Science Gateways for Distributed Computing Infrastructures: Development Framework and Exploitation by Scientific User Communities

308 Pages·2014·8.628 MB·English

by  Péter Kacsuk (eds.)

Péter Kacsuk Editor
Science Gateways
for Distributed
Computing
Infrastructures
Development Framework and
Exploitation by Scientific User
Communities
Science Gateways for Distributed Computing
Infrastructures
é
P ter Kacsuk
Editor
Science Gateways for
Distributed Computing
Infrastructures
Development Framework and Exploitation by
Scientific User Communities
123
Editor
Péter Kacsuk
Laboratory ofParallel andDistributed
Systems
HungarianAcademy ofSciences (MTA)
Budapest
Hungary
ISBN 978-3-319-11267-1 ISBN 978-3-319-11268-8 (eBook)
DOI 10.1007/978-3-319-11268-8
LibraryofCongressControlNumber:2014951697
SpringerChamHeidelbergNewYorkDordrechtLondon
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Acknowledgments
I would like to say thanks to all the SCI-BUS partners, subcontractors and asso-
ciated members for their constant feedback by which they helped with continuous
improvement of the SCI-BUS technology. I owe special thanks to Tibor Gottdank
for his help in editing the book.
Peter Kacsuk
Coordinator of SCI-BUS
SCI-BUS project: Chaps. 1–19
ThisworkisfinanciallysupportedbytheSCI-BUSprojectfundedbyEuropean
Union Seventh Framework Programme (FP7/2007-2013) under grant agreement
no. 28348.
ER-flow project: Chaps. 5, 9, 10, 11, and 18
The research leading to these results has received funding from the European
UnionSeventhFrameworkProgramme(FP7/2007-2013)undergrantagreementno
312579 (ER-Flow).
agINFRA project: Chap. 17
TheagINFRAsection, whichissupportedbyEUFP7-InfrastructuresagINFRA
project no. 283770, was written in close contribution with Charalampos Thanop-
oulos, Nikos Manolis, and Andreas Drakos from AgroKnow and Valeria Pesce
from FAO. The authors would like to say a special thank you to the project
coordinator, Miguel-Angel Sicilia.
CloudSME project: Chaps. 5 and 19
TheresearchleadingtotheseresultsreceivedfundingfromtheEuropeanUnion
Seventh Framework Programme (FP7/2007-2013) under grant agreement no.
608886 (CloudSME).
SHIWA project: Chap. 9
The development of the Coarse-Grained Interoperability concept and the SHI-
WA Simulation Platform was supported by the EU funded FP7 Sharing Interop-
erable Workflow for Large-Scale Scientific Simulation on Available DCIs
(SHIWA) project (grant no. 261585).
v
vi Acknowledgments
VIALACTEA project: Chap. 5
The research leading to these results has received funding from the European
Union Seventh Framework Programme (FP7/2007-2013) under grant agreement
no. 607380 (VIALACTEA).
Further Acknowledgments
Chapter 10: We thank the colleagues who participated in the development,
deployment and testing of the AMC-NSG: Paul F.C. Groot, Hurng-Chun Lee,
Mostapha al Mourabit, Mark Santcroos, Gerbrand Spaans and Jalmar Teeuw.
ThisworkisfinanciallysupportedbytheCOMMITproject“e-Biobankingwith
imaging for healthcare”, funded by the Nederlandse Organisatie voor Wet-
enschappelijk Onderzoek (Netherlands Organization for Scientific Research,
NWO), and the HPCN UvA project “Computational Neuroscience Gateway”,
funded by the University of Amsterdam.
Chapter 11: The authors would like to thank the German Federal Ministry of
EducationandResearch(BMBF)fortheopportunitytodoresearchintheMoSGrid
project (reference 01IG09006).
The research leading to these results has also partially been supported by the
LSDMA project of the Helmholtz Association of German Research Centers. Spe-
cialthanksareduetoNGI-DEformanagingtheGermanGridinfrastructureandall
compute centres supporting MoSGrid.
