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© 2009 Open Grid Forum Interoperability of HTC & HPC e-Science Infrastructures WISDOM - Improving the in-silico drug discovery process Morris Riedel (DEISA & Jülich Supercomputing Centre) et al. Group Co-Chair Grid Interoperation Now & Production Grid Infrastructure
© 2009 Open Grid Forum 2 Outline
© 2009 Open Grid Forum 3 Outline Scientific Project WISDOM Addressing Project Description and Project Participants e-Infrastructure Setup Addressing how is the infrastructure provided Interoperability Framework Addressing what level of interoperability is required Other Scientific Applications Conclusions References Outline
© 2009 Open Grid Forum 4 Scientific Project WISDOM
© 2009 Open Grid Forum 5 Wide In Silicio Docking On Malaria (WISDOM) Developing new drugs for neglected and emerging diseases with an initial particular focus on malaria More recently WISDOM stands for a broader science collaboration Fundamental goals Accelerate research & drug development for emerging and neglected diseases (e.g. Malaria, Avian Flu, etc.) Reduced research & drug development costs Basic project ideas Use of computational-based so called in-silico methods & push in-vitro afterwards Intensive use of (European) e-science (i.e. Grid) infrastructures Scientific Project WISDOM
© 2009 Open Grid Forum 6 TBD: Slides Scientific Project WISDOM  Dr. Nicolas Jacq
© 2009 Open Grid Forum 7 Jülich Supercomputing Centre as DEISA contact Project Members  EGEE WISDOM  DEISA
© 2009 Open Grid Forum 8 e-Science Infrastructure Setup
© 2009 Open Grid Forum 9 e-Science Infrastructures High Performance Computing (HPC) InfrastructuresHigh Throughput Computing (HTC) Infrastructures
© 2009 Open Grid Forum 10 WISDOM uses EGEE for large scale in silicio docking Computational method for prediction of whether one molecule will bind to another Using AutoDock and FlexX software provided via gLite in EGEE Output is a list of best chemical compounds (potential drugs) That is not the final solution, only a potential list of drugs Refine best compound list via molecular dynamics (MD) Simulate the docked compounds over time for verification Fast MD computations use AMBER (or scalable NAMD) in DEISA AMBER (Assisted Model Building with Energy Refinement), version 9 Goal: Accelerate drug discovery using EGEE + DEISA e-Science Infrastructure Setup  Riedel et al., Improving e-Science with Interoperability of the e-Infrastructures EGEE and DEISA
© 2009 Open Grid Forum 11 Interoperability Framework
© 2009 Open Grid Forum 12 Interoperability Framework HPC InfrastructuresHTC Infrastructures AMBER AUTODOCK FlexX  Riedel et al., Improving e-Science with Interoperability of the e-Infrastructures EGEE and DEISA HTC Jobs HPC Jobs
© 2009 Open Grid Forum Initial Proprietary Approach  Riedel et al., Interoperation of world-wide production e-science Infrastructures
© 2009 Open Grid Forum Interoperability Components (1)  Riedel et al., Research Advances by using Interoperable e-Science Infrastructures – The Infrastructure Interoperability Reference Model applied in e-Science
© 2009 Open Grid Forum Interoperability Components (2)  Riedel et al., Research Advances by using Interoperable e-Science Infrastructures – The Infrastructure Interoperability Reference Model applied in e-Science
© 2009 Open Grid Forum Interoperability Components (3)  Riedel et al., Research Advances by using Interoperable e-Science Infrastructures – The Infrastructure Interoperability Reference Model applied in e-Science
© 2009 Open Grid Forum 17 Other Scientific Applications
© 2009 Open Grid Forum 18 European Fusion for ITER Applications Towards future electricity producing power plants Goal: Provide a comprehensive framework/infrastructure for core and edge transport and turbulence simulation using HTC/Grid and HPC to support the modelling community GIN Demonstration at Supercomputing 2009 Production e-science infrastructures EGEE for HTC codes DEISA for HPC codes Scientific software Kepler workflow tool orchestrating HPC/HTC ~80 codes for HTC and HPC computations Other Scientific Application
© 2009 Open Grid Forum 19 Conclusions
© 2009 Open Grid Forum 20 More and more projects evolve that require interoperability between HTC- & HPC-driven e-science infrastructures Interoperability requirements with respect to policies&usage… WISDOM is one project that can take advantage of this However the access to computational paradigms (i.e. HTC, HPC) must be significantly easier More work needs to be done with licenses E.g. FlexX is good, but commercial – licenses per user vs. per sites More work needs to be done in usage policies / access HPC systems overbooked, applying for time with proposals not easy Step from HTC infrastructure to HPC is a very big one requiring experience in coding (i.e. MPI) in order to achieve a speed-up Conclusions (1)
© 2009 Open Grid Forum 21 Interoperability requirements with respect to technology… Transparency for end-users is the key – one client only(!) Different security models are major showstoppers Open Standards already provide a first good step into the right direction – but some need to be refined / improved E.g. High Performance Computing – Basic Profile (HPC-BP) E.g. Storage Ressource Manager (SRM), GridFTP E.g. GLUE2 Information Model WISDOM use case experience significantly contributes to the Production Grid Infrastructure (PGI) Working Group Improvements and feedback to common open standards Missing links between OGSA-BES, JSDL, SRM, GridFTP, GLUE2,… Conclusions (2)
© 2009 Open Grid Forum 22 References
© 2009 Open Grid Forum 23  Dr Nicolas Jacq, International Symposium on Grids for Science and Business 12 June 2007, e33f554e2dd5 e33f554e2dd5  M. Riedel et al., Improving e-Science with Interoperability of the e-Infrastructures EGEE and DEISA, Proceedings of the 31st International Convention MIPRO, Conference on Grid and Visualization Systems (GVS), May 2008, Opatija, Croatia, Croatian Society for Information and Communication Technology, Electronics and Microelectronics, ISBN , pages 225 – 231  M. Riedel, F. Wolf, D. Kranzlmüller, A. Streit, T. Lippert, Research Advances by using Interoperable e-Science Infrastructures - The Infrastructure Interoperability Reference Model applied in e-Science, Journal of Cluster Computing, Special Issue Recent Advances in e-Science  Enabling Grids for e-Science (EGEE),  WISDOM Web-page:  Distributed European Infrastructure for Supercomputing Applications (DEISA),  M.Riedel and E. Laure et al., Interoperation of World-Wide Production e-Science Infrastructures, Concurrency and Computation: Practice and Experience, 21 (2009) 8, 961 – 990, DOI: /cpe.1402DOI: /cpe.1402 References
© 2009 Open Grid Forum 24 Full Copyright Notice Copyright (C) Open Grid Forum (2009). All Rights Reserved. This document and translations of it may be copied and furnished to others, and derivative works that comment on or otherwise explain it or assist in its implementation may be prepared, copied, published and distributed, in whole or in part, without restriction of any kind, provided that the above copyright notice and this paragraph are included on all such copies and derivative works. The limited permissions granted above are perpetual and will not be revoked by the OGF or its successors or assignees.
