Lecture Notes in Computer Science 3402 CommencedPublicationin1973 FoundingandFormerSeriesEditors: GerhardGoos,JurisHartmanis,andJanvanLeeuwen EditorialBoard DavidHutchison LancasterUniversity,UK TakeoKanade CarnegieMellonUniversity,Pittsburgh,PA,USA JosefKittler UniversityofSurrey,Guildford,UK JonM.Kleinberg CornellUniversity,Ithaca,NY,USA FriedemannMattern ETHZurich,Switzerland JohnC.Mitchell StanfordUniversity,CA,USA MoniNaor WeizmannInstituteofScience,Rehovot,Israel OscarNierstrasz UniversityofBern,Switzerland C.PanduRangan IndianInstituteofTechnology,Madras,India BernhardSteffen UniversityofDortmund,Germany MadhuSudan MassachusettsInstituteofTechnology,MA,USA DemetriTerzopoulos NewYorkUniversity,NY,USA DougTygar UniversityofCalifornia,Berkeley,CA,USA MosheY.Vardi RiceUniversity,Houston,TX,USA GerhardWeikum Max-PlanckInstituteofComputerScience,Saarbruecken,Germany Michel Daydé Jack J. Dongarra Vicente Hernández José M.L.M. Palma (Eds.) High Performance Computing for Computational Science – VECPAR 2004 6th International Conference Valencia, Spain, June 28-30, 2004 Revised Selected and Invited Papers 1 3 VolumeEditors MichelDaydé ENSEEIHT 2,RueCamichel,31071ToulouseCedex7,France E-mail:[email protected] JackJ.Dongarra UniversityofTennessee,TN37996-1301,USA E-mail:[email protected] VicenteHernández UniversidadPolitecnicadeValencia CaminodeVera,s/n,46022Valencia,Spain E-mail:[email protected] JoséM.L.M.Palma UniversidadedoPorto FaculdadedeEngenharia RuaDr.RobertoFriass/n,4200-465Porto,Portugal E-mail:[email protected] LibraryofCongressControlNumber:Appliedfor CRSubjectClassification(1998):D,F,C.2,G,J.2,J.3 ISSN 0302-9743 ISBN-10 3-540-25424-2SpringerBerlinHeidelbergNewYork ISBN-13 978-3-540-25424-9SpringerBerlinHeidelbergNewYork Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned,specificallytherightsoftranslation,reprinting,re-useofillustrations,recitation,broadcasting, reproductiononmicrofilmsorinanyotherway,andstorageindatabanks.Duplicationofthispublication orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9,1965, initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violationsareliable toprosecutionundertheGermanCopyrightLaw. SpringerisapartofSpringerScience+BusinessMedia springeronline.com ©Springer-VerlagBerlinHeidelberg2005 PrintedinGermany Typesetting:Camera-readybyauthor,dataconversionbyScientificPublishingServices,Chennai,India Printedonacid-freepaper SPIN:11403937 06/3142 543210 Preface VECPARisaseriesofinternationalconferencesdedicatedtothepromotionand advancement of all aspects of high-performance computing for computational science, as an industrial technique and academic discipline, extending the fron- tier of both the state of the art and the state of practice. The audience for and participants in VECPAR are seen as researchers in academic departments, gov- ernment laboratories and industrial organizations. There is now a permanent website for the series, http://vecpar.fe.up.pt, where the history of the confer- ences is described. ThesixtheditionofVECPARwasthefirsttimetheconferencewascelebrated outside Porto – at the Universitad Politecnica de Valencia (Spain), June 28–30, 2004. The whole conference programme consisted of 6 invited talks, 61 papers and26posters,outof130contributionsthatwereinitiallysubmitted.Themajor themes were divided into large-scale numerical and non-numerical simulations, parallelandgridcomputing,biosciences,numericalalgorithms,dataminingand visualization. This postconference book includes the best 48 papers and 5 invited talks presented during the three days of the conference. The book is organized into 6 chapters, with a prominent position reserved for the invited talks and the Best Student Paper. As a whole it appeals to a wide research community, from those involved in the engineering applications to those interested in the actual details of the hardware or software implementations, in line with what, in these days, tends to be considered as computational science and engineering (CSE). Chapter 1 is concerned with large-scale computations; the first paper in the chapter, and in the book, was also the opening talk at the conference. Tetsuya Sato gives an overview of the greatest computations