Lecture Notes in Computer Science 8500

Lecture Notes in Computer Science 8500 Commenced Publication in 1973 Founding and Former Series Editors: Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen Editorial Board David Hutchison Lancaster University, UK Takeo Kanade Carnegie Mellon University, Pittsburgh, PA, USA Josef Kittler University of Surrey, Guildford, UK Jon M. Kleinberg Cornell University, Ithaca, NY, USA Alfred Kobsa University of California, Irvine, CA, USA Friedemann Mattern ETH Zurich, Switzerland John C. Mitchell Stanford University, CA, USA Moni Naor Weizmann Institute of Science, Rehovot, Israel Oscar Nierstrasz University of Bern, Switzerland C. Pandu Rangan Indian Institute of Technology, Madras, India Bernhard Steffen TU Dortmund University, Germany Demetri Terzopoulos University of California, Los Angeles, CA, USA Doug Tygar University of California, Berkeley, CA, USA Gerhard Weikum Max Planck Institute for Informatics, Saarbruecken, Germany

Marian Bubak Jacek Kitowski Kazimierz Wiatr (Eds.) escience on Distributed Computing Infrastructure Achievements of PLGrid Plus Domain-Specific Services and Tools 13

Volume Editors Marian Bubak AGH University of Science and Technology Department of Computer Science and ACC Cyfronet AGH Kraków, Poland E-mail: bubak@agh.edu.pl Jacek Kitowski AGH University of Science and Technology Department of Computer Science and ACC Cyfronet AGH Kraków, Poland E-mail: kito@agh.edu.pl Kazimierz Wiatr AGH University of Science and Technology ACC Cyfronet AGH and Department of Electronics Kraków, Poland E-mail: k.wiatr@cyfronet.pl ISSN 0302-9743 e-issn 1611-3349 ISBN 978-3-319-10893-3 e-isbn 978-3-319-10894-0 DOI 10.1007/978-3-319-10894-0 Springer Cham Heidelberg New York Dordrecht London Library of Congress Control Number: 2014946919 LNCS Sublibrary: SL 3 Information Systems and Application, incl. Internet/Web and HCI Springer International Publishing Switzerland 2014 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work. Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher s location, in ist current version, and permission for use must always be obtained from Springer. Permissions for use may be obtained through RightsLink at the Copyright Clearance Center. Violations are liable to prosecution under the respective Copyright Law. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made. The publisher makes no warranty, express or implied, with respect to the material contained herein. Typesetting: Camera-ready by author, data conversion by Scientific Publishing Services, Chennai, India Printed on acid-free paper Springer is part of Springer Science+Business Media (www.springer.com)

Preface Nowadays, science requires powerful e-infrastructures: computing, data storage, visualization, and networking. One such e-infrastructure was built in Poland in the years 2009-2012, in the framework of the PLGrid project, whose main results were presented in the book: Marian Bubak, Tomasz Szepieniec, Kazimierz Wiatr (Eds.): Building a National Distributed e-infrastructure PLGrid, Scientific and Technical Achievements. Lecture Notes in Computer Science, vol. 7136. Springer 2012, ISBN 978-3-642-28266-9. In spite of this progress, for many domain scientists direct, efficient, and transparent usage of such e-infrastructures often remains relatively difficult and time-consuming. Scientists frequently require assistance and close collaboration with service providers in order to access computational resources. Due to the diversity of scientists requirements, a number of domain-specific computing environments have been developed. These include solutions, services, and extended infrastructures (including software) tailored to the needs of various groups of scientists. Such an effort has been undertaken in the framework of the PLGrid Plus project, the main results of which are presented in this book. To help researchers from different areas of science understand and unlock the potential of the Polish Grid Infrastructure and to define their requirements and expectations, the following 13 pilot communities have been organized and involved in the PLGrid Plus project, helping refine and enhance the shared e- infrastructure: Acoustics, AstroGrid-PL, Bioinformatics, Ecology, Energy Sector, Health Sciences, HEPGrid, Life Science, Materials, Metallurgy, Nanotechnologies, Quantum Chemistry and Molecular Physics, and SynchroGrid. Introduction of domain-oriented solutions for these communities enables various research groups of users to make further use of scientific data and computations. However, the scope is not limited to selected domains: indeed, by applying the generic infrastructure services more custom-tailored solutions, integration of new groups should proceed smoothly and at lower cost. The book describes the experience and scientific results attained by project partners and the outcome of research and development activities carried out within the project. The book is split into three parts: the first (chapters 1 to 8) provides a general overview of research and development activities in the framework of the PLGrid Plus project with emphasis on services for different scientific areas and an update on the status of the PLGrid e-infrastructure, describing new developments in security and middleware. The second part (chapters 9 to 13) discusses new environments and services, which may be applied by all of the communities mentioned above. The third part (chapters 14 to 36) presents how the PLGrid Plus environments, tools and services are used by advanced domainspecific computer simulations performed by individual groups of researchers. These chapters present computational models, new algorithms, and ways, in

