CANS2006, 12/7/2006

Cindy ZhengPeter Arzberger

Philip PapadopoulosMason Katz

Pacific Rim Application and Grid Middleware AssemblyUniversity of California, San Diego

http://www.pragma-grid.nethttp://goc.pragma-grid.net

PRAGMA: A Framework For Collaborations

CANS2006, 12/7/2006

Overview• PRAGMA

– Goal and approach

• Collaborations– In testbed

• Applications and middleware

– With technology teams• security, data, sensor network, Rocks, Optputer

– With science teams• GEON, GLEON, bioscience

– With other Grids• GIN-OPS, Peer grids

– In education and training• PRIME, PRIUS, NBCR institute

• Looking forward for more collaborations

CANS2006, 12/7/2006http://www.pragma-grid.net

Overarching GoalsPRAGMA

“A Practical Collaborative Framework”.

Strengthen Existing and Establish New Collaborations

Work with Science Teams to Advance Grid Technologies and Improve the

Underlying Infrastructure

In the Pacific Rim and Globally

CANS2006, 12/7/2006

Overview and ApproachProcess to Promote Routine Use Team Science

Application-Driven CollaborationsApplications Middleware

Routine Use Lab/TestbedTesting Applications

Building Grid and GOC

Multiway DisseminationKey Middleware

Workshops and Organization

Information Exchange

Planning and Review

New Collaborations

New Members

Expand Users

Expand Impact

Outcomes

Improved middlewareBroader Use

New CollaborationsTransfer Tech.

StandardsPublications

New KnowledgeData AccessEducation

CANS2006, 12/7/2006

PRAGMA Grid TestbedPRAGMA Grid Testbed

29 Clusters from 26 institutions in 14 countries/regions (+9 in preparation)

UZurichSwitzerland

KUNECTECThailand

UoHydIndia

MIMOSUSMMalaysia

CUHKHongKong

ASGCNCHCTaiwan

IOIT-HCMVietnam

AISTOsakaUUTsukubaTITechJapan

BIIIHPCNGOSingapore MU

Australia

APACQUTAustralia

KISTIKorea

JLUChina

SDSCUSA

CICESEMexico

UNAMMexico

UCNChile

UChileChile

UMCUSA

UUtahUSA

NCSAUSA BU

USA

ASURCCosta Rica

BESTGridNew Zealand

CNICGUCASChina

CANS2006, 12/7/2006

Applications http://goc.pragma-grid.net

• Achieved long run and scientific results– Savannah/Nimrod, MU, Australia– TDDFT/Ninf-G, FMO/Ninf-G, AIST, Japan

• Successful run– MM5/Mpich-Gx, CICESE/KISTI,

Mexico/Korea

• 12 applications continue run in testbed, various middleware and scientific domains

– Savannah/Nimrod: climate model, MU, Australia– MM5/Mpich-Gx: climate model, CICESE, Mexico– QM-MD, FMO/Ninf-G: quantum-mechanics,

AIST, Japan– iGAP/Gfarm/CSF: genomics, UCSD, USA– HPM: genomics, IOIT-HCM, Vietnam– mpiBlast/Mpich-G2: genomics, ASGC, Taiwan– Gamess-APBS/Nimrod: organic chemistry,

UZurich, Switzerland– Siesta/Nimrod: molecular simulation, UZurich,

Switzerland– Amber/Rsh: molecular simulation, USM,

Malaysia

CANS2006, 12/7/2006

Mutually beneficial• Nimrod based Gamess-APBS

– Gamess-APBS: UZurich, Switzerland– Nimrod: MU, Australia

• Mpich-Gx based MM5 and WRF– MM5 and WRF: CICESE, Mexico– Mpich-Gx: KISTI, Korea

• Test/develop Gfarm and CSF with iGAP– Gfarm: AIST, Japan– CSF: JLU, China– iGAP: UCSD, USA

Application/Middleware Collaborationshttp://wiki.pragma-grid.net http://goc.pragma-grid.net

CANS2006, 12/7/2006

• Grid security– IGTF accredition

APGrid PMA, http://www.apgridpma.org/• AIST, ASGC, CNIC, NCSA, …• PRAGMA CA, catch-all

– GSI credential management• Naregi-CA (Naregi, Japan)• GAMA (SDSC, USA)

• Computation + data + sensor– Gfarm-fuse (TsukubaU/AIST, Japan)– Grid monitoring and accounting (ThaiGrid, NTU

