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PRAGMA Grid A Multi-Application Route-Use Global Grid

PRAGMA Grid A Multi-Application Route-Use Global Grid. Cindy Zheng PRAGMA Grid Coordinator P acific R im A pplication and G rid M iddleware A ssembly University of California, San Diego San Diego Supercomputer Center http://www.pragma-grid.net http://goc.pragma-grid.net. Overview.

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PRAGMA Grid A Multi-Application Route-Use Global Grid

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  1. PRAGMA Grid A Multi-Application Route-Use Global Grid Cindy Zheng PRAGMA Grid Coordinator Pacific Rim Application and Grid Middleware Assembly University of California, San Diego San Diego Supercomputer Center http://www.pragma-grid.net http://goc.pragma-grid.net

  2. Overview • PRAGMA • Goals, Characteristics, Working groups, Workshops • PRAGMA Grid testbed • Goals, Characteristics, Resources • Applications • Application middleware • Infrastructure middleware • Benefit summary • Multi-Grid interoperation • Goals, Resources • Applications • Infrastructure testing matrix • Lessons learned • Forward

  3. PRAGMAhttp://www.pragma-grid.net • 2002 - • Goals • Open international organization • Grid applications, practical issues • Build international scientific collaborations • Members and community • 28 institutional members, 11 countries • >38 inst. >14 countries are actively involved • Characteristics • No central funding, but mutual interests • Build friendship, trust, help, community • Do, act • Working groups • Bio, data, resources, telescience, geosciences, … • Semi-annual Workshops

  4. The PRAGMA Steering Committee http://www.pragma-grid.net/steering_committee.htm

  5. Pragma Grid testbed and Routine-basis Experiements • 2004 - • Goal – make grid easier for scientists to use, by improving • middleware interoperability • Global grid usability and productivity • Method • For applications. Let applications drive • More organized testbed operation • Full-scale and integrated testing/research • Long application runs • Learn issues, develop/research/test solutions • Manners • Grass-roots • Voluntary, contribute of resources and work • long term, persistent • Inclusion: don’t have to be PRAGMA member or pacific rim • General science grid

  6. PRAGMA Grid Resources

  7. PRAGMA Grid Testbed JLU China UZurich Switzerland BU USA CNIC GUCAS China KISTI Korea SDSC USA NCSA USA AIST OSAKAU TITECH Japan KU NECTEC Thailand UMC USA ASCC NCHC Taiwan CICESE Mexico UoHyd India IOIT-HCM Vietnam UNAM Mexico MIMOS USM Malaysia QUT Australia BII IHPC NGO Singapore UChile Chile MU Australia

  8. PRAGMA Grid Software Layers

  9. Applicationshttp://goc.pragma-grid.net • Real science, multi-applications (11) • TDDFT: quantum-chemistry, AIST, Japan • Savannah: climate model, MU, Australia • MM5: climate model, CICESE, Mexico • QM-MD, FMO: quantum-mechanics, AIST, Japan • iGAP: genomics, UCSD, USA • HPM: genomics, IOIT-HCM, Vietnam • mpiBlast: genomics, ASCC, Taiwan • Gamess-APBS: organic chemistry, UZurich, Switzerland • Siesta: molecular simulation, UZurich, Switzerland • Amber: molecular simulation, USM, Malaysia • Learn • How to grid-enable, run • Application needs, issues

  10. Grid Application Middleware • Why grid application middleware • Enable applications to run on grid(s) • Make easier • Example grid application middleware development/testing • Ninf-G (AIST, Japan) • Nimrod/G (Monash University, Australia) • Mpich-Gx (KISTI, Korea)

  11. Ninf-Ghttp://ninf.apgrid.org • Developed by AIST, Japan • Support GridRPC model which will be a GGF standard • Integrated to NMI release 8 (first non-US software in NMI) • Ninf roll for Rocks 4.x is also available • 3 applications ran in PRAGMA grid and 1 ran on GIN testbed (multi-grids) • TDDFT • QM/MD • FMO • Achieved long runs(1 week ~ 50 days) • Improved fault-tolerance (papers) - hang • Simplified deployment procedures • Speed-up development cycles

  12. Nimrod/Ghttp://ninf.apgrid.org • Developed by Monash University, Australia • Supports large scale parameter sweeps on Grid infrastructure • Easy user interface - portal • 3 applications ran in PRAGMA grid and 1 will run in GIN testbed (multi-grids) • Savanah climate simulation (MU) • GAMESS/APBS (UZurich) • Siesta (UZurich) • Achieved long runs (90 different scenarios of 6 weeks each • Improved fault-tolerance (innovate time_step) • Speed-up enhancements

  13. Mpich-Gxhttp://www.moredream.org/mpich.htm • KISTI, Korea • Grid-enabled MPI, support • Private IP • Fault tolerance • Application run on KGrid • MM5 • Climate simulation • CICESE, Mexico

