek, Roland Wismuller . . . . . . . . . . . . . . . 108
Parallel Machine Scheduling of Deteriorating Jobs by Modified SteepestDescent Search
Stanis�law Gawiejnowicz, Wies�law Kurc, Lidia Pankowska . . . . . . . . . . . 116
A Study on Load Imbalance in Parallel Hypermatrix MultiplicationUsing OpenMP
Jose R. Herrero, Juan J. Navarro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124
Common Due Window Assignment in Parallel Processor SchedulingProblem with Nonlinear Penalty Functions
Adam Janiak, Marcin Winczaszek . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
Distributed Architecture System for Computer Performance TestingEzequiel Herruzo, Andres J. Mesones, Jose I. Benavides,Oscar Plata, Emilo L. Zapata . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
Data Access Time Estimation for the CASTOR HSM SystemMarcin Kuta, Darin Nikolow, Renata S�lota, Jacek Kitowski . . . . . . . . . 148
Towards Distributed Monitoring and Performance Analysis Services inthe K-WfGrid Project
Hong-Linh Truong, Bartosz Balis, Marian Bubak, Jakub Dziwisz,Thomas Fahringer, Andreas Hoheisel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
A New Diagonal Blocking Format and Model of Cache Behavior forSparse Matrices
Pavel Tvrdık, Ivan Simecek . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Table of Contents XIII
Grid Programming
GridSpace – Semantic Programming Environment for the GridTomasz Guba�la, Marian Bubak . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
Applications Control on Grid with SynchronizersDamian Kopanski, Marek Tudruj, Janusz Borkowski . . . . . . . . . . . . . . . . 180
Alchemi+: An Agent-Based Approach to Grid ProgrammingRoohollah Mafi, Hossein Deldari, Mojtaba Mazoochi . . . . . . . . . . . . . . . . 188
Tools and Environments for Clusters and Grids
Bridging the Gap Between Cluster and Grid ComputingAlbano Alves, Antonio Pina . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
A Broker Based Architecture for Automated Discovery and Invocationof Stateful Services
Marian Babik, Ladislav Hluchy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Remote Parallel I/O in Grid EnvironmentsRudolf Berrendorf, Marc-Andre Hermanns, Jan Seidel . . . . . . . . . . . . . . 212
Remote Task Submission and Publishing in BeesyCluster: Security andEfficiency of Web Service Interface
Pawe�l Czarnul, Micha�l Bajor, Marcin Fr ↪aczak, Anna Banaszczyk,Marcin Fiszer, Katarzyna Ramczykowska . . . . . . . . . . . . . . . . . . . . . . . . . 220
Open MPI: A Flexible High Performance MPIRichard L. Graham, Timothy S. Woodall, Jeffrey M. Squyres . . . . . . . . 228
ClusteriX Data Management System and Its Integration withApplications
Lukasz Kuczynski, Konrad Karczewski, Roman Wyrzykowski . . . . . . . . 240
Grid Access and User Interface in CLUSTERIX ProjectPiotr Kopta, Tomasz Kuczynski, Roman Wyrzykowski . . . . . . . . . . . . . . 249
An Architecture for Reconfigurable Iterative MPI Applications inDynamic Environments
Kaoutar El Maghraoui, Boleslaw K. Szymanski, Carlos Varela . . . . . . . 258
Parallel Computing in Java: Looking for the Most Effective RMIImplementation for Clusters
Rafa�l Metkowski, Piotr Ba�la . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 272
XIV Table of Contents
Practical Experience in Building an Agent System for Semantics-BasedProvision and Selection of Grid Services
Gustaf Nimar, Vladimir Vlassov, Konstantin Popov . . . . . . . . . . . . . . . . 278
A Framework for Managing Large Scale Computing Fabrics and ItsComputational Complexity
Piotr Poznanski, Jacek Kitowski . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 288
Domus – An Architecture for Cluster-Oriented Distributed Hash TablesJose Rufino, Antonio Pina, Albano Alves,Jose Exposto . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 296
Applications of Parallel/Distributed/GridComputing
Iterative Reconstruction of Tomographic Scans in Dynamic SMPClusters with Communication on the Fly
Boguslaw Butrylo, Marek Tudruj, Lukasz Masko . . . . . . . . . . . . . . . . . . . 304
Parallel Tool for Solution of Multiphase Flow ProblemsRaimondas Ciegis, Alexander Jakusev, Vadimas Starikovicius . . . . . . . . 312
