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Cindy Zheng, Pragma Grid, 5/30/2006 The PRAGMA Testbed Building a Multi-Application International Grid Cindy Zheng P acific R im A pplication and G rid.

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Presentation on theme: "Cindy Zheng, Pragma Grid, 5/30/2006 The PRAGMA Testbed Building a Multi-Application International Grid Cindy Zheng P acific R im A pplication and G rid."— Presentation transcript:

1 Cindy Zheng, Pragma Grid, 5/30/2006 The PRAGMA Testbed Building a Multi-Application International Grid Cindy Zheng P acific R im A pplication and G rid M iddleware A ssembly University of California, San Diego San Diego Supercomputer Center

2 Cindy Zheng, Pragma Grid, 5/30/2006 Overview PRAGMA PRAGMA Grid testbed Routine-basis experiments –Applications –Grid middleware –Grid infrastructure software Grid interoperation Lessons Learned

3 Cindy Zheng, Pragma Grid, 5/30/2006 PRAGMA PRAGMA ( ) –Open international organization –Grid applications, practical issues –Build international scientific collaborations Characteristics –No central funding, but mutual interests –Friendship, trust, help among people –Doers Working groups –Bio, telescience, data, Geon, resources Meetings

4 Cindy Zheng, Pragma Grid, 5/30/2006 Resources working group Improve –middleware interoperability –Global grid usability and productivity –Grid interoperability How to make a global grid easy to use? –For applications. Let applications drive –More organized testbed operation –Full-scale and integrated testing/research –Long daily application runs –Find problems, develop/research/test solutions

5 Cindy Zheng, Pragma Grid, 5/30/2006 Routine-basis Experiments Run applications while building testbed –Started 2004 –Grass-roots, PRAGMA membership not necessary –Voluntary contribution of resources/work –long term, persistent –General grid Coordinator Site supporters Application drivers Developers

6 Cindy Zheng, Pragma Grid, 5/30/2006 How We Operate Heterogeneity –fundings, policies, environments Motivation –learn, develop, test, interop Communication – , VTC, Skype, workshop, timezone, language Create operation procedures –joining testbed –running applications –resources, contacts, requirements, instructions, monitoring, status, tools, etc.

7 Cindy Zheng, Pragma Grid, 5/30/2006 How We Operate

8 Cindy Zheng, Pragma Grid, 5/30/2006 PRAGMA Grid Testbed AIST, Japan CNIC, China KISTI, Korea ASCC, Taiwan NCHC, Taiwan UoHyd, India MU, Australia BII, Singapore KU, Thailand USM, Malaysia NCSA, USA SDSC, USA CICESE, Mexico UNAM, Mexico UChile, Chile TITECH, Japan QUT, Australia UZurich, Switzerland JLU, China NGO, Singapore MIMOS, Malaysia OSAKAU, Japan IOIT-HCM, Vietnam

9 Cindy Zheng, Pragma Grid, 5/30/2006 PRAGMA Grid resources

10 Cindy Zheng, Pragma Grid, 5/30/2006 Software Layers Globus 2, 3, 4 GT4 pre-WS, 9 sites GT4 WS, 1 Moving requirements

11 Cindy Zheng, Pragma Grid, 5/30/2006 Trust Trust all site CAs –tarball Experimental -> production Setup PRAGMA CA –GAMA/Naregi-CA APGRID PMA, IGTF (5 accr.)

12 Cindy Zheng, Pragma Grid, 5/30/2006 Applications Real science, multiple applications –Resource sharing Mpich-g2 Reservation and meta-scheduling –TDDFT: quantum-chemistry, AIST, Japan –Savannah: climate Model, MU, Australia –QM-MD: quantum-mechanic, AIST, Japan –iGAP: bioinformatic, UCSD, USA –Gamess-APBS: organic chemistry, UZurich, Switzerland –Siesta: molecular simulation, UZurich, Switzerland –Amber: molecular simulation, USM, Malaysia –FMO: quantum-mechanics, AIST, Japan –HPM: Genomics, IOIT-HCM, Vietnam –(GEON, Sensor, … )

13 Cindy Zheng, Pragma Grid, 5/30/2006 Middleware Application middleware –enable application to run in grid –Ninf-G AIST, Japan TDDFT, QM/MD, FMO –Nimrod/G MU, Australia Savannah, Siesta, Gamess –Mpich-Gx KISTI, Korea MM5, CICESE, Mexico Infrastructure middleware –provide grid services –Gfarm AIST, Japan iGAP, testbed, 6 sites –SCMSWeb KU, Thailand Testbed, 20 sites –MOGAS NTU, Singapore Testbed, 14 sites

