Lecture Notes in Computer Science 7136

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1 Lecture Notes in Computer Science 7136 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 Madhu Sudan Microsoft Research, Cambridge, MA, USA 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

2 Marian Bubak Tomasz Szepieniec Kazimierz Wiatr (Eds.) Building a National Distributed e-infrastructure PL-Grid Scientific and Technical Achievements 13

3 Volume Editors Marian Bubak AGH University of Science and Technology Department of Computer Science and ACC Cyfronet AGH Kraków, Poland Tomasz Szepieniec AGH University of Science and Technology ACC Cyfronet AGH Kraków, Poland Kazimierz Wiatr AGH University of Science and Technology ACC Cyfronet AGH and Department of Electronics Kraków, Poland ISSN e-issn ISBN e-isbn DOI / Springer Heidelberg Dordrecht London New York Library of Congress Control Number: CR Subject Classification (1998): C.2, H.4, I.2, D.2, H.3, F.1 LNCS Sublibrary: SL 3 Information Systems and Application, incl. Internet/Web and HCI Springer-Verlag Berlin Heidelberg 2012 This work is subject to copyright. All rights are reserved, whether the whole or part of the material is concerned, 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 publication or 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 liable to prosecution under the German Copyright Law. The use of general descriptive names, registered names, trademarks, 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. 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 (

4 Preface The main objective of the PL-Grid project was to provide the Polish scientific community with a grid-based e-infrastructure enabling research in various domains of e-science. Our infrastructure supports scientific investigations by integrating experimental data and results of advanced computer simulations carried out by geographically distributed research teams. PL-Grid not only extends the amount of computational resources provided to the Polish scientific community by 215 Tflops of computing power and 2500 TB of storage space, but more importantly facilitates effective use of these resources by providing innovative grid services and end-user tools, as well as continuous technical support. Extensive collaboration between project developers and domain scientists has led to the release of new domain-specific services and applications. Another important achievement of PL-Grid was the introduction of a professional separation of responsibilities upon which the infrastructure is based. This organizational schema enables better user support and ensures consistent quality of service, in line with European Commission policies which actively encourage development and integration of distributed computing infrastructures under the EGI InSPIRE and PRACE umbrella projects. This book describes the experience and the scientific results obtained by the project partners as well as the outcome of research and development activities carried out within the project. The first chapter provides an overview of motivation, current status and future development within the PL-Grid e-infrastructure. The second chapter presents the way in which three main grid middleware suites (glite, UNICORE and QosCosGrid) are integrated in the PL-Grid platform and extended with additional support services. The third chapter describes the experience and current status of service operations. This is followed by three chapters which provide details on the middleware implemented in PL-Grid. The next four chapters are dedicated to essential security mechanisms, including the tools and security solutions implemented in our e-infrastructure. We also present chapters devoted to new methods of infrastructure monitoring, storage provisioning and implementation of service level agreements. Subsequently, seven consecutive chapters provide an in-depth description of user environments: the Eclipse Parallel Tools Platform integrated with QosCosGrid, the Migrating Desktop, Science Gateways based on the Vine Toolkit, the GridSpace Experiment Platform, and the InSilico- Lab environment. A very important contribution to the book comes in the form of five chapters prepared by end-user teams. They describe how the PL-Grid middleware and infrastructure are applied to solving such scientific problems as grain morphology analysis, seeking common structural motifs in protein families, chemistry computations, molecular dynamics models, LHC computing, and

5 VI Preface Monte Carlo simulations for the Cherenkov Telescope Array. Finally, the last two chapters describe activities which are of great importance in any emerging computing infrastructure namely, training and dissemination. The book is supplemented with a glossary of terms. We hope that it will serve as an important intellectual resource for researchers, developers and system administrators working on their own grid infrastructures and promote 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 which ensures the high quality of this book. We would like to express our gratitude to Jacek Kitowski, Director of PL-Grid, for his personal involvement. We are also indebted to Zofia Mosurska, Robert Paj ak, Milena Zaj ac, Piotr Nowakowski, Magdalena Szopa, and Joanna Kocot for their enthusiastic editorial work, as well as to numerous colleagues from ACC Cyfronet AGH for their help. Finally, we wish to thank Springer for the fruitful collaboration during the preparation of the book. We invite you to visit the PL-Grid website ( which carries up-to-date information regarding our e-infrastructure. This book, like all PL-Grid project activities, was co-funded by the European Regional Development Fund as part of the Innovative Economy Program. December 2011 Marian Bubak Tomasz Szepieniec Kazimierz Wiatr