Grids for Real Time Data ApplicationsGeoffrey C. Fox, Mehmet S. Aktas, Galip Aydin, Hasan Bulut,Harshawardhan Gadgil, Sangyoon Oh, Shrideep Pallickara,Marlon E. Pierce, Ahmet Sayar, Gang Zhai . . . . . . . . . . . . . . . . . . . . . . . 320
Modeling of People Flow in Public Transport VehiclesBart�lomiej Gudowski, Jaros�law W ↪as . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 333
Parallel Processing in Discrimination Between Models of DynamicSystems
Bartosz Kuczewski, Przemys�law Baranowski, Dariusz Ucinski . . . . . . . . 340
Real Terrain Visualisation with a Distributed PC-ClusterJacek Lebiedz, Krzysztof Mieloszyk, Bogdan Wiszniewski . . . . . . . . . . . . 349
Service Oriented Architecture for Risk Assessment of Natural DisastersMartin Maliska, Branislav Simo, Marek Ciglan, Peter Slizik,Ladislav Hluchy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 357
Porting Thermomechanical Applications to Grid EnvironmentTomasz Olas, Roman Wyrzykowski . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 364
Table of Contents XV
Parallel Implementation of Software Package for Modelling Bi–phaseGas–Particle Flows
Sebastian Pluta, Roman Wyrzykowski . . . . . . . . . . . . . . . . . . . . . . . . . . . . 373
Parallel Resolution of the Satisfiability Problem (SAT) with OpenMPand MPI
Daniel Singer, Alain Vagner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 380
Grid Technology for the Collaborative EnterpriseZiga Turk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 389
Large Scalable Simulations of Mammalian Visual CortexGrzegorz M. Wojcik, Wieslaw A. Kaminski . . . . . . . . . . . . . . . . . . . . . . . 399
Evolutionary Computing with Applications
Optimised Scheduling of Grid Resources Using Hybrid EvolutionaryAlgorithms
Wilfried Jakob, Alexander Quinte, Karl-Uwe Stucky,Wolfgang Suß . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 406
A New Library for Evolutionary AlgorithmsStanis�law Gawiejnowicz, Tomasz Onak, Cezary Suwalski . . . . . . . . . . . . 414
Grid-Based Evolutionary Optimization of StructuresWac�law Kus, Tadeusz Burczynski . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 422
Parallelizing Evolutionary Algorithms for Clustering DataWojciech Kwedlo . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 430
Evolutionary Adaptation in Non-stationary Environments: A CaseStudy
Andrzej Obuchowicz, Dariusz Wawrzyniak . . . . . . . . . . . . . . . . . . . . . . . . 439
Hierarchical Representation and Operators in Evolutionary DesignBarbara Strug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 447
Parallel Data Mining
Improving Parallelism in Structural Data MiningMin Cai, Istvan Jonyer, Marcin Paprzycki . . . . . . . . . . . . . . . . . . . . . . . . 455
Parallel Query Processing and Edge Ranking of GraphsDariusz Dereniowski, Marek Kubale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 463
XVI Table of Contents
Online Balancing of aR-Tree Indexed Distributed Spatial DataWarehouse
Marcin Gorawski, Robert Chechelski . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 470
Resumption of Data Extraction Process in Parallel Data WarehousesMarcin Gorawski, Pawel Marks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 478
Parallel Numerics
An Efficient Parallel Solution of Complex Toeplitz Linear SystemsPedro Alonso, Antonio M. Vidal . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 486
Monitoring the Block Conjugate Gradient Convergence Within theInexact Inverse Subspace Iteration
Carlos Balsa, Michel Dayde, Ronan Guivarc’h, Jose Laginha Palma,Daniel Ruiz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 494
Parallel Schwarz Methods: Algebraic Construction of Coarse Problems,Implementation and Testing
Radim Blaheta, Petr Byczanski, Ondrej Jakl, Jirı Stary . . . . . . . . . . . . . 505
Direct Solution of Linear Systems of Size 109 Arising in Optimizationwith Interior Point Methods
Jacek Gondzio, Andreas Grothey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 513
FPGA Implementation of the Conjugate Gradient MethodOleg Maslennikow, Volodymyr Lepekha, Anatoli Sergyienko . . . . . . . . . . 526
A Parallel Preconditioning for the Nonlinear Stokes ProblemPawe�l J. Matuszyk, Krzysztof Boryczko . . . . . . . . . . . . . . . . . . . . . . . . . . . 534
Optimization of Parallel FDTD Computations Based on StructuralRedeployment of Macro Data Flow Nodes
