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Cindy Zheng Peter Arzberger Philip Papadopoulos Mason Katz PowerPoint Presentation
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Cindy Zheng Peter Arzberger Philip Papadopoulos Mason Katz

Cindy Zheng Peter Arzberger Philip Papadopoulos Mason Katz

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Cindy Zheng Peter Arzberger Philip Papadopoulos Mason Katz

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  1. PRAGMA: A Framework For Collaborations Cindy Zheng Peter Arzberger Philip Papadopoulos Mason Katz Pacific Rim Application and Grid Middleware Assembly University of California, San Diego

  2. Overview • PRAGMA • Goal and approach • Collaborations • In testbed • Applications and middleware • With technology teams • security, data, sensor network, Rocks, Optputer • With science teams • GEON, GLEON, bioscience • With other Grids • GIN-OPS, Peer grids • In education and training • PRIME, PRIUS, NBCR institute • Looking forward for more collaborations

  3. PRAGMA Overarching Goals Strengthen Existing and Establish New Collaborations Work with Science Teams to Advance Grid Technologies and Improve the Underlying Infrastructure In the Pacific Rim and Globally “A Practical Collaborative Framework”.

  4. Workshops and Organization Information Exchange Planning and Review New Collaborations New Members Expand Users Expand Impact Routine Use Lab/Testbed Testing Applications Building Grid and GOC Multiway Dissemination Key Middleware Overview and ApproachProcess to Promote Routine Use Team Science Application-Driven Collaborations Applications Middleware Outcomes Improved middleware Broader Use New Collaborations Transfer Tech. Standards Publications New Knowledge Data Access Education

  5. PRAGMA Grid Testbed JLU China UZurich Switzerland CNIC GUCAS China AIST OsakaU UTsukuba TITech Japan NCSA USA KISTI Korea BU USA UUtah USA SDSC USA KU NECTEC Thailand ASGC NCHC Taiwan UMC USA CICESE Mexico UoHyd India CUHK HongKong UNAM Mexico MIMOS USM Malaysia IOIT-HCM Vietnam ASURC Costa Rica APAC QUT Australia BII IHPC NGO Singapore UCN Chile BESTGrid New Zealand UChile Chile MU Australia 29 Clusters from 26 institutions in 14 countries/regions (+9 in preparation)

  6. Applications • Achieved long run and scientific results • Savannah/Nimrod, MU, Australia • TDDFT/Ninf-G, FMO/Ninf-G, AIST, Japan • Successful run • MM5/Mpich-Gx, CICESE/KISTI, Mexico/Korea • 12 applications continue run in testbed, various middleware and scientific domains • Savannah/Nimrod: climate model, MU, Australia • MM5/Mpich-Gx: climate model, CICESE, Mexico • QM-MD, FMO/Ninf-G: quantum-mechanics, AIST, Japan • iGAP/Gfarm/CSF: genomics, UCSD, USA • HPM: genomics, IOIT-HCM, Vietnam • mpiBlast/Mpich-G2: genomics, ASGC, Taiwan • Gamess-APBS/Nimrod: organic chemistry, UZurich, Switzerland • Siesta/Nimrod: molecular simulation, UZurich, Switzerland • Amber/Rsh: molecular simulation, USM, Malaysia

  7. Application/Middleware Collaborationshttp://wiki.pragma-grid.net Mutually beneficial • Nimrod based Gamess-APBS • Gamess-APBS: UZurich, Switzerland • Nimrod: MU, Australia • Mpich-Gx based MM5 and WRF • MM5 and WRF: CICESE, Mexico • Mpich-Gx: KISTI, Korea • Test/develop Gfarm and CSF with iGAP • Gfarm: AIST, Japan • CSF: JLU, China • iGAP: UCSD, USA

