Cindy Zheng
Peter Arzberger
Philip Papadopoulos
Mason Katz
P acific R im A pplication and G rid M iddleware A ssembly
University of California, San Diego
CANS2006, 12/7/2006 http://www.pragma-grid.net
http://goc.pragma-grid.net

• 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, 12/7/2006

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
“A Practical Collaborative Framework”
.
pragma -grid.net

Process to Promote Routine Use Team Science
Application-Driven Collaborations
Applications Middleware
Workshops and
Organization
Information Exchange
Planning and Review
New Collaborations
New Members
Expand Users
Expand Impact
Multiway Dissemination
Key Middleware
Outcomes
Routine Use Lab/Testbed
Testing Applications
Building Grid and GOC
Improved middleware
Broader Use
New Collaborations
Transfer Tech.
Standards
Publications
New Knowledge
Data Access
Education
CANS2006, 12/7/2006

UZurich
Switzerland
CNIC
GUCAS
China
KU
NECTEC
Thailand
JLU
China KISTI
Korea
AIST
OsakaU
UTsukuba
TITech
Japan
SDSC
USA
UUtah
USA
NCSA
USA
UoHyd
India
CUHK
HongKong
ASGC
NCHC
Taiwan
CICESE
Mexico
UNAM
Mexico
UMC
USA
BU
USA
MIMOS
USM
Malaysia
IOIT-HCM
Vietnam
ASURC
Costa Rica APAC
QUT
Australia BII
IHPC
NGO
Singapore
MU
Australia
BESTGrid
New Zealand
UCN
Chile
UChile
Chile
29 Clusters from 26 institutions in 14 countries/regions ( +9 in preparation )
CANS2006, 12/7/2006

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

http://wiki.pragma-grid.net
http://goc.pragma-grid.net
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
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, …)
CANS2006, 12/7/2006

TDW/OptIPuter Example
Controlling @ CNIC
Source: Elaine Liu, PRIME 2006
Viewing @ UCSD
CANS2006, 12/7/2006

• 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 www.geongrid.org

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

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

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

• 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
Kangwon U
B.Kim
Maintain Soyang
Public Policy
NCHC
F.P.Lin
Maintain YYL
Parallelize Codes
NIGLAS
B.Q Qin
Maintain Taihu
Physical Limnology
U.Waikato
D.Hamilton
Models
UCSD
F.Vernon, S.Peltier,
T.Fountain P.Arzberger
ROADNet, Telescience
Moore Fnd, PRAGMA
U.Wisconsin
T.Kratz
Maintain Trout Bog
Lake Metabolism
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
Lake Taihu
Nanjing Institute of Geography and Limnology,
CANS2006, 12/7/2006
Chinese Academy of Science

http://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps
• 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
CANS2006, 12/7/2006

http://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 schema http://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

– QM/MD by AIST, run on PRAGMA Grid and
TeraGrid
– 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 21 st century
•
Built on top of PRAGMA R&D network and activities for
Undergraduate Research
• A Pilot Project for Global Engagement
• 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
CANS2006, 12/7/2006
PRIME Class 2006

Host Institutions and Projects at a Glance
Prime Students 2006
Hosted by CNIC, China
At Lao She Tea House
•
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 analysis

Pacific Rim International UniverSity
Based at Osaka University http://prius.ics.es.osaka-u.ac.jp/en/index.html
• Establish a consistent educational program for graduate students.
• On-the-Job-training and education with PRAGMA
P.D
P.D Exchange prgm: produces liquidity in human resource
Doc
M2
Long Abroad Internship:
Provide skill building chances
Short Abroad Internship:
Offer trial opportunities
Research Part
Educational Part
M1 Lecture course:
Stimulate students’ ambitious
CANS2006, 12/7/2006
Source: Susumu Date, Osaka University

• 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

• 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

• 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

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