Adam Smyk, Marek Tudruj . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 542
A Note on the Numerical Inversion of the Laplace TransformPrzemys�law Stpiczynski . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 551
Computer Methods
Mesh Adaptation Based on Discrete DataBarbara G�lut, Tomasz Jurczyk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 559
Table of Contents XVII
Applying Cooperating Distributed Graph Grammars in ComputerAided Design
Ewa Grabska, Barbara Strug . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 567
An Adaptive Filter Mechanism of Random Number Generator in aCrypto Module
Jin Keun Hong, Ki Hong Kim . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 575
Computer Analysis of the Sensitivity of the Integrated AssessmentModel MERGE-5I
Vyacheslav Maksimov, Leo Schrattenholzer,Yaroslav Minullin . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 583
Hierarchical ClassifierIgor T. Podolak, S�lawomir Biel, Marcin Bobrowski . . . . . . . . . . . . . . . . . 591
The Second Grid Application and MiddlewareWorkshop (GAMW’2005)
Knowledge-Based Runtime Prediction of Stateful Web Services forOptimal Workflow Construction
Zoltan Balogh, Emil Gatial, Michal Laclavik, Martin Maliska,Ladislav Hluchy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 599
Real-Time Visualization in the Grid Using UNICORE MiddlewareKrzysztof Benedyczak, Aleksander Nowinski, Krzysztof Nowinski,Piotr Ba�la . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 608
Development of a Grid Service for Scalable Decision Tree Constructionfrom Grid Databases
Peter Brezany, Christian Kloner, A. Min Tjoa . . . . . . . . . . . . . . . . . . . . 616
Block Matrix Multiplication in a Distributed Computing Environment:Experiments with NetSolve
Luisa D’Amore, Giuliano Laccetti, Marco Lapegna . . . . . . . . . . . . . . . . . 625
Best Practices of User Account Management with Virtual OrganizationBased Access to Grid
Jirı Denemark, Micha�l Jankowski, Ales Krenek, Ludek Matyska,Norbert Meyer, Miroslav Ruda, Pawe�l Wolniewicz . . . . . . . . . . . . . . . . . 633
Manageable Dynamic Execution Environments on the Grid UsingVirtual Machines
Sai Srinivas Dharanikota, Ralf Ratering . . . . . . . . . . . . . . . . . . . . . . . . . . 643
XVIII Table of Contents
Semantic-Based Grid Workflow CompositionTomasz Guba�la, Marian Bubak, Maciej Malawski,Katarzyna Rycerz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 651
Towards Checkpointing Grid ArchitectureGracjan Jankowski, Jozsef Kovacs, Norbert Meyer,Radoslaw Januszewski, Rafal Mikolajczak . . . . . . . . . . . . . . . . . . . . . . . . . 659
Enabling Remote Method Invocations in Peer-to-Peer Environments:RMIX over JXTA
Pawel Jurczyk, Maciej Golenia, Maciej Malawski, Dawid Kurzyniec,Marian Bubak, Vaidy S. Sunderam . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 667
Transparency in Object-Oriented Grid Database SystemsKrzysztof Kaczmarski, Piotr Habela, Hanna Kozankiewicz,Krzysztof Stencel, Kazimierz Subieta . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 675
Unifying Grid Metadata Representations Through OntologiesBartosz Kryza, Marta Majewska, Renata S�lota, Jacek Kitowski . . . . . . 683
The Grid Portlets Web Application: A Grid Portal FrameworkMichael Russell, Jason Novotny, Oliver Wehrens . . . . . . . . . . . . . . . . . . 691
A Grid Service for Management of Multiple HLA Federate ProcessesKatarzyna Rycerz, Marian Bubak, Maciej Malawski, Peter M.A. Sloot 699
Algorithms for Automatic Data Replication in Grid EnvironmentRenata S�lota, �Lukasz Skita�l, Darin Nikolow, Jacek Kitowski . . . . . . . . . 707
The Second Grid Resource Management Workshop(GRMW’2005)
A Grid Workflow Language Using High-Level Petri NetsMartin Alt, Andreas Hoheisel, Hans-Werner Pohl, Sergei Gorlatch . . . 715
Towards a Language for a Satisfaction-Based Selection of Grid ServicesSergio Andreozzi, Paolo Ciancarini, Danilo Montesi, Rocco Moretti . . 723
HMM: A Static Mapping Algorithm to Map Parallel Applications onGrids
Ranieri Baraglia, Renato Ferrini, Pierluigi Ritrovato . . . . . . . . . . . . . . . 731
Agent-Based Grid Scheduling with CalanaMathias Dalheimer, Franz-Josef Pfreundt, Peter Merz . . . . . . . . . . . . . . 741
Table of Contents XIX