14 Cindy Zheng, Pragma Grid, 5/30/2006 Server Client Compuer Func. Handle Client Component Info. Manager Remote Executables GridRPC: A Programming Model based on RPC GridRPC API is a proposed recommendation at the GGF Three components Information Manager - Manages and provides interface info Client Component - Manages remote executables via function handles Remote Executables - Dynamically generated on remote servers Built on top of Globus Toolkit (MDS, GRAM, GSI) Simple and easy-to-use programming interface Hiding complicated mechanism of the grid Providing RPC semantics

15 Cindy Zheng, Pragma Grid, 5/30/2006 Nimrod Development Cycle Prepare Jobs using Portal Jobs Scheduled Executed Dynamically Results displayed & interpreted Sent to available machines

16 Cindy Zheng, Pragma Grid, 5/30/2006 Application Middleware Ninf-G –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 –On PRAGMA testbed, TDDFT and QM/MD application achieved long time executions (1 week ~ 50 days runs). Nimrod –Supports large scale parameter sweeps on Grid infrastructure Study the behaviour of some of the output variables against a range of different input scenarios. Computer parameters that optimize model output Computations are uncoupled (file transfer) Allows robust analysis and more realistic simulations Very wide range of applications from quantum chemistry to public health policy –Climate experiment ran some 90 different scenarios of 6 weeks each

17 Cindy Zheng, Pragma Grid, 5/30/2006 Fault-Tolerance Enhanced Ninf-G monitors each RPC call –Return error code for failures Explicit Faults : Server down, Disconnection of network Implicit Faults : Jobs not activated, unknown faults Timeout - grpc_wait*() –Retry/restart Nimrod/G monitors remote services and restarts failed jobs –Long jobs are split into many sequentially dependent jobs which can be restarted using sequential parameters called seqameters Improvement in the routine-basis experiment –developers test code on heterogeneous global grid –results guide developers to improve detection and handle faults

18 Cindy Zheng, Pragma Grid, 5/30/2006 Application Setup and Resource Management Heterogeneous platforms –Manual build, deploy applications, manage resources Labor intensive, time consuming, tidious Middleware solutions –For deployment Automatic distribution of executables use staging functions –For resource management Ninf-G client configuration allow description of server attributes –Port number of the Globus gatekeeper –Local scheduler type –Queue name for submitting jobs –Protocol for data transfer –Library path for dynamic linking Nimrod/G portal allows a user to generate a testbed and helps maintain information about resources, including use of different certificates.

19 Cindy Zheng, Pragma Grid, 5/30/2006 Gfarm – Grid Virtual File System -High transfer rate (parallel transfer, localization) -Scalable -File replication – user/application setup, fault tolerance -Support Linux, Solaris; also scp, gridftp, SMB -POSIX compliant -Gfarm-FUSE -6 sites, 3786 GBytes, 1527 MB/sec (70 I/O nodes)

20 Cindy Zheng, Pragma Grid, 5/30/2006 Application Benefit No modification required –Existing legacy application can access files in Gfarm file system without any modification Easy application deployment –Install Application in Gfarm file system, run everywhere It supports binary execution and shared library loading Different kinds of binaries can be stored at the same pathname, which will be automatically selected depending on client architecture Fault tolerance –Automatic selection of file replicas in access time tolerates disk and network failure File sharing – Community Software Area

21 Cindy Zheng, Pragma Grid, 5/30/2006 Performance Enhancements OriginalImproved metadata management W/ metadata cache server Performance for small files – Improve meta-cache management – add meta-cache server Directory listing of 16,393 files

22 Cindy Zheng, Pragma Grid, 5/30/2006 SCMSWeb Web-based monitoring system for clusters and grid –System usage –Performance metrics Reliability –Grid service monitoring –Spot problems at a glance

23 Cindy Zheng, Pragma Grid, 5/30/2006 PRAGMA-Driven Development Heterogeneity –Add platform support Solaris (CICESE, Mexico) IA64 (CNIC, China) Software deployment –NPACI Rocks Roll Support ROCKS – 4.1 –Native Linux RPM for various Linux platform Enhancement –Hierarchical monitoring on large scale Grid –Compress data exchange between Grid side For some site with slow network –Better and cleaner graphics user interfaces Standardize & more collaboration –GRMAP (Grid Resource Management & Account Project) – Collaboration between NTU and TNGC –GIN (Grid Interoperation Now) Monitoring – standardize data exchange between monitoring softwares

24 Cindy Zheng, Pragma Grid, 5/30/2006 Multi-organisation Grid Accounting System

25 Cindy Zheng, Pragma Grid, 5/30/2006 Information for grid resource managers/administrators: –Resource usage based on organization –Daily, weekly, monthly, yearly records –Resource usage based on project/individual/organisation –Individual log of jobs –Metering and charging tool, can decide a pricing system, e.g. Price = f(hardware specifications, software license, usage measurement) MOGAS Web information