being performed on the Earth Simulator in Japan, followed by a series of 7 papers on equally large problems. Patrick Valduriez authors an invited talk on data management in large P2P systems; the companion to 4 more papers put together in Chapter 2. The Grid technology in the roughly 5 years since it emerged has become one of the major driving forces in computer and also computational science and en- gineering.FabrizioGagliardiandVincentBretoninthetwofirstpapers(invited talks)inchapter3present,respectively,theEGEEEuropeanGridInfrastructure and applications of the Grid technology in medical applications. The 8 remain- ing papers in the chapter are a further example of the impact that the Grid is making in many areas of application. Chapter4isthelargestofallandthe12papersinthischapterareanindica- tionoftheimportanceofclustercomputing.Parallelanddistributedcomputing is the title of chapter 5, which, despite its similarity with the previous chapter, includes papers where the emphasis has been put on the physical modelling and not so much on the strictly computing aspects of the simulations. The invited VI Preface talk by Michael Heath opens chapter 5 and is a good example of how complex the computer simulation of real-life engineering systems can be. Since its early editions, linear algebra has occupied a relatively large proportion of the confer- ence programme; linear algebra was the topic we chose to bring this book to a closure – Chapter 6. Best Student Paper There were 10 papers of high quality registered for the Best Student Paper competition. The laureate of the prize was German Molto for the paper: – Three-Dimensional Cardiac Electrical Activity Simulation on Cluster and Grid Platforms,byGermanMolto,andalsoco-authoredbyJoseM.Alonso, Jose M. Ferrero, Vicente Hernandez, Marta Monserrat and Javier Saiz, all at Universidad Politecnica de Valencia. To conclude, we would like to state in writing our gratitude to all the mem- bers of the Scientific Committee and the additional referees. Their opinions and commentswereessentialinthepreparationofthisbookandtheconferencepro- gramme. We hope that the knowledge and the experience of many contributors to this book can be useful to a large number of readers. December 2004 Michel Dayd´e, Jack Dongarra, Vicente Hern´andez, Jos´e M.L.M. Palma VECPAR is a series of conferences organized by the Faculty of Engineering of Porto (FEUP) since 1993 Acknowledgments The sixth edition of the VECPAR conference brought new organizational chal- lenges. The work was split between people in different countries. While the conference was held in Valencia (Spain), both the Web-based submission sys- tems and the conference page were maintained at the Faculty of Engineering of the University of Porto (Portugal). Vitor Carvalho, once again, was responsible for the conference webpage and did an excellent job. Miguel Caballer, Gemma Cabrelles and Gabriel Garcia at the University of Valencia, under the guidance of Vicente Hernandez, did invaluable work on the Organizing Committee. Joa˜o Correia Lopes took care of the VECPAR databases and the Web-based submission systems; his collaboration was precious. Committees Organizing Committee Vicente Hernandez (Chairman) Antonio Vidal Vicente Vidal Victor Garc´ıa Enrique Ramos Ignacio Blanquer Jose Roman Jose Miguel Alonso Fernando Alvarruiz Jesus Peinado Pedro Alonso Joa˜o Correia Lopes (Webchair) Steering Committee Jos´e Laginha Palma (Chairman), Universidade do Porto, Portugal Jack Dongarra, University of Tennessee, USA Jos´e Fortes, University of Purdue, USA A´lvaro Coutinho, Universidade Federal do Rio de Janeiro, Brazil Lionel Ni, Hong Kong University of Science and Technology, Hong Kong, China Scientific Committee M. Dayd´e (Chairman) ENSEEIHT-IRIT, France O. Coulaud INRIA, France J.C. Cunha Univ. Nova de Lisboa, Portugal I.S. Duff RutherfordAppletonLab.,UKandCERFACS, France N. Ebecken Univ. Federal do Rio de Janeiro, Brazil W. Gentzsch SUN, USA A. George Univ. of Florida, USA L. Giraud CERFACS, France R. Guivarch ENSEEIHT-IRIT, France D. Knight Rutgers Univ., USA J. Koster Bergen Center for Comp. Science, Norway V. Kumar Univ. of Minnesota, USA R. Lohner George Mason