  8. Collaborations With Technology Teams • Grid security • IGTF accredition APGrid PMA, • AIST, ASGC, CNIC, NCSA, … • PRAGMA CA, catch-all • GSI credential management • Naregi-CA (Naregi, Japan) • GAMA (SDSC, USA) • Computation + data + sensor • Gfarm-fuse (TsukubaU/AIST, Japan) • Grid monitoring and accounting (ThaiGrid, NTU Singapore) • GEON data network • GLEON sensor network • Rocks and middleware • Ninf-G, SCE, Gfarm, Bio, K*Rocks, Condor, … • AIST, ThaiGrid, NBCR, KISTI, UWSC, … • Rocks (SDSC, USA) • OptIPuter • High performance networked TDW (CalIT2/UCSD, KISTI, AIST, OsakaU, NCHC, CNIC, …)

  9. Source: Elaine Liu, PRIME 2006 TDW/OptIPuter Example Viewing @ UCSD Controlling @ CNIC

  10. Collaborations in BioScience • Avian Flu Research Project • UCSD, CNIC, JLU, Uni. Of Tskuba/AIST, University of Hawaii and Konkuk University • EGEE – Academia Sinica • Biosciences Portal • Collaboration between Osaka University, University of Queensland, JLU, UCSD. • Involves PRIME, PRIUS and summer students from UCSD, Osaka and JLU. • Metagenomics Research and Genome Informatics • Bioinformatics, computational biology software • Gfarm/CSF4, TskubaU/JLU, Japan/China • With University of Wisconsin, UCSD, PRIME project

  11. GEON-iGEON-PRAGMA • GEON is a coalition among IT and Earth Science researchers with the goal of developing advanced information technologies to enable new modes of geosciences research • GEON is developing technologies for information integration and knowledge discovery • Internationalization of GEON – iGEON • PRAGMA • Some sites already working on geoscience projects • Building a datagrid • Welcome geoscience applications • Seeking collaboration in grid interoperation

  12. PRAGMA and GEON/iGEON collaboration Sharing data, software know-how, interoperate grids • Geoscience workgroup established at PRAGMA11 • GUCAS (China) • Setup a GEON node in PRAGMA testbed • UMC (USA) and GUCAS • Preparing a GEON application to run in PRAGMA testbed • CNIC (China) • Is setting up a GEON data node in PRAGMA testbed • UoHyd (India) • has setup a GEON node, will join PRAGMA testbed • AIST Geogrid (Japan) plan • Share data with GEON • Interoperate with PRAGMA testbed

  13. Collaboration in Environmental Science • GLEON • A grassroots network of • People: lake scientists, engineers, information technology experts • Institutions: universities, national laboratories, agencies • Programs: PRAGMA, AS-Forest Biogeochemistry,US-LTER, TERN, KING, EcoGrid, etc. • Instruments • Data • Linked by a common purpose and cyberinfrastructure • With a goal of understanding lake dynamics at local, regional, continental, and global scales

  14. New Paradigm: Global Team Science Kangwon U B.Kim Maintain Soyang Public Policy U.Wisconsin T.Kratz Maintain Trout Bog Lake Metabolism NCHC F.P.Lin Maintain YYL Parallelize Codes UCSD F.Vernon, S.Peltier, T.Fountain P.Arzberger ROADNet, Telescience Moore Fnd, PRAGMA NIGLAS B.Q Qin Maintain Taihu Physical Limnology U.Waikato D.Hamilton Models

  15. Collaboration with GLEON • BU (USA) • Joining PRAGMA grid testbed • Preparing a sensor network application to run in the testbed • NCHC (Taiwan) • preparing a sensor application to run in testbed • PRAGMA Grid + GLEON sensor network • link GLEON sites to PRAGMA testbed computing and data grids Lake Taihu Nanjing Institute of Geography and Limnology, Chinese Academy of Science

  16. Grid Interoperation Now (GIN) • GIN – a project under OGF • GIN testbed (started Feb. 2006) • PRAGMA, TeraGrid, EGEE, OSG, NorduGrid • Applications • TDDFT/Ninf-G • Yoshio Tanaka, Yusuke Tanimura (AIST, Japan) • Deployed and run • PRAGMA - AIST, NCSA, SDSC • TeraGrid – ANL • OSG – UCSD • NorduGrid • Working on deployment to EGEE • Savanah fire simulation (data intensive) • Colin Enticott (MU, Australia) • Started in GIN testbed