Towards an Intelligent Grid Scheduling SystemRalf Gruber, Vincent Keller, Pierre Kuonen,Marie-Christine Sawley, Basile Schaeli, Ali Tolou,Marc Torruella, Trach-Minh Tran . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 751
Running Interactive Jobs in the Grid EnvironmentMarcin Lawenda, Marcin Okon, Ariel Oleksiak, Bogdan Ludwiczak,Tomasz Piontek, Juliusz Pukacki, Norbert Meyer,Jaros�law Nabrzyski, Maciej Stroinski . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 758
Comparison of Pricing Policies for a Computational Grid MarketOmer Ozan Sonmez, Attila Gursoy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 766
Two Level Job-Scheduling Strategies for a Computational GridAndrei Tchernykh, Juan Manuel Ramırez, Arutyun Avetisyan,Nikolai Kuzjurin, Dmitri Grushin, Sergey Zhuk . . . . . . . . . . . . . . . . . . . . 774
A Meta-Scheduling Service for Co-allocating Arbitrary Types ofResources
Oliver Waldrich, Philipp Wieder, Wolfgang Ziegler . . . . . . . . . . . . . . . . . 782
Comparison of Workflow Scheduling Strategies on the GridMarek Wieczorek, Radu Prodan, Thomas Fahringer . . . . . . . . . . . . . . . . 792
Workshop on Large Scale Computations on Grids
A Web Computing Environment for Parallel Algorithms in JavaOlaf Bonorden, Joachim Gehweiler,Friedhelm Meyer auf der Heide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 801
Matchmaking of Mathematical Web ServicesSimone A. Ludwig, William Naylor, Omer F. Rana, Julian Padget . . . 809
Porting CFD Codes Towards Grids: A Case StudyDana Petcu, Daniel Vizman, Marcin Paprzycki . . . . . . . . . . . . . . . . . . . . 817
Parallelization of Numerical CFD Codes in Cluster and GridEnvironments
Jacek Rokicki, Marian Krause, Micha�l Wichulski . . . . . . . . . . . . . . . . . . . 825
Execution of a Bioinformatics Application in a Joint IRISGrid/EGEETestbed
Jose Luis Vazquez-Poletti, E. Huedo, Ruben S. Montero,Ignacio M. Llorente . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 831
XX Table of Contents
Workshop on Scheduling for Parallel Computing
Load Balancing Strategies in a Web Computing EnvironmentOlaf Bonorden, Joachim Gehweiler,Friedhelm Meyer auf der Heide . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 839
Multi-installment Divisible Load Processing in Heterogeneous Systemswith Limited Memory
Maciej Drozdowski, Marcin Lawenda . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 847
Chromatic Scheduling of 1- and 2-Processor UET Tasks on DedicatedMachines with Availability Constraints
Krzysztof Giaro, Marek Kubale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 855
Task Scheduling for Look–Ahead Reconfigurable Systems in Presenceof Conditional Branches
Eryk Laskowski, Marek Tudruj . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 863
Scheduling Task Graphs for Execution in Dynamic SMP Clusters withBounded Number of Resources
Lukasz Masko . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 871
Scheduling Moldable Tasks for Dynamic SMP Clusters in SoCTechnology
Lukasz Masko, Pierre–Francois Dutot, Gregory Mounie,Denis Trystram, Marek Tudruj . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 879
Model Driven Scheduling Framework for Multiprocessor SoC DesignAshish Meena, Pierre Boulet . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 888
Asymmetric Scheduling and Load Balancing for Real-Time on LinuxSMP
Eric Piel, Philippe Marquet, Julien Soula, Jean-Luc Dekeyser . . . . . . . 896
Artificial Immune Systems Applied to Multiprocessor SchedulingGrzegorz Wojtyla, Krzysztof Rzadca, Franciszek Seredynski . . . . . . . . . . 904
Workshop on Language-Based Parallel ProgrammingModels
Toward an Application Support Layer: Numerical Computation inUnified Parallel C
Jonathan Leighton Brown, Zhaofang Wen . . . . . . . . . . . . . . . . . . . . . . . . . 912
Table of Contents XXI
Simple, List-Based Parallel Programming with Transparent LoadBalancing
Jorge Buenabad-Chavez, Miguel A. Castro-Garcıa,Graciela Roman-Alonso . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 920
SILC: A Flexible and Environment-Independent Interface for MatrixComputation Libraries
Tamito Kajiyama, Akira Nukada, Hidehiko Hasegawa, Reiji Suda,Akira Nishida . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 928
