PRAGMA: A Framework For
Collaborations
Cindy Zheng
Peter Arzberger
Philip Papadopoulos
Mason Katz
Pacific Rim Application and Grid Middleware Assembly
University of California, San Diego
http://www.pragma-grid.net
http://goc.pragma-grid.net
OSG All Hands, 3/5/2007
Overview
• PRAGMA
– Goal and approach
• Collaborations
– In testbed
• Applications and middleware
• With science and technology teams
– With other Grids
• GIN-OPS, Peer-grids
– In education and training
• PRIME, PRIUS, NBCR institute
OSG All Hands, 3/5/2007
PRAGMA
Overarching Goals
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”.
http://www.pragma-grid.net
OSG All Hands, 3/5/2007
Overview and Approach
Process to Promote Routine Use Team Science
Workshops and
Organization
Application-Driven Collaborations
Applications
Middleware
Information Exchange
Planning and Review
Routine Use Lab/Testbed
Testing Applications
Building Grid and GOC
New Collaborations
New Members
Expand Users
Expand Impact
OSG All Hands, 3/5/2007
Multiway Dissemination
Key Middleware
Outcomes
Improved middleware
Broader Use
New Collaborations
Transfer Tech.
Standards
Publications
New Knowledge
Data Access
Education
PRAGMA Grid Testbed
UZurich
Switzerland
CNIC
GUCAS
China
JLU
China
NECTEC
NECTEC
ThaiGrid
ThaiGrid
Thailand
UoHyd
India
CUHK
HongKong
MIMOS
USM
Malaysia
BII
IHPC
NGO
NGO
Singapore
AIST
AIST
OsakaU
UTsukuba
TITech
Japan
KISTI
Korea
ASGC
NCHC
Taiwan
IOIT-HCM
Vietnam
MU
Australia
UUtah
USA
NCSA
USA
SDSC
USA
UMC
USA
CICESE
Mexico
UNAM
Mexico
APAC
QUT
Australia
BESTGrid
New Zealand
ASURC
Costa Rica
UCN
Chile
UChile
Chile
31 Clusters from 27 institutions in 14 countries/regions (+8 in preparation) 5 gfarm sites
OSG All Hands, 3/5/2007
BU
USA
Applications and Middleware
http://goc.pragma-grid.net/applications/default.html
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Real science applications pair and drive
middleware development
Achieve long-run and scientific results
Open to applications of all scientific disciplines
– Climate simulation
• Savannah/Nimrod (MU, Australia)
• MM5/Mpich-Gx (CICESE, Mexico; KISTI, Korea)
– Quantum-mechanics, quantum-chemistry:
• TDDFT, QM-MD, FMO/Ninf-G (AIST, Japan)
– Genomics
• iGAP/Gfarm/CSF (UCSD, USA; AIST, Japan; JLU,
China)
• HPM: genomics (IOIT-HCM, Vietnam)
• mpiBlast/Mpich-G2 (ASGC, Taiwan)
– Organic chemistry
• Gamess-APBS/Nimrod (UZurich, Switzerland)
– Molecular simulation
• Siesta/Nimrod (UZurich, Switzerland; MU, Australia)
• Amber/Rsh ( USM, Malaysia)
– Compute Science
• Load Balancer (VAST-HCM, Vietnam)
• GriddLeS (MU, Australia)
OSG All Hands, 3/5/2007
Application/Middleware Collaborations
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
OSG All Hands, 3/5/2007
Collaborations With Science and
Technology Teams
• Grid security
– Naregi (Japan), APGrid, GAMA (SDSC, USA)
• Grid infrastructure
– Monitoring - SCMSWeb (ThaiGrid, Thailand)
– Accounting - MOGAS (NTU Singapore)
– Metascheduling - Community Scheduling
Forum (JLU, China)
– Cyber-environment - CSE-Online (UUtah,
USA)
– Rocks and middleware (SDSC, USA; …)
• Ninf-G, SCE, Gfarm, Bio, K*Rocks, Condor, …
• Datagrid, sensor, network
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Gfarm-fuse (AIST, Japan)
GEON data network
GLEON sensor network
OptIPuter
• High performance networked TDW
• Telescience
OSG All Hands, 3/5/2007
Source: Elaine Liu, PRIME 2006
TDW/OptIPuter Example
Controlling @ CNIC
OSG All Hands, 3/5/2007
Viewing @ UCSD
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
OSG All Hands, 3/5/2007
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
OSG All Hands, 3/5/2007
 Internationalization of GEON – iGEON
 PRAGMA
 Some sites already working on
geoscience projects
 Building a datagrid
 Welcome geoscience applications
 Seeking collaboration in grid
interoperation
PRAGMA and GEON/iGEON collaboration
Sharing data, software know-how, interoperate grids
• Geoscience workgroup established at
PRAGMA11, joint conferences with PRAGMA
• 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
OSG All Hands, 3/5/2007
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
OSG All Hands, 3/5/2007
Collaborate in Publishing Research
Results
Some published papers in 2006:
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Arzberger P, Papadopoulos P. PRAGMA: Example of Grass-Roots Grid Promoting
Collaborative EScience Teams. CTWatch. Vol 2, No. 1 Feb 2006.