6 Book Preparation This book was prepared with the help of the members of the PL-Grid project. Editors Support Team Help in editing the book: English proofreading: Z. Mosurska, R. Paj ak and M. Zaj ac J. Kocot, P. Nowakowski and M. Szopa Reviewers P. Ar lukowicz P. Ba la T. Bartyński K. Benedyczak M. Borcz B. Bosak M. Bubak E. Ciepiela L. Dutka A. Eilmes M. Filocha L. Flis G. Frankowski W. Funika T. Guba la D. Harȩżlak T. Jadczyk M. Jarz ab M. Kasztelnik J. Kocot P. Kopta J. Kosiński M. Krakowian B. Kryza K. Kurowski M. Malawski M. Mamoński J. Meizner N. Meyer D. Niko low K. Nowiński L. Olejnik A. Oziȩb lo B. Palak T. Piontek M. Radecki I. Roterman K. Rycerz R. S lota M. Sterzel B. Szurgot T. Szymocha M. Teodorczyk M. Tomanek M. Tura la M. Tykierko R. Tylman M. Uchroński W. Waga W. Wiślicki M. Witek P. Wolniewcz S. Zieliński

7 Table of Contents List of Contributions PL-Grid: Foundations and Perspectives of National Computing Infrastructure... 1 Jacek Kitowski, Micha l Tura la, Kazimierz Wiatr, and Lukasz Dutka Integrating Various Grid Middleware Components and User Services into a Single Platform Marcin Radecki, Tadeusz Szymocha, Daniel Harȩżlak, Maciej Pawlik, Jakub Andrzejewski, Wojciech Ziajka, and Marcin Szelc Towards Professional Service Operations in Grids Marcin Radecki, Tomasz Szepieniec, Tadeusz Szymocha, Magda Szopa, and Ma lgorzata Krakowian New Capabilities in QosCosGrid Middleware for Advanced Job Management, Advance Reservation and Co-allocation of Computing Resources Quantum Chemistry Application Use Case Bartosz Bosak, Jacek Komasa, Piotr Kopta, Krzysztof Kurowski, Mariusz Mamoński, and Tomasz Piontek Seamless Access to the PL-Grid e-infrastructure Using UNICORE Middleware Krzysztof Benedyczak, Marcin Stolarek, Rados law Rowicki, Rafa l Kluszczyński, Marcelina Borcz, Grzegorz Marczak, Maciej Filocha, and Piotr Ba la User-Oriented Provisioning of Secure Virtualized Infrastructure Marcin Jarz ab, Jacek Kosiński, Krzysztof Zieliński, and S lawomir Zieliński Flexible and Extendable Mechanism Enabling Secure Access to e-infrastructures and Storage of Confidential Data for the GridSpace2 Virtual Laboratory Jan Meizner, Eryk Ciepiela, Piotr Nowakowski, Joanna Kocot, Maciej Malawski, and Marian Bubak