Chapter14:TheauthorsareparticularlygratefultoProf.PeterGallagherandhis
team for the invaluable help and support.
Chapter 15: This work was supported in part by the Ministry of Education,
Science and Technological Development of the Republic of Serbia under projects
ON171017,III43007andNAI-DBEC;byGermanAcademicandExchangeService
(DAAD) under project; NAI-DBEC; and by the European Commission under EU
FP7projectSCI-BUS(grantno.283481),PRACE-3IP(grantno.312763),HP-SEE
(grant no. 261499) and EGI-InSPIRE (grant no. 261323).
Chapter17:TheauthorsoftheVERCEsciencegatewaysection,whoseworkis
supported by EU FP7-Infrastructures VERCE project (no. 283543), represent a
larger team including Emanuele Cesarotti, Claudia Ramos Garcia, Leong Siew
Hoon,AmreyKrause, LionKrischer, Federica Magnoni,Jonas Matser and Visakh
Muraleedharan, who contributed to the implementation.
The authors of the DRIHM Gateway section, which is supported by EU FP7-
Infrastructures DRIHM (project no. 28356), are only representatives of a larger
team composed of Andrea Clematis, Antonella Galizia, Alfonso Quarati. Luca
Roverelli and Gabriele Zereik from CNR-IMATI; and Dieter Kranzlmüller, Nils
GentschenFeldeandChristianStraubefromLMU.Theywouldliketosayaspecial
thank you to the project coordinator, Antonio Parodi.
Contents
Part I WS-PGRADE/gUSE Science Gateway Framework
1 Introduction to Science Gateways and Science Gateway
Frameworks. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Péter Kacsuk
2 Introduction to the WS-PGRADE/gUSE Science Gateway
Framework . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Tibor Gottdank
3 Workflow Concept of WS-PGRADE/gUSE. . . . . . . . . . . . . . . . . . 33
Ákos Balaskó
4 DCI Bridge: Executing WS-PGRADE Workflows
in Distributed Computing Infrastructures . . . . . . . . . . . . . . . . . . 51
Miklos Kozlovszky, Krisztián Karóczkai, István Márton,
Péter Kacsuk and Tibor Gottdank
5 Remote Storage Resource Management
in WS-PGRADE/gUSE. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
Ákos Hajnal, Zoltán Farkas, Péter Kacsuk and Tamás Pintér
6 WS-PGRADE/gUSE Security . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Zoltán Farkas
7 WS-PGRADE/gUSE and Clouds. . . . . . . . . . . . . . . . . . . . . . . . . 97
Zoltán Farkas, Ákos Hajnal and Péter Kacsuk
vii
viii Contents
8 Developing Science Gateways at Various Levels
of Granularity Using WS-PGRADE/gUSE. . . . . . . . . . . . . . . . . . 111
Tamás Kiss, Gábor Terstyánszky, Péter Borsody,
Péter Kacsuk and Ákos Balaskó
9 Sharing Science Gateway Artefacts Through Repositories. . . . . . . 123
Gábor Terstyánszky, Edward Michniak, Tamás Kiss
and Ákos Balaskó
Part II Domain-Specific Science Gateways Customized
from the WS-PGRADE/gUSE Framework
10 Computational Neuroscience Gateway: A Science Gateway
Based on the WS-PGRADE/gUSE. . . . . . . . . . . . . . . . . . . . . . . . 139
Shayan Shahand, Mohammad Mahdi Jaghoori,
Ammar Benabdelkader, Juan Luis Font-Calvo, Jordi Huguet,
Matthan W.A. Caan, Antoine H.C. van Kampen
and Sílvia D. Olabarriaga
11 Molecular Simulation Grid (MoSGrid): A Science Gateway
Tailored to the Molecular Simulation Community . . . . . . . . . . . . 151
