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Supporting Molecular Modeling Workflows within a Grid Services Cloud

Identifieur interne : 000285 ( Istex/Corpus ); précédent : 000284; suivant : 000286

Supporting Molecular Modeling Workflows within a Grid Services Cloud

Auteurs : Martin Koehler ; Matthias Ruckenbauer ; Ivan Janciak ; Siegfried Benkner ; Hans Lischka ; N. Gansterer

Source :

RBID : ISTEX:70BABEB8A977D51570B30B71EA435FA38B036B2E

Abstract

Abstract: Seamless integrated support for scientific workflows accessing HPC applications, deployed on globally distributed computing resources, has become a major challenge in scientific computing. Scientific workflows in the domain of theoretical chemistry are typically long running, deal with huge files, and have a need for dynamic execution control mechanisms. In this paper, we describe a service-oriented approach based on the Vienna Grid Environment (VGE) that tackles these challenges by seamlessly integrating the Ubuntu Cloud infrastructure supporting the scheduling of dynamic and partitioned workflows. The VGE service environment, which enables the provisioning of HPC applications and data sources as Web services, has been enhanced with support for virtualized workflows. The generic scientific workflow infrastructure is utilized in the context of the CPAMMS project, an interdisciplinary research initiative in the area of computational molecular modeling and simulation. A case study implementing a complex scientific workflow for computing photodynamics of biologically relevant molecules, a simulation of the nonadiabatic dynamics of 2,4-pentadieneiminum-cation (Protonated Schiff Base 3, PSB3) solvated in water, is realized via the presented infrastructure.

Url:
DOI: 10.1007/978-3-642-12189-0_2

Links to Exploration step

ISTEX:70BABEB8A977D51570B30B71EA435FA38B036B2E

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<forename type="first">David</forename>
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<forename type="first">Osvaldo</forename>
<surname>Gervasi</surname>
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<forename type="first">Beniamino</forename>
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<forename type="first">Eric</forename>
<surname>Pardede</surname>
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<email>e.pardede@latrobe.edu.au</email>
<affiliation>Department of Computer Science and Computer Engineeering, LaTrobe University, VIC 3086, Bundoora, Australia</affiliation>
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<forename type="first">Bernady</forename>
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<surname>Apduhan</surname>
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<email>bob@is.kyusan-u.ac.jp</email>
<affiliation>Department of Intelligent Informatics, Kyushu Sangyo University, 813-8503, Fukuoka, Japan</affiliation>
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<forename type="first">David</forename>
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<affiliation>Lancaster University, Lancaster, UK</affiliation>
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<forename type="first">Takeo</forename>
<surname>Kanade</surname>
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<affiliation>Carnegie Mellon University, Pittsburgh, PA, USA</affiliation>
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<forename type="first">Josef</forename>
<surname>Kittler</surname>
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<affiliation>University of Surrey, Guildford, UK</affiliation>
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<forename type="first">Jon</forename>
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<surname>Kleinberg</surname>
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<forename type="first">John</forename>
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<forename type="first">Moni</forename>
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<affiliation>Weizmann Institute of Science, Rehovot, Israel</affiliation>
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<forename type="first">Oscar</forename>
<surname>Nierstrasz</surname>
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<affiliation>University of Bern, Bern, Switzerland</affiliation>
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<forename type="first">C.</forename>
<surname>Pandu Rangan</surname>
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<affiliation>Indian Institute of Technology, Madras, India</affiliation>
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<forename type="first">Bernhard</forename>
<surname>Steffen</surname>
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<affiliation>University of Dortmund, Dortmund, Germany</affiliation>
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<forename type="first">Madhu</forename>
<surname>Sudan</surname>
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<affiliation>Massachusetts Institute of Technology, MA, USA</affiliation>
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<forename type="first">Demetri</forename>
<surname>Terzopoulos</surname>
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<persName>
<forename type="first">Doug</forename>
<surname>Tygar</surname>
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<affiliation>University of California, Berkeley, CA, USA</affiliation>
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<persName>
<forename type="first">Moshe</forename>
<forename type="first">Y.</forename>
<surname>Vardi</surname>
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<affiliation>Rice University, Houston, TX, USA</affiliation>
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<forename type="first">Gerhard</forename>
<surname>Weikum</surname>
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<affiliation>Max-Planck Institute of Computer Science, Saarbrücken, Germany</affiliation>
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<p>Abstract: Seamless integrated support for scientific workflows accessing HPC applications, deployed on globally distributed computing resources, has become a major challenge in scientific computing. Scientific workflows in the domain of theoretical chemistry are typically long running, deal with huge files, and have a need for dynamic execution control mechanisms. In this paper, we describe a service-oriented approach based on the Vienna Grid Environment (VGE) that tackles these challenges by seamlessly integrating the Ubuntu Cloud infrastructure supporting the scheduling of dynamic and partitioned workflows. The VGE service environment, which enables the provisioning of HPC applications and data sources as Web services, has been enhanced with support for virtualized workflows. The generic scientific workflow infrastructure is utilized in the context of the CPAMMS project, an interdisciplinary research initiative in the area of computational molecular modeling and simulation. A case study implementing a complex scientific workflow for computing photodynamics of biologically relevant molecules, a simulation of the nonadiabatic dynamics of 2,4-pentadieneiminum-cation (Protonated Schiff Base 3, PSB3) solvated in water, is realized via the presented infrastructure.</p>
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<Para>Seamless integrated support for scientific workflows accessing HPC applications, deployed on globally distributed computing resources, has become a major challenge in scientific computing. Scientific workflows in the domain of theoretical chemistry are typically long running, deal with huge files, and have a need for dynamic execution control mechanisms. In this paper, we describe a service-oriented approach based on the Vienna Grid Environment (VGE) that tackles these challenges by seamlessly integrating the Ubuntu Cloud infrastructure supporting the scheduling of dynamic and partitioned workflows. The VGE service environment, which enables the provisioning of HPC applications and data sources as Web services, has been enhanced with support for virtualized workflows. The generic scientific workflow infrastructure is utilized in the context of the CPAMMS project, an interdisciplinary research initiative in the area of computational molecular modeling and simulation. A case study implementing a complex scientific workflow for computing photodynamics of biologically relevant molecules, a simulation of the nonadiabatic dynamics of 2,4-pentadieneiminum-cation (Protonated Schiff Base 3, PSB3) solvated in water, is realized via the presented infrastructure.</Para>
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<abstract lang="en">Abstract: Seamless integrated support for scientific workflows accessing HPC applications, deployed on globally distributed computing resources, has become a major challenge in scientific computing. Scientific workflows in the domain of theoretical chemistry are typically long running, deal with huge files, and have a need for dynamic execution control mechanisms. In this paper, we describe a service-oriented approach based on the Vienna Grid Environment (VGE) that tackles these challenges by seamlessly integrating the Ubuntu Cloud infrastructure supporting the scheduling of dynamic and partitioned workflows. The VGE service environment, which enables the provisioning of HPC applications and data sources as Web services, has been enhanced with support for virtualized workflows. The generic scientific workflow infrastructure is utilized in the context of the CPAMMS project, an interdisciplinary research initiative in the area of computational molecular modeling and simulation. A case study implementing a complex scientific workflow for computing photodynamics of biologically relevant molecules, a simulation of the nonadiabatic dynamics of 2,4-pentadieneiminum-cation (Protonated Schiff Base 3, PSB3) solvated in water, is realized via the presented infrastructure.</abstract>
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