VI Preface which they are implemented with available tools and services. The book also provides a glossary of important terms and concepts. We hope that this book, much like its predecessor mentioned at the beginning of this preface, will serve as an important intellectual resource for researchers, developers, and system administrators working on efficient exploitation of available e-infrastructures, promoting collaboration and exchange of ideas in the process of constructing a common European e-infrastructure. We owe our thanks to all authors and reviewers for their diligent work in ensuring quality of this publication. We would like to express our sincere gratitude to Zofia Mosurska and Robert Paj ak for their enthusiastic day-to-day management of the editorial process, for collecting new versions of papers and liaising with reviewers. We are also indebted to Bartosz Baliś, W lodzimierz Funika, Joanna Kocot, Piotr Nowakowski, and Milena Zaj ac for their editorial contributions. Finally, we wish to thank Springer Verlag for very fruitful collaboration at all stages of the book s preparation. We invite you to visit the PLGrid Plus web site (http://www.plgrid.pl/en), which carries up-to-date information regarding our e-infrastructure. July 2014 Marian Bubak Jacek Kitowski Kazimierz Wiatr Acknowledgments. This book, like all PLGrid Plus project activities, was cofunded by the European Regional Development Fund as part of the Innovative Economy Program.

Book Preparation This book was prepared with the help of the members of the PLGrid Plus project. Editors Support Team Help in editing the book: English proofreading: R. Paj ak, M. Zaj ac B. Baliś,W.Funika,J.Kocot,P.Nowakowski Reviewers P. Ba la M. Baranowski A. Belloum K. Benedyczak A. Bożek I. Campos R. Cushing M. Czuchry C. Engwer N. Ferreira M. Filocha P. Flaszyński W. Funika (2x) P. Goryl P. Grabowski D. Groen T. Guba la M. Hanasz I. Hidalgo-Gonzalez (2x) S. Jezequel M. Kasztelnik M. Kȩsek J. Kocot J. Komasa J. Koz lowska D. Kranzlmueller V. Krzhizhanovskaya M. Krzyżanowski M. Kupczyk J. Kusiak W. Kuś A. Kwiecień (2x) L. Madej G. Mazur J. Meizner N. Meyer K. Michalek Z. Mosurska J. Mrozek K. Muszka K. Noga A. Olszewski P. Pa lka G. Papanikolaou P. Petrov M. Pietrzyk T. Piontek M. P lóciennik (2x) P. Rafaj L. Rauch (2x) M. Romberg R. Różańska J. Rybicki (2x) K. Rycerz (2x) M. Schaap B. Schuller H. Siejkowski (2x) G. Siemieniec-Oziȩb lo M. Sitko P. Siudek R. S lota M. Stahl M. Sterzel M. Stolarek C. Straube W. Suwa la T. Szepieniec R. Szwaba T. Szymocha (2x) J. Świrydczuk M. Tomanek I. Tsukrov M. Uchroński P. Wolniewicz (2x) M. Zdyba l W. Ziajka

