Post on 11-Jan-2016
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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
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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
CANS2006, 12/7/2006
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
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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
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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
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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