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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 Cindy Zheng, Geon Workshop, 7/20/2006 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 Cindy Zheng, Geon Workshop, 7/20/2006 PRAGMA http://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 Cindy Zheng, Geon Workshop, 7/20/2006 The PRAGMA Steering Committee http://www.pragma-grid.net/steering_committee.htm Cindy Zheng, Geon Workshop, 7/20/2006 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 Cindy Zheng, Geon Workshop, 7/20/2006 PRAGMA Grid Resources Cindy Zheng, Geon Workshop, 7/20/2006 PRAGMA Grid Testbed UZurich Switzerland CNIC GUCAS China KU NECTEC Thailand UoHyd India MIMOS USM Malaysia JLU China BU USA KISTI Korea AIST OSAKAU TITECH Japan ASCC NCHC Taiwan Cindy Zheng, Geon Workshop, 7/20/2006 NCSA USA UMC USA CICESE Mexico IOIT-HCM Vietnam BII IHPC NGO Singapore SDSC USA UNAM Mexico QUT Australia MU Australia UChile Chile PRAGMA Grid Software Layers Cindy Zheng, Geon Workshop, 7/20/2006 Applications http://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 Cindy Zheng, Geon Workshop, 7/20/2006 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) Cindy Zheng, Geon Workshop, 7/20/2006 Ninf-G http://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 Cindy Zheng, Geon Workshop, 7/20/2006 Nimrod/G http://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 Cindy Zheng, Geon Workshop, 7/20/2006 Mpich-Gx http://www.moredream.org/mpich.htm • KISTI, Korea • Grid-enabled MPI, support – Private IP – Fault tolerance • Application run on KGrid – MM5 • Climate simulation • CICESE, Mexico Cindy Zheng, Geon Workshop, 7/20/2006 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) Cindy Zheng, Geon Workshop, 7/20/2006 Gfarm – Grid Virtual File System http://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 Cindy Zheng, Geon Workshop, 7/20/2006 SCMSWeb http://www.opensce.org/components/SCMSWeb • • Developed by Kasetsart University, Thailand Web-based monitoring system for clusters and grid – • • Easy user interface, rapid support Testing in PRAGMA grid, get user feedbacks and sites help – – – • System usage, functional/performance metrics, job/queue status Speed-up development, enhancement, platform support expansion Improve fault tolerance, functionalities, user interface Popularize the software GIN, common schema Cindy Zheng, Geon Workshop, 7/20/2006 Multi-organisation Grid Accounting System http://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 Cindy Zheng, Geon Workshop, 7/20/2006 PRAGMA Grid Brings Together • 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) – … Cindy Zheng, Geon Workshop, 7/20/2006 GAMA 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 Cindy Zheng, Geon Workshop, 7/20/2006 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) Cindy Zheng, Geon Workshop, 7/20/2006 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 Cindy Zheng, Geon Workshop, 7/20/2006 One Possible Collaboration with AIST Cindy Zheng, Geon Workshop, 7/20/2006 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 Cindy Zheng, Geon Workshop, 7/20/2006 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 Cindy Zheng, Geon Workshop, 7/20/2006 Other Collaborations • Exchanges: – Calit2 – Students (PRIME) – GEON willing to support this • OptIPuter Cindy Zheng, Geon Workshop, 7/20/2006 New Paradigm: Global Team Science Kangwon U B.Kim Maintain Soyang Public Policy U.Wisconsin 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 Cindy Zheng, Geon Workshop, 7/20/2006 T.Kratz Maintain Trout Bog Lake Metabolism Everyone is welcome to join us! Either to build grid and/or to run applications. Thank You zhengc@sdsc.edu http://goc.pragma-grid.net Cindy Zheng, Geon Workshop, 7/20/2006
