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: roman@icis.pcz.pl

Jack DongarraUniversity of TennesseeComputer Science Department1122 Volunteer Blvd., Knoxville, TN 37996-3450, USAE-mail: dongarra@cs.utk.edu

Norbert MeyerPoznan Supercomputing and Networking CenterNoskowskiego 10, 61-704 Poznan, PolandE-mail: meyer@man.poznan.pl

Jerzy WasniewskiTechnical University of DenmarkDepartment of Informatics and Mathematical ModellingRichard Petersens Plads, Building 321, 2800 Kongens Lyngby, DenmarkE-mail: jw@imm.dtu.dk

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

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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