© 2007 Open Grid Forum GIN-CG Session I – Charter/Docs Morris Riedel (Forschungszentrum Jülich & OMII - Europe) GIN Secretary …and many others…
© 2007 Open Grid Forum OGSA-RUS Specification Update, Adoption and WS-RF Profile Discussions (Molly Pitcher) Morris Riedel (Forschungszentrum Jülich –
Grid Interoperability Through Standards Dr. Alistair Dunlop Project Manager.
© 2007 Open Grid Forum GIN-CG Session I – GIN Update Morris Riedel (Forschungszentrum Jülich - JSC & OMII - Europe) GIN Secretary …and many others…
© 2006 Open Grid Forum Workflow Management Research Group - WFM-RG OGF 22 Ian Taylor, Andrew Harrison and Ewa Deelman.
© 2007 Open Grid Forum JSDL-WG Session 1 OGF25 – General Session 11:00-12:30, 3 March 2009 Catania.
© 2006 Open Grid Forum Storage Networking Community Group.
© 2007 Open Grid Forum DMTF-OGF Work Register Current and Proposed Items OGF 22 Boston, MA 26 February 2008.
© 2007 Open Grid Forum Towards Usage Record 2.0 Usage Record Working Group OGF21 – Seattle, WA October 2007 Donal Fellows University of Manchester, UK.
© 2007 Open Grid Forum JSDL-WG Session OGF27 – General Session 10:30-12:00, 14 October 2009 Banff, Canada.
© 2006 Open Grid Forum JSDL Optional Elements OGF 24 Singapore.
© 2006 Open Grid Forum Joint Session on Information Modeling for Computing Resources OGF 20 - Manchester, 7 May 2007.
© 2007Open Grid Forum OGF22, 25th February 2008 OGSA Data Architecture Mario Antonioletti.
EGEE-III INFSO-RI Enabling Grids for E-sciencE EGEE and gLite are registered trademarks Experiences with using the EGEE grid infrastructure.
© 2008 Open Grid Forum Resource Selection Services OGF22 – Boston, Feb
© 2006 Open Grid Forum Network Services Interface Introduction to NSI Guy Roberts.
Promoting and Standardizing Grid Computing Defining the Grid: Open Grid Services Architecture Current and Future Generation Grid Technology Summer School.
© 2006 Open Grid Forum RISGE-RG use case Telecommunication measurement instrumentation on the eInfrastructure Evaluating the effects of noise and fading.
EGEE 08, Istanbul, September 25th, Support for experimental science communities Istanbul, September 25th, 2008 Norbert Meyer, Marcin Płóciennik.
Slide David Britton, University of Glasgow IET, Oct 09 1 Prof. David Britton GridPP Project leader University of Glasgow GridPP delivering The UK Grid.
© 2006 Open Grid Forum JSDL 1.0: Parameter Sweeps: Examples OGF 22, February 2008, Cambridge, MA.
©2010Open Grid Forum OGF28 OGSA-DMI Status Chairs: Mario Antonioletti, EPCC Stephen Crouch, Southampton Shahbaz Memon, FZJ Ravi Madduri, UoC.
© 2006 Open Grid Forum Joint Session on Information Modeling for Computing Resources (OGSA Modeling Activities) OGF 21 - Seattle, 16 October 2007.
Adoption Status of the OGSA-BES interface Morris Riedel, Mohammad Shahbaz Memon … and many others from the UNICORE community Jülich.
© 2006 Open Grid Forum GHPN-RG Status update co-chairss:Cees de Laat Dimitra Simeonidou GGF22, Boston, February 2008.
© 2006 Open Grid Forum GridRPC Interoperability Test Response to comments Yusuke Tanimura.
© 2007 Open Grid Forum JSDL-WG Session OGF21 – Activity schema session 17 October 2007 Seattle, U.S.
© 2007Open Grid Forum GGF19, 1'st February 2007 OGSA Data Architecture Services Dave Berry & Allen Luniewski.
© 2006 Open Grid Forum Federated Identity in the Cloud OGF 32, Salt Lake City.
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