Singapore)– GEON data network– GLEON sensor network

• Rocks and middleware– Ninf-G, SCE, Gfarm, Bio, K*Rocks, Condor, …

• AIST, ThaiGrid, NBCR, KISTI, UWSC, … – Rocks (SDSC, USA)

• OptIPuter– High performance networked TDW (CalIT2/UCSD,

KISTI, AIST, OsakaU, NCHC, CNIC, …)

Collaborations With Technology Teams

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Controlling @ CNIC Viewing @ UCSD

TDW/OptIPuter ExampleSource: Elaine Liu, PRIME 2006

CANS2006, 12/7/2006

Collaborations in BioScience

• Avian Flu Research Project– UCSD, CNIC, JLU, Uni. Of Tskuba/AIST,

University of Hawaii and Konkuk University– EGEE – Academia Sinica

• Biosciences Portal– Collaboration between Osaka University,

University of Queensland, JLU, UCSD.– Involves PRIME, PRIUS and summer students

from UCSD, Osaka and JLU.• Metagenomics Research and Genome

Informatics– Bioinformatics, computational biology software– Gfarm/CSF4, TskubaU/JLU, Japan/China– With University of Wisconsin, UCSD, PRIME

project

CANS2006, 12/7/2006

GEON-iGEON-PRAGMA

GEON is a coalition among IT and Earth Science researchers with the goal of developing advanced information technologies to enable new modes of geosciences research GEON is developing technologies for information integration and knowledge discovery

www.geongrid.org

Internationalization of GEON – iGEON PRAGMA

Some sites already working on geoscience projects Building a datagrid Welcome geoscience applications Seeking collaboration in grid interoperation

CANS2006, 12/7/2006

PRAGMA and GEON/iGEON collaboration

Sharing data, software know-how, interoperate grids• Geoscience workgroup established at

PRAGMA11• GUCAS (China)

– Setup a GEON node in PRAGMA testbed

• UMC (USA) and GUCAS– Preparing a GEON application to run in PRAGMA

testbed

• CNIC (China) – Is setting up a GEON data node in PRAGMA

testbed

• UoHyd (India) – has setup a GEON node, will join PRAGMA testbed

• AIST Geogrid (Japan) plan– Share data with GEON– Interoperate with PRAGMA testbed

CANS2006, 12/7/2006

Collaboration in Environmental Science• GLEON

– A grassroots network of• People: lake scientists,

engineers, information technology experts

• Institutions: universities, national laboratories, agencies

• Programs: PRAGMA, AS-Forest Biogeochemistry,US-LTER, TERN, KING, EcoGrid, etc.

• Instruments • Data

– Linked by a common purpose and cyberinfrastructure

– With a goal of understanding lake dynamics at local, regional, continental, and global scales

CANS2006, 12/7/2006

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

CANS2006, 12/7/2006

• BU (USA)– Joining PRAGMA grid testbed– Preparing a sensor network application to run

in the testbed

• NCHC (Taiwan)– preparing a sensor application to run in

testbed

• PRAGMA Grid + GLEON sensor network– link GLEON sites to PRAGMA testbed

computing and data grids

Collaboration with GLEON

Lake Taihu

Nanjing Institute of Geography and Limnology, Chinese Academy of Science

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• GIN – a project under OGF• GIN testbed (started Feb. 2006)

– PRAGMA, TeraGrid, EGEE, OSG, NorduGrid• Applications

– TDDFT/Ninf-G• Yoshio Tanaka, Yusuke Tanimura (AIST, Japan)• Deployed and run

– PRAGMA - AIST, NCSA, SDSC– TeraGrid – ANL– OSG – UCSD– NorduGrid

• Working on deployment to EGEE– Savanah fire simulation (data intensive)

• Colin Enticott (MU, Australia)• Started in GIN testbed

Grid Interoperation Now (GIN)http://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps

CANS2006, 12/7/2006

GIN Testbed Monitoringhttp://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps

• Infrastructure testing matrix http://goc.pragma-grid.net/cgi-bin/scmsweb/probe.cgi – SCMSWeb (by Thaigrid)– Working with PRAGMA Grid, TeraGrid, OSG, NorduGrid, EGEE– New version to handle various grid service configurations/tests

• GIN map http://maps.google.com/maps?q=http://lfield.home.cern.ch/lfield/gin.kml– Implemented a XML-> LDIF translator for GIN map– Collaboration of ThaiGrid and CERN

• Cross-grid monitoring - Common schemahttp://wiki.pragma-grid.net/index.php?title=GIN_%28Grid_Inter-operation_Now%29_Monitoring– Working with PRAGMA Grid, TeraGrid, OSG, NorduGrid, EGEE