A Fortran Evolution of mpC Parallel Programming LanguageAlexey Kalinov, Ilya Ledovskikh, Mikhail Posypkin,Zakhar Levchenko, Vladimir Chizhov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 936
Java Programs Optimization Based on the Most–Often–Used–PathsApproach
Eryk Laskowski, Marek Tudruj, Richard Olejnik,Bernard Toursel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 944
Vertex-Magic Total Labeling of a Graph by Distributed ConstraintSolving in the Mozart System
Adam Meissner, Krzysztof Zwierzynski . . . . . . . . . . . . . . . . . . . . . . . . . . . 952
A Parallel Numerical Library for Co-array FortranRobert W. Numrich . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 960
A Hybrid MPI/OpenMP Implementation of a Parallel 3-D FFT onSMP Clusters
Daisuke Takahashi . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 970
Workshop on Dependability of the DistributedSystems
Safety of an Object-Based Version Vector Consistency Protocol ofSession Guarantees
Jerzy Brzezinski, Cezary Sobaniec . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 978
Minimizing Cost and Minimizing Schedule Length in Synthesis of FaultTolerant Multiprocessors Systems
Mieczyslaw Drabowski, Krzysztof Czajkowski . . . . . . . . . . . . . . . . . . . . . . . 986
A Model of Exception Propagation in Distributed ApplicationsPawe�l L. Kaczmarek, Henryk Krawczyk . . . . . . . . . . . . . . . . . . . . . . . . . . . 994
XXII Table of Contents
Parallel Processing Subsystems with Redundancy in a DistributedEnvironment
Adrian Kosowski, Micha�l Ma�lafiejski, Pawe�l Zylinski . . . . . . . . . . . . . . . 1002
Dependable Information Service for Distributed SystemsJan Kwiatkowski, Piotr Karwaczynski, Marcin Pawlik . . . . . . . . . . . . . . 1010
Fault-Tolerant Protocols for Scalable Distributed Data StructuresKrzysztof Sapiecha, Grzegorz Lukawski . . . . . . . . . . . . . . . . . . . . . . . . . . . 1018
Quantifying the Security of Composed SystemsMax Walter, Carsten Trinitis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1026
Increasing Dependability by Means of Model-Based Acceptance TestInside RTOS
Yuhong Zhao, Simon Oberthur, Norma Montealegre,Franz J. Rammig, Martin Kardos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1034
Workshop on HPC Linear Algebra Libraries forComputers with Multilevel Memories
A Cache Oblivious Algorithm for Matrix Multiplication Based onPeano’s Space Filling Curve
Michael Bader, Christoph Zenger . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1042
On Using an Hybrid MPI-Thread Programming for the Implementationof a Parallel Sparse Direct Solver on a Network of SMP Nodes
Pascal Henon, Pierre Ramet, Jean Roman . . . . . . . . . . . . . . . . . . . . . . . . 1050
Adapting Linear Algebra Codes to the Memory Hierarchy Using aHypermatrix Scheme
Jose R. Herrero, Juan J. Navarro . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1058
Measuring the Scalability of Heterogeneous Parallel SystemsAlexey Kalinov . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1066
A Variable Group Block Distribution Strategy for Dense Factorizationson Networks of Heterogeneous Computers
Alexey Lastovetsky, Ravi Reddy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1074
Minimizing Associativity Conflicts in Morton LayoutJeyarajan Thiyagalingam, Olav Beckmann,Paul H.J. Kelly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1082
Table of Contents XXIII
Workshop on Parallel Bio-computing
A Parallel Algorithm for Solving the Reversal Median ProblemMatthias Bernt, Daniel Merkle, Martin Middendorf . . . . . . . . . . . . . . . . 1089
The Parallel Genetic Algorithm for Designing DNA Randomizations ina Combinatorial Protein Experiment
Jacek B�lazewicz, Beniamin Dziurdza, Wojciech T. Markiewicz,Ceyda Oguz . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1097
Introducing Dependencies into Alignment Analysis and Its Use forLocal Structure Prediction in Proteins
Szymon Nowakowski, Krzysztof Fidelis, Jerzy Tiuryn . . . . . . . . . . . . . . . 1106
Parallel Implementation of Logical Analysis of Data (LAD) forDiscriminatory Analysis of Protein Mass Spectrometry Data
Krzysztof Puszynski . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1114
Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1123