Table of Contents Domain-Specific Services in Polish e-infrastructure... 1 Jacek Kitowski, Kazimierz Wiatr, Lukasz Dutka, Tomasz Szepieniec, Mariusz Sterzel, and Robert Paj ak National Distributed High Performance Computing Infrastructure for PL-Grid Users... 16 Pawe l Dziekoński, Franciszek Klajn, Lukasz Flis, Patryk Lasoń, Marek Magryś, Andrzej Oziȩb lo, Rados law Rowicki, Marcin Stolarek, Dominik Bartkiewicz, Marek Zawadzki, Marcin Pospieszny, Rafa l Miko lajczak, Maciej Brzeźniak, Norbert Meyer, and Marcin Samson New QosCosGrid Middleware Capabilities and Its Integration with European e-infrastructure... 34 Bartosz Bosak, Piotr Kopta, Krzysztof Kurowski, Tomasz Piontek, and Mariusz Mamoński Recent Advances of the Cloud Platform Delivered in the Infrastructure as a Service Model for the PL-Grid Scientific Communities... 54 Jan Meizner, Maciej Nabożny, Marcin Radecki, Tomasz Szepieniec, and Mi losz Zdyba l Multilayered IT Security Requirements and Measures for the Complex Protection of Polish Domain-Specific Grid Infrastructure... 61 Bart lomiej Balcerek, Gerard Frankowski, Agnieszka Kwiecień, Norbert Meyer, Micha l Nowak, and Adam Smutnicki Reservations for Compute Resources in Federated e-infrastructure... 80 Marcin Radecki, Tadeusz Szymocha, Tomasz Piontek, Bartosz Bosak, Mariusz Mamoński, Pawe l Wolniewicz, Krzysztof Benedyczak, and Rafa l Kluszczyński Improving PL-Grid Operations Based on FitSM Standard... 94 Marcin Radecki, Tadeusz Szymocha, Tomasz Szepieniec, and Roksana Różańska Integrating Slurm Batch System with European and Polish Grid Infrastructures... 106 Dominik Bartkiewicz, Krzysztof Benedyczak, Rafa l Kluszczyński, Marcin Stolarek, and Tomasz Rȩkawek

X Table of Contents Towards Provisioning of Reproducible, Reviewable and Reusable In-Silico Experiments with the GridSpace2 Platform... 118 Eryk Ciepiela, Bartosz Wilk, Daniel Harȩżlak, Marek Kasztelnik, Maciej Pawlik, and Marian Bubak A Framework for Domain-Specific Science Gateways... 130 Joanna Kocot, Tomasz Szepieniec, Piotr Wójcik, Micha l Trzeciak, Maciej Golik, Tomasz Grabarczyk, Hubert Siejkowski, and Mariusz Sterzel Easy Development and Integration of Science Gateways with Vine Toolkit... 147 Krzysztof Kurowski, Piotr Dziubecki, Piotr Grabowski, Micha l Krysiński, Tomasz Piontek, and Dawid Szejnfeld A Lightweight Method of Metadata and Data Management with DataNet... 164 Daniel Harȩżlak, Marek Kasztelnik, Maciej Pawlik, Bartosz Wilk, and Marian Bubak Uniform and Efficient Access to Data in Organizationally Distributed Environments... 178 Lukasz Dutka, Renata S lota, Micha l Wrzeszcz, Dariusz Król, and Jacek Kitowski Enabling Multiscale Fusion Simulations on Distributed Computing Resources... 195 Katarzyna Rycerz, Marian Bubak, Eryk Ciepiela, Maciej Pawlik, Olivier Hoenen, Daniel Harȩżlak, Bartosz Wilk, Tomasz Guba la, Jan Meizner, and David Coster Auxiliar Experimentorum An Innovative Approach for Creating and Deploying Scientific Applications... 211 Miko laj M. Miko lajczyk, Mariusz Uchroński, Kamil Mowiński, Marcin Lubimow, Sebastian Bijak, Marcin Teodorczyk, Mariusz Hruszowiec, Sebastian Szkoda, Bartosz Majster, Grzegorz Banach, and Mateusz Tykierko Domain-Oriented Services for High Energy Physics in Polish Computing Centers... 226 Krzysztof Nawrocki, Andrzej Olszewski, Adam Padée, Anna Padée, Mariusz Witek, Piotr Wójcik, and Mi losz Zdyba l Services for Synchrotron Deployment and Operation... 238 Tadeusz Szymocha, Marek Stankiewicz, Adriana Wawrzyniak, Piotr Goryl, Marcin Zaj ac, Marcin Nowak, Lukasz Żytniak, and Fryderyk Melka