26 Cindy Zheng, Pragma Grid, 5/30/2006 PRAGMA MOGAS status (27/3/2006) AIST, Japan CNIC, China KISTI, Korea ASCC, Taiwan NCHC, Taiwan UoHyd, India MU, Australia BII, Singapore KU, Thailand USM, Malaysia NCSA, USA SDSC, USA CICESE, Mexico UNAM, Mexico UChile, Chile TITECH, Japan Cindy Zheng, GGF13, 3/14/05 modified by A/Prof. Bu-Sung Lee MIMOS IOIT-HCM GT4 GT2 NGO, Singapore QUT

27 Cindy Zheng, Pragma Grid, 5/30/2006 Integrations and Collaborations Naregi-CA (AIST, Japan) and Gama (SDSC, USA) Integration Rocks (SDSC, USA) and SCE (KU, Thailand), Ninf-G (AIST), Gfarm (AIST), KISTI etc. PRAGMA and NLANR PRAGMA and GEON –PRAGMA grid testbed –UMC, SDSC (USA) –GSCAS, CNIC (China) –UoHyd (India) –AIST (Japan) PRAGMA and sensor networks –PRAGMA grid testbed –NCHC, Taiwan –Binghamton University, NY, USA GAMA

28 Cindy Zheng, Pragma Grid, 5/30/2006 Grid Interoperation Now (GIN) GIN testbed (started Feb. 2006) –PRAGMA –TeraGrid –EGEE Fist application: TDDFT/Ninf-G –Lead: Yoshio Tanaka, Yusuke Tanimura (AIST) –Deployed and run PRAGMA - AIST, NCSA, SDSC TeraGrid – ANL –Working on deployment to EGEE – LCG Middleware interoperability problem –Assumptions by middleware about local architecture –Standard protocol

29 Cindy Zheng, Pragma Grid, 5/30/2006 Lessons Learned, Issues and Work (1) Authentication –User obtain initial access Process documented by Cindy Zheng, goc.rocksclusters.org/gin/gin-egee.htmhttp://pragma- goc.rocksclusters.org/gin/gin-egee.htm Not easy, not simple Need documentation to guide users Develop software to simply the process –DN incompatibility Summarized by Oscar Koeroo, grid.net/gin/Cert-probs-GIN.pdfhttp://goc.pragma- grid.net/gin/Cert-probs-GIN.pdf Commented by Charles Bacon (Globus), Need both standard and flexibility Voms server is modified to handle both styles of DN strings

30 Cindy Zheng, Pragma Grid, 5/30/2006 Lessons Learned, Issues and Work (2) Software stack and Community Software Area (CSA) –Software stack is different among grids. Problems with conflicting requirements. CSA as a solution for users to deploy their sub- stack and share installed software –Near term - work on CSA within each grid Gfarm-FUSE –Need focused discussion on solution for GIN

31 Cindy Zheng, Pragma Grid, 5/30/2006 Lessons Learned, Issues and Work (3) Cross-grid monitoring –Summary by Somsak Sriprayoonsakul, monitor.htm monitor.htm Get some monitoring software together, develop a common schema –Wiki - grid.net/index.php?title=GIN_%28Grid_I nter-operation_Now%29_Monitoringhttp://wiki.pragma- grid.net/index.php?title=GIN_%28Grid_I nter-operation_Now%29_Monitoring

32 Cindy Zheng, Pragma Grid, 5/30/2006 Lessons Summary Problems and solutions –Information sharing (pragma-goc) –Trust and access (Naregi-CA, GAMA, myproxy) –Resource requirements (INCA) –User/application environment (Gfarm) –Job submission (Portal/service/middleware) –System/job monitoring (SCMSWeb, +) –Network monitoring (APAN, NLANR) –Resource/job accounting (SCMSWeb, NTU) –Fault tolerance (Ninf-G, Nimrod) Publications –Infrastructure, applications, software integration, organization

33 Cindy Zheng, Pragma Grid, 5/30/2006 Thank You Pointers PRAGMA: PRAGMA Testbed: PRAGMA: Example of Grass-Roots Grid Promoting Collaborative e-science Teams. CTWatch. Vol 2, No. 1 Feb 2006 The PRAGMA testbed – Building a Multi- application International Grid, CCGrid2006 Deploying Scientific Applications to the PRAGMA Grid Testbed: Strategies and Lessons, CCGrid2006 MOGAS: Analysis of Job in a Multi- Organizational Grid Test-bed, CCGrid2006


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