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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. - PowerPoint PPT Presentation
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Cindy Zheng, Geon Workshop, 7/20/2006
PRAGMA GridA Multi-Application Route-Use Global Grid
Cindy Zheng
PRAGMA Grid Coordinator
Pacific Rim Application and Grid Middleware AssemblyUniversity of California, San DiegoSan Diego Supercomputer Center
http://www.pragma-grid.nethttp://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
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
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 TestbedPRAGMA Grid Testbed
AISTOSAKAUTITECHJapan
CNICGUCASChina
KISTIKorea
ASCCNCHCTaiwanUoHyd
India
MUAustralia
BIIIHPCNGO
Singapore
KUNECTECThailand
NCSAUSA
SDSCUSA
CICESEMexico
UNAMMexico
UChileChile
QUTAustralia
UZurichSwitzerland
JLUChina
MIMOSUSM
Malaysia
IOIT-HCMVietnam
BUUSA
UMCUSA
Cindy Zheng, Geon Workshop, 7/20/2006
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-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
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 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
Cindy Zheng, Geon Workshop, 7/20/2006
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
Cindy Zheng, Geon Workshop, 7/20/2006
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
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)
– …
GAMAGAMA
Cindy Zheng, Geon Workshop, 7/20/2006
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 stacksTakes a lot of learning to understandTakes 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
U.WaikatoD.Hamilton
Models
NCHCF.P.Lin
Maintain YYLParallelize Codes
U.WisconsinT.Kratz
Maintain Trout BogLake MetabolismUCSD
F.Vernon, S.Peltier,T.Fountain P.ArzbergerROADNet, TelescienceMoore Fnd, PRAGMANIGLAS
B.Q QinMaintain Taihu
Physical Limnology
Kangwon UB.Kim
Maintain SoyangPublic Policy
Cindy Zheng, Geon Workshop, 7/20/2006
Thank You
Everyone is welcome to join us!Either to build grid and/or
to run applications.
zhengc@sdsc.eduhttp://goc.pragma-grid.net
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