  14. Infrastructure Middleware • Why grid infrastructure middleware • Provide grid services • Make grid easier to use and manage • Example grid infrastructure middleware • Grid file system • Gfarm (AIST, Japan) • Grid monitoring system • SCMSWeb (Kasetsart University, Thailand) • Grid accounting system • MOGAS (Nanyang Technological University, Singapore)

  15. Gfarm – Grid Virtual File Systemhttp://datafarm.apgrid.org/ • Developed by AIST, Japan • High performance, scalable grid file system • Support Linux, Solaris; also scp, gridftp, SMB • Meta-server, file replication, Gfarm-FUSE • Ease user/application setup, file sharing (CSA), fault tolerance • 6 sites, 3786 GBytes, 1527 MB/sec (70 I/O nodes) • Tested with iGAP, large number of files, performance up >10x

  16. SCMSWebhttp://www.opensce.org/components/SCMSWeb • Developed by Kasetsart University, Thailand • Web-based monitoring system for clusters and grid • System usage, functional/performance metrics, job/queue status • Easy user interface, rapid support • Testing in PRAGMA grid, get user feedbacks and sites help • Speed-up development, enhancement, platform support expansion • Improve fault tolerance, functionalities, user interface • Popularize the software • GIN, common schema

  17. Multi-organisation Grid Accounting Systemhttp://ntu-cg.ntu.edu.sg/pragma • Developed by NTU, Singapore • Resource usage based on project/individual/organization • Daily, weekly, monthly, yearly • Pie charts and detail job logs • Metering and charging tool, easily customizable pricing system • Database and data analysis tools • Run on 17 sites in PRAGMA testbed • Improved interface to various globus and local schedulers

  18. PRAGMA Grid Brings Together GAMA • People • Hands-on learning to make grid work • Software development • Heterogeneity and reality check • Check software Integration and interface both horizontally and vertically • User feedback steers better direction • Popularize grid software • Collaborations • Naregi-CA (AIST, Japan) and Gama (SDSC, USA) Integration • Rocks (SDSC, USA) and SCE (KU, Thailand), Ninf-G (AIST, Japan), Gfarm (AIST), KRocks (KISTI, Korea) • PRAGMA and NLANR • PRAGMA and GEON • PRAGMA testbed and sensor networks (NCHC, Taiwan; Binghamton University, USA) • …

  19. Grid Interoperation Now (GIN)http://goc.pragma-grid.net/gin/default.html • GIN testbed (started Feb. 2006) • PRAGMA, TeraGrid, EGEE, OSG, NorduGrid • Applications • TDDFT/Ninf-G • Lead: Yoshio Tanaka, Yusuke Tanimura (AIST, Japan) • Deployed and run • PRAGMA - AIST, NCSA, SDSC • TeraGrid – ANL • Working on deployment to EGEE, OSG and NorduGrid • Savanah Study • Lead: Colin Enticott (MU, Australia) • Infrastructure testing matrix • Cindy Zheng (SDSC, USA) and Somsak Sriprayoonsakul (KU, Thailand) • Use SCMSWeb

  20. Lessons Learned • Differences among grids • Organization structures • Authentication (GSI, VOMS) • Job submission (GRAM, Gridftp) • Software stacks Takes a lot of learning to understand Takes a lot of work to interoperate • Resolved some problems (GSI-VOM, GT2-GT4) • Stimulated new initiatives (Cross grid monitoring) • Learned some from each other (Community Software Area) • Many more still yet to work on (File sharing, easy user access, direction and standards)

  21. Forward • More resources • More computational resources • GUCAS, China; UMC, USA; … • Add data resources (geo, atro, bio, …) • Add sensor network resources • NCHC, Taiwan; BU, USA; … • More applications • Geoscience (Mian Liu, Huai Zhang) • More and better grid middleware • Credential management systems (SDSC, USA; Naregi, Japan) • Portals (NCHC, Taiwan; QUT, Australia; …) • Meta-schedulers (AIST, Japan; IHPC, Singapore; …) • More grids interoperation • More grids • More applications • More collaboration on grid technology research and development

  22. One Possible Collaboration with AIST

  23. Collaborations with GSCAS and CNIC • GSCAS (Shi Yaolin, Huai Zhang), U Missouri (Mian Liu), UCSD (Chaitan Baru, Cindy Zheng), CNIC (Kai Nan) • Develop PRAGMA/iGEON Node at GSCAS • Develop initial parallel finite element codes • Run a geodynamics models on this cluster and then the PRAGMA testbed • Ensure user-friendly, Web interfaces to access and execute finite element codes developed by China on PRAGMA grid as well as TeraGrid

  24. Collaborations with U Hyderabad • Collaborators A. Agarwal, K.V. Subbarao (U Hyderabad) and Chaitan Baru (UCSD) • Establish GEON node at U Hyderabad • Experiment with sharing data • Register new datasets

  25. Other Collaborations • Exchanges: • Calit2 • Students (PRIME) • GEON willing to support this OptIPuter

  26. 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

  27. Thank You Everyone is welcome to join us! Either to build grid and/or to run applications. zhengc@sdsc.edu http://goc.pragma-grid.net

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