Univ., USA O. Marques Lawrence Berkeley National Laboratory, USA X Committees A. Nachbin Inst. Matema´tica Pura e Aplicada, Brazil A. Padilha Univ. do Porto, Portugal B. Plateau Lab. Informatique et Distribution, France T. Priol IRISA/INRIA, France R. Ralha Univ. do Minho, Portugal H. Ruskin Dublin City Univ., Ireland E. Seidel Louisiana State University, USA A. Sousa Univ. do Porto, Portugal M. Stadtherr Univ. of Notre Dame, USA F. Tirado Univ. Complutense de Madrid, Spain B. Tourancheau E´cole Normale Sup´erieure de Lyon, France M. Valero Univ. Polit´ecnica de Catalunya, Spain E. Zapata Univ. de Malaga, Spain Invited Lecturers – Tetsuya Sato Earth Simulator Center, Japan – Patrick Valduriez INRIA and IRIN, Nantes, France – Fabrizio Gagliardi EGEE, CERN, Switzerland – Vincent Breton LPC Clermont-Ferrand, CNRS-IN2p3, France – Michael T. Heath Computational Science and Engineering University of Illinois at Urbana-Champaign, USA Sponsoring Organizations The Organizing Committee is very grateful to the following organizations for their support: UPV -Universidad Polit´ecnica de Valencia UP -Universidade do Porto FEUP-Faculdade de Engenharia da Universidade do Porto GVA -Generalitat Valenciana Conselleria de Empresa, Universidad y Ciencia Committees XI Additional Referees Alberto Pascual Jorge Barbosa Albino dos Anjos Aveleda Jose M. Cela Aleksandar Lazarevic Jose Roman Alfredo Bautista Joseph Gergaud B. Uygar Oztekin Jos´e Carlos Alves Boniface Nkonga Jos´e L.D. Alves Bruno Carpentieri Jos´e Miguel Alonso Byung Il Koh Joa˜o Manuel Tavares Carlos Balsa Joa˜o Tom´e Saraiva Carlos Silva Santos K. Park Christian Perez Kil Seok Cho Christine Morin Luis F. Romero Congduc Pham Luis Pin˜uel Daniel Ruiz Miguel Pimenta Monteiro David Bueno M.C. Counilh Eric Eilertson Manuel Prieto Matias Eric Grobelny Manuel Pro´spero dos Santos Eugenius Kaszkurewicz Marc Pantel Fernando Alvarruiz Marchand Corine Gabriel Antoniu Matt Radlinski Ga¨el Utard Michael Steinbach Germ´an Molto´ Myrian C.A. Costa Gerson Zaverucha Nicolas Chepurnyi Gregory Mounie Nuno Correia Guillaume Huard Olivier Richard G´erard Padiou Pascal Henon Helge Avlesen Paulo Lopes Hui Xiong Pedro Medeiros Hung-Hsun Su Pierre Ramet Ian A. Troxel Ragnhild Blikberg Ignacio Blanquer Rajagopal Subramaniyan Inˆes de Castro Dutra Ramesh Balasubramanian J. Magalha˜es Cruz Sarp Oral J.M. Nlong Uygar Oztekin Jan-Frode Myklebust Yves Denneulin Jean-Baptiste Caillau Yvon J´egou Jean-Louis Pazat Table of Contents Chapter 1: Large Scale Computations Large Scale Simulations Sato Tetsuya .................................................. 1 Development and Integration of Parallel Multidisciplinary Computational Software for Modeling a Modern Manufacturing Process Brian J. Henz, Dale R. Shires, Ram V. Mohan .................... 10 Automatically Tuned FFTs for BlueGene/L’s Double FPU Franz Franchetti, Stefan Kral, Juergen Lorenz, Markus Pu¨schel, Christoph W. Ueberhuber ....................................... 23 A Survey of High-Quality Computational Libraries and Their Impact in Science and Engineering Applications Leroy A. Drummond, Vicente Hernandez, Osni Marques, Jose E. Roman, Vicente Vidal ................................... 37 A Performance Evaluation of the Cray X1 for Scientific Applications Leonid Oliker, Rupak Biswas, Julian Borrill, Andrew Canning, Jonathan Carter, M. Jahed Djomehri, Hongzhang Shan, David Skinner ................................................. 51 Modelling Overhead of Tuple Spaces with Design of Experiments Frederic Hancke, Tom Dhaene, Jan Broeckhove .................... 66 Analysis of the Interaction of Electromagnetic Signals with Thin-Wire Structures. Multiprocessing Issues for an Iterative Method Ester Mart´ın Garzo´n, Siham Tabik, Amelia Rubio Bretones, Inmaculada Garc´ıa............................................. 78 A Performance Prediction Model for Tomographic Reconstruction in Structural Biology Paula Cecilia Fritzsche, Jos´e-Jesu´s Ferna´ndez, Ana Ripoll, Inmaculada Garc´ıa, Emilio Luque................................ 90 Chapter 2: Data Management and Data Mining Data Management in Large-Scale P2P Systems Patrick Valduriez, Esther Pacitti................................. 104