  17. GIN Testbed Monitoring • Infrastructure testing matrix • SCMSWeb (by Thaigrid) • Working with PRAGMA Grid, TeraGrid, OSG, NorduGrid, EGEE • New version to handle various grid service configurations/tests • GIN map • Implemented a XML-> LDIF translator for GIN map • Collaboration of ThaiGrid and CERN • Cross-grid monitoring - Common schema • Working with PRAGMA Grid, TeraGrid, OSG, NorduGrid, EGEE

  18. Peer Grids Interoperations • PRAGMA application developers running applications across grids • QM/MD by AIST, run on PRAGMA Grid and TeraGrid • Talking with OSG, LSU, UCGrid • Running applications across grids • Bi-directional • Develop a minimum set of tools to enable interoperation

  19. PRIME • Providing UCSD undergraduate students international interdisciplinary research internships and Cultural experiences • Preparing the global work place of the 21st century • Built on top of PRAGMA R&D network and activities for Undergraduate Research • A Pilot Project for Global Engagement • Summer research abroad • Mentors from UCSD and host institutions • Real science and practical projects • Learning science, technology and culture • Demo’s and talks • Continuing research involvement thereafter PRIME Class 2006

  20. PRIME 2006 (Thrid Year)Host Institutions and Projects at a Glance • CNIC, China • Virtual Screening of Avian Influenza H5N1 Neuraminidase and Hemagglutinin proteins against two libraries of ligands • High-resolution astronomial visualization and visual collaboration environment • MU, Australia • Computational analysis of biological structures using GAMESS-APBS/Nimrod programs • Develop efficient method for large scale virtual screening of ligands • More stable ionic model of ventricular myocytes • OsakaU, Japan • Homology modeling of the protein kinases and binding site prediction • Docking simulations of protein kinases and virtual screening of ligands for inhibitors • Established networked Tile Display Wall • NCHC, Taiwan • implementing image-processing software for neural networks • Develop software tools for earthquake experiments, monitoring and analysis Prime Students 2006 Hosted by CNIC, China At Lao She Tea House

  21. Establish a consistent educational program for graduate students. On-the-Job-training and education with PRAGMA PRIUS - Pacific Rim International UniverSity Based at Osaka University P.D Exchange prgm: produces liquidity in human resource P.D Long Abroad Internship: Provide skill building chances Doc Research Part Educational Part Short Abroad Internship: Offer trial opportunities M2 M1 Lecture course: Stimulate students’ ambitious Source: Susumu Date, Osaka University

  22. 10 International instructors All from PRAGMA members UCSD, USA NCHC, Taiwan NTU, Singapore QUT, MU, Australia Grid computing/applications Grid and web services Clustering tools Optical network computing Grid accounting systems Biomedical grid applications Economic and social impact of cyberinfrastructure Interaction with students Internship abroad UCSD, USA Develop QM/MM hybrid simulation program for protein research using OPAL NTU, Singapore Design/prototype a grid security monitoring system as an add-on to MOGAS QUT, Australia Develop a bioscience portal for PRAGMA NCHC, Taiwan Implement high-definition-quality streaming video over a high-speed network with various TDW technologies PRIUS (First Year)

  23. More Collaborations Forward • Testing Gfarm with applications • More peer grids interoperation experiments • More collaborations with science teams • GEON, GLEON, CAMERA, … • More collaboration with technology groups • Meta-schedulling, portal, … • Greater use of the network • Using optical networks and tile display walls • Cyber-environment • More exchange of students, replicate PRIME, PRIUS • More trainings • Globally, especially with technology and science teams in China

  24. Future Meeting • 20 – 22 March 2007, Bangkok Thailand • PRAGMA 12 Hosted by NECTEC and Thai National Grid Center • 18 – 20 March 2007: GEOGrid Workshop • Fall 2007, Urbana-Champaign USA • PRAGMA 13 Hosted by NCSA • Spring 2008, Hsinchu Taiwan • PRAGMA 14 Hosted by NCHC • Fall 2008, Penang Malaysia • PRAGMA 15 Hosted by USM

  25. PRAGMA is supported by the National Science Foundation (Grant No. INT-0216895, INT-0314015, OCI -0627026), and member institutions PRIME is supported by the National Science Foundation under NSF INT 04007508 Thank You