Table of Contents XI Comprehensive Support for Chemistry Computations in PL-Grid Infrastructure... 250 Andrzej Eilmes, Mariusz Sterzel, Tomasz Szepieniec, Joanna Kocot, Klemens Noga, and Maciej Golik Supercomputing Grid-Based Services for Hearing Protection and Acoustical Urban Planning, Research and Education... 263 Maciej Szczodrak, Andrzej Czyżewski, Józef Kotus, and Bożena Kostek Kepler-Based Workflow Environment for Astronomy... 278 Pawe l Cieciel ag, Marcin P lóciennik, Piotr Spyra, Micha l Urbaniak, Tomasz Żok, Wojciech Pych, and Arkadiusz Hypki High Performance Astrophysical Fluid Simulations Using InSilicoLab Framework... 293 Micha l Hanasz, Kacper Kowalik, Artur Gawryszczak, and Dominik Wóltański Services for Astronomical Data Management and Sharing... 305 Tomasz Kundera, Greg Stachowski, Arkadiusz Wierzbowski, Jerzy Borkowski, and Pawe l Cieciel ag A Modern Tool for Modelling and Optimisation of Production in Underground Coal Mine... 317 Edyta Brzychczy Automatic Monitoring as a Tool for Collection of Information on Fitophenological Cycle... 335 Przemys law Mager, Ma lgorzata Kȩpińska-Kasprzak, Norbert Meyer, Szymon Mueller, Dominik Stok losa, Wanda Wójtowicz, and Joanna Jaskulska Preliminary Data Classification in COMPASS Experiment Using HEP-Grid Tools... 351 Anna Padée Application of Sensitivity Analysis to Grid-Based Procedure Dedicated to Creation of SSRVE... 364 Lukasz Rauch, Danuta Szeliga, Daniel Bachniak, Krzysztof Bzowski, and Maciej Pietrzyk Optimization of Profile Extrusion Processes Using the Finite Element Method and Distributed Computing... 378 Andrzej Milenin and Piotr Kustra Adaptive Finite Element Modelling of Welding Processes... 391 Krzysztof Banaś, Kazimierz Ch loń, Pawe l Cybu lka, Kazimierz Michalik, Przemys law P laszewski, and Aleksander Siwek

XII Table of Contents Numerical Simulation of the Continuous Casting of Steel on a Grid Platform... 407 Lechos law Trȩbacz, Katarzyna Mi lkowska-piszczek, Krzysztof Konopka, and Jan Falkus Experimental and Numerical Database of EU Research Projects Investigating Shock Wave-Boundary Layer Interaction in Transonic/Supersonic Flows... 419 Piotr Doerffer and Oskar Szulc Aerodynamic and Aero-acoustic Analysis of Helicopter Rotor Blades in Hover... 429 Piotr Doerffer, Oskar Szulc, Fernando Tejero Embuena, and Javier Martinez Suarez Parallelization of the Monte Carlo Static Recrystallization Model... 445 Lukasz Madej and Mateusz Sitko Convergence of Explicitly Correlated Gaussian Wave Functions... 459 Piotr Kopta, Tomasz Piontek, Krzysztof Kurowski, Mariusz Puchalski, and Jacek Komasa Analysing a Power Generation Sector Using the MILP Approach... 475 Jacek Kamiński, Przemys law Kaszyński, and Tomasz Mirowski Modelling the Long-Term Development of an Energy System with the Use of a Technology Explicit Partial Equilibrium Model... 489 Artur Wyrwa, Marcin Pluta, Szymon Skoneczny, and Tomasz Mirowski Assessment of Environmental Impacts of Energy Scenarios Using the πesa Platform... 504 Artur Wyrwa, Janusz Zyśk, and Tomasz Mirowski Glossary of Terms... 519 Author Index... 533 Subject Index... 535