cindy zheng, geon workshop, 7/20/2006 pragma grid a multi-application route-use global grid cindy...

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


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


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


The PRAGMA Steering Committee

http://www.pragma-grid.net/steering_committee.htm


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


PRAGMA Grid Resources


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


PRAGMA Grid Software Layers


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


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)


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


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


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


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)


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


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


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


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


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


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)


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


One Possible Collaboration with AIST


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


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


Other Collaborations

• Exchanges: – Calit2– Students (PRIME)– GEON willing to

support this

• OptIPuter


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


Thank You

Everyone is welcome to join us!Either to build grid and/or

to run applications.

[email protected]://goc.pragma-grid.net

cindy zheng, geon workshop, 7/20/2006 pragma grid a multi-application route-use global grid cindy...

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