8 X Table of Contents SARA System for Inventory and Static Security Control in a Grid Infrastructure Gerard Frankowski and Micha l Rzepka ACARM-ng: Next Generation Correlation Framework Bart lomiej Balcerek, Bartosz Szurgot, Mariusz Uchroński, and Wojciech Waga Security Best Practices: Applying Defense-in-Depth Strategy to Protect the NGI PL Bart lomiej Balcerek, Gerard Frankowski, Agnieszka Kwiecień, Adam Smutnicki, and Marcin Teodorczyk Automation of System Monitoring Based on Fuzzy Logic or Rules; Comparison of Two Designed Approaches with Regard to Computational Infrastructures W lodzimierz Funika, Filip Szura, and Jacek Kitowski A Toolkit for Storage QoS Provisioning for Data-Intensive Applications Renata S lota, Dariusz Król, Kornel Ska lkowski, Bartosz Kryza, Darin Niko low, Micha l Orzechowski, and Jacek Kitowski Implementation of Service Level Management in PL-Grid Infrastructure Tomasz Szepieniec, Ma lgorzata Tomanek, Marcin Radecki, Magda Szopa, and Marian Bubak Highly Integrated Environment for Parallel Application Development Using QosCosGrid Middleware Bartosz Bosak, Jan Konczak, Krzysztof Kurowski, Mariusz Mamoński, and Tomasz Piontek User-Friendly Frameworks for Accessing Computational Resources Bartek Palak, Pawe l Wolniewicz, Marcin P lóciennik, Micha l Owsiak, and Tomasz Żok Online Web-Based Science Gateway for Nanotechnology Research Piotr Dziubecki, Piotr Grabowski, Micha l Krysiński, Tomasz Kuczyński, Krzysztof Kurowski, Tomasz Piontek, and Dawid Szejnfeld Scripting Language Extensions Offered by the GridSpace Experiment Platform Daniel Harȩżlak, Marek Kasztelnik, Eryk Ciepiela, and Marian Bubak

9 Table of Contents XI Managing Entire Lifecycles of e-science Applications in the GridSpace2 Virtual Laboratory From Motivation through Idea to Operable Web-Accessible Environment Built on Top of PL-Grid e-infrastructure Eryk Ciepiela, Piotr Nowakowski, Joanna Kocot, Daniel Harȩżlak, Tomasz Guba la, Jan Meizner, Marek Kasztelnik, Tomasz Bartyński, Maciej Malawski, and Marian Bubak GridSpace2 Virtual Laboratory Case Study: Implementation of Algorithms for Quantitative Analysis of Grain Morphology in Self-assembled Hexagonal Lattices According to the Hillebrand Method Eryk Ciepiela, Leszek Zaraska, and Grzegorz D. Sulka Examining Protein Folding Process Simulation and Searching for Common Structure Motifs in a Protein Family as Experiments in the GridSpace2 Virtual Laboratory Tomasz Jadczyk, Maciej Malawski, Marian Bubak, and Irena Roterman InSilicoLab Managing Complexity of Chemistry Computations Joanna Kocot, Tomasz Szepieniec, Daniel Harȩżlak, Klemens Noga, and Mariusz Sterzel Ab Initio Molecular Dynamics Simulations of Ketocyanine Dyes in Organic Solvents Andrzej Eilmes Polish Contribution to the Worldwide LHC Computing Artur Binczewski, Micha l Bluj, Antoni Cyz, Micha l Dwużnik, Maciej Filocha, Lukasz Flis, Ryszard Gokieli, Jaros law Iwaszkiewicz, Marek Kowalski, Patryk Lasoń, Rafa l Lichwa la, Micha l Lopuszyński, Marek Magryś, Piotr Malecki, Norbert Meyer, Krzysztof Nawrocki, Andrzej Olszewski, Andrzej Oziȩb lo, Adam Padée, Henryk Pa lka, Marcin Pospieszny, Marcin Radecki, Rados law Rowicki, Dorota Stojda, Marcin Stolarek, Tomasz Szepieniec, Tadeusz Szymocha, Micha l Tura la, Karol Wawrzyniak, Wojciech Wiślicki, Mariusz Witek, and Pawe l Wolniewicz PL-Grid e-infrastructure for the Cherenkov Telescope Array Observatory Anna Barnacka, Leszek Bogacz, Micha l Gochna, Mateusz Janiak, Nukri Komin, Giovanni Lamanna, Rafa l Moderski, and Ma lgorzata Siudek

10 XII Table of Contents Training in the PL-Grid as Key Component to Attract Users to Grid e-infrastructures Marcelina Borcz, Krzysztof Benedyczak, Adam Padée, Rafa l Kluszczyński, Grzegorz Marczak, Miros law Zdybek, Maciej Pawlik, Maciej Filocha, and Piotr Ba la Dissemination Activities Conducted within the PL-Grid Project as a Successful Means of Promotion of Its Offer and Achievements Robert Paj ak and Zofia Mosurska Glossary of Terms Subject Index Author Index