Sandra Gesing, Jens Krüger, Richard Grunzke,
Luis de la Garza, Sonja Herres-Pawlis and Alexander Hoffmann
12 Statistical Seismology Science Gateway . . . . . . . . . . . . . . . . . . . . 167
Çelebi Kocair, Cevat Şener and Ayşen D. Akkaya
13 VisIVO Gateway and VisIVO Mobile for the Astrophysics
Community . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 181
Eva Sciacca, Fabio Vitello, Ugo Becciani,
Alessandro Costa and Piero Massimino
14 HELIOGate, a Portal for the Heliophysics Community . . . . . . . . 195
Gabriele Pierantoni and Eoin Carley
15 Science Gateway for the Serbian Condensed Matter
Physics Community . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
Dušan Vudragović and Antun Balaž
Contents ix
Part III Further Applications of WS-PGRADE/gUSE
16 WS-PGRADE/gUSE-Based Science Gateways in Teaching . . . . . . 223
Sílvia Delgado Olabarriaga, Ammar Benabdelkader,
Matthan W.A. Caan, Mohammad Mahdi Jaghoori,
Jens Krüger, Luis de la Garza, Christopher Mohr,
Benjamin Schubert, Anatoli Danezi and Tamas Kiss
17 WS-PGRADE/gUSE in European Projects. . . . . . . . . . . . . . . . . . 235
Tamás Kiss, Péter Kacsuk, Róbert Lovas, Ákos Balaskó,
Alessandro Spinuso, Malcolm Atkinson, Daniele D’Agostino,
Emanuele Danovaro and Michael Schiffers
18 Creating Gateway Alliances Using WS-PGRADE/gUSE . . . . . . . . 255
Ugo Becciani, Eva Sciacca, Alessandro Costa, Piero Massimino,
Fabio Vitello, Santi Cassisi, Adriano Pietrinferni, Giuliano Castelli,
Cristina Knapic, Riccardo Smareglia, Giuliano Taffoni,
Claudio Vuerli, Marian Jakubik, Lubos Neslusan, Mel Krokos
and Gong-Bo Zhao
19 Commercial Use of WS-PGRADE/gUSE . . . . . . . . . . . . . . . . . . . 271
Tamás Kiss, Péter Kacsuk, Éva Takács, Áron Szabó,
Péter Tihanyi and Simon J.E. Taylor
Conclusions and Outlook. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 287
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 291
Contributors
Ayşen D. Akkaya Middle East Technical University, Ankara, Turkey
Malcolm Atkinson School of Informatics, Data-Intensive Research Group, Uni-
versity of Edinburgh, Edinburgh, Scotland
Ákos Balaskó Laboratory of Parallel and Distributed Systems, Institute for
Computer Science and Control, Hungarian Academy of Sciences, Budapest,
Hungary
Antun Balaž Scientific Computing Laboratory, Institute of Physics Belgrade,
University of Belgrade, Belgrade, Serbia
Ugo Becciani Astrophysical Observatory of Catania, National Institute for
Astrophysics (INAF), Catania, Italy
AmmarBenabdelkader AcademicMedicalCentreoftheUniversityofAmsterdam,
Amsterdam,TheNetherlands
PéterBorsody CentreforParallelComputing,UniversityofWestminster,London,
UK
MatthanW.A.Caan AcademicMedical Centre oftheUniversityof Amsterdam,
Amsterdam, The Netherlands
Eoin Carley School of Computer Science and Statistics and School of Physics,
Trinity College Dublin, Dublin, Ireland
Santi Cassisi Astronomical Observatory of Teramo, National Institute for Astro-
physics (INAF), Teramo, Italy
Giuliano Castelli Astronomical Observatory of Trieste, National Institute for
Astrophysics (INAF), Trieste, Italy
Alessandro Costa Astrophysical Observatory of Catania, National Institute for
Astrophysics (INAF), Catania, Italy
xi