CANS2006, 12/7/2006

Peer Grids Interoperations

• PRAGMA application developers running applications across grids– QM/MD by AIST, run on PRAGMA Grid and

TeraGrid

• Talking with OSG, LSU, UCGrid– Running applications across grids

• Bi-directional• Develop a minimum set of tools to enable

interoperation

CANS2006, 12/7/2006

PRIME http://prime.ucsd.edu

• Providing UCSD undergraduate students international interdisciplinary research internships and Cultural experiences

• Preparing the global work place of the 21st century• Built on top of PRAGMA R&D network and activities for

Undergraduate Research• A Pilot Project for Global Engagement

PRIME Class 2006

• Summer research abroad• Mentors from UCSD and

host institutions• Real science and practical

projects• Learning science,

technology and culture• Demo’s and talks• Continuing research

involvement thereafter

PRIME 2006 (Thrid Year)Host Institutions and Projects at a Glance

• CNIC, China– Virtual Screening of Avian Influenza H5N1

Neuraminidase and Hemagglutinin proteins against two libraries of ligands

– High-resolution astronomial visualization and visual collaboration environment

• MU, Australia– Computational analysis of biological structures

using GAMESS-APBS/Nimrod programs– Develop efficient method for large scale virtual

screening of ligands– More stable ionic model of ventricular myocytes

• OsakaU, Japan– Homology modeling of the protein kinases and

binding site prediction– Docking simulations of protein kinases and virtual

screening of ligands for inhibitors– Established networked Tile Display Wall

• NCHC, Taiwan– implementing image-processing software for

neural networks– Develop software tools for earthquake

experiments, monitoring and analysisPrime Students 2006Prime Students 2006Hosted by CNIC, China Hosted by CNIC, China At Lao She Tea HouseAt Lao She Tea House

CANS2006, 12/7/2006

PRIUS - Pacific Rim International UniverSity Based at Osaka University

• Establish a consistent educational program for graduate students.

• On-the-Job-training and education with PRAGMA

Lecture course:Stimulate students’ ambitious

Short Abroad Internship:Offer trial opportunities

Long Abroad Internship:Provide skill building chances

M1

M2

Doc

P.D Exchange prgm: produces liquidity in human resource

P.D

Educational Part

Research Part

Source: Susumu Date, Osaka University

http://prius.ics.es.osaka-u.ac.jp/en/index.html

CANS2006, 12/7/2006

PRIUS (First Year)

• 10 International instructors– All from PRAGMA members

• UCSD, USA• NCHC, Taiwan• NTU, Singapore• QUT, MU, Australia

– Grid computing/applications• Grid and web services• Clustering tools• Optical network computing• Grid accounting systems• Biomedical grid applications• Economic and social impact of

cyberinfrastructure– Interaction with students

• Internship abroad– UCSD, USA

• Develop QM/MM hybrid simulation program for protein research using OPAL

– NTU, Singapore• Design/prototype a grid security

monitoring system as an add-on to MOGAS

– QUT, Australia• Develop a bioscience portal for

PRAGMA– NCHC, Taiwan

• Implement high-definition-quality streaming video over a high-speed network with various TDW technologies

CANS2006, 12/7/2006

More Collaborations Forward

• Testing Gfarm with applications• More peer grids interoperation experiments• More collaborations with science teams

– GEON, GLEON, CAMERA, …• More collaboration with technology groups

– Meta-schedulling, portal, …• Greater use of the network

– Using optical networks and tile display walls• Cyber-environment• More exchange of students, replicate PRIME,

PRIUS• More trainings• Globally, especially with technology and

science teams in China

CANS2006, 12/7/2006

Future Meeting

• 20 – 22 March 2007, Bangkok Thailand– PRAGMA 12 Hosted by NECTEC and Thai

National Grid Center– 18 – 20 March 2007: GEOGrid Workshop

• Fall 2007, Urbana-Champaign USA– PRAGMA 13 Hosted by NCSA

• Spring 2008, Hsinchu Taiwan– PRAGMA 14 Hosted by NCHC

• Fall 2008, Penang Malaysia– PRAGMA 15 Hosted by USM

CANS2006, 12/7/2006

http://www.pragma-grid.nethttp://goc.pragma-grid.net

Thank You

• PRAGMA is supported by the National Science Foundation (Grant No. INT-0216895, INT-0314015, OCI -0627026), and member institutions

• PRIME is supported by the National Science Foundation under NSF INT 04007508