www.ctwatch.org/quarterly/articles/2006/02/pragmaexample-of-grass-roots-grid-promotingcollaborativee-science-teams
Abramson D, Lynch A, Takemiya H, Tanimura Y, Date S, Nakamura H, Jeong K, Hwang S, Zhu J,
Lu Z, Amoreira C, Baldridge K, Lee H, Wang C, Shih HL, Molina T, Li, W, Arzberger P. Deploying
Scientific Applications on the PRAGMA Grid testbed: Ways, Means and Lessons.
IEEE/CCGRID International Workshop on Grid Computing, 2006, Singapore.
Lee B-S, Tang M, Zhang J, Soon O Y, Zheng C, Arzberger P. Analysis of Jobs on a MultiOrganizational Grid Testbed. IEEE/CCGRID Int’l Workshop on Grid Computing, 2006,
Singapore.
Zheng C, Abramson D, Arzberger P, Ayuub S, Enticott C, Garic S, Katz M, Kwak J, Lee B S,
Papadopoulos P, Phatanapherom S, Sriprayoonsakul S, Tanaka Y, Tanimura Y, Tatebe O,
Uthayopas P. The PRAGMA Testbed: Building a Multi-Application International Grid. 2005
IEEE/CCGRID International Workshop on Grid Computing, 2006, Singapore.
Li WW, Arzberger PW, Yeo CL, Ang L, Tatebe O, Sekiguchi S, Jeong K, Wuang S, Date S,
Kwak JH. Proteome Analysis Using iGAP in Gfarm. The Second International Life Science
Grid Workshop 2005, Grid Asia 2005, Singapore 2005.
Wei X, Ding Z, Li W W, Tatebe O, Jiang J, et al. GDIA: A Scalable Grid Infrastructure for Data
Intensive Applications. IEEE Int’l Conference on Hybrid Information Technology, ICHIT 2006,
Cheju Island, Korea.
Krishnan S, Baldridge K K, Greenberg J. P, Stearn B, Bhatia K. An End-to-End Web ServicesBased Infrastructure for Biomedical Applications. Proceedings of Grid 2005, 6th IEEE/ACM
Int’l Workshop on Grid Computing, November 13-14, 2005, Seattle, WA, U.S.
…
OSG All Hands, 3/5/2007
Grid Interoperation Now (GIN)
http://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps
OGF – GIN-OPS
• GIN testbed (February, 2006 – on-going)
• TDDFT/Ninf-G (PRAGMA - AIST, Japan)
– PRAGMA, TeraGrid, OSG, NorduGrid; EGEE
• Savanah fire simulation (PRAGMA - MU, Australia)
– PRAGMA, TeraGrid, OSG
• Multi-Grid monitoring
– SCMSWeb probe matrix (PRAGMA - ThaiGrid, Thailand)
– Common schema (PRAGMA, TeraGrid, EGEE,
NorduGrid)
OSG All Hands, 3/5/2007
Peer-grid Interoperation Experiments
http://goc.pragma-grid.net/wiki/index.php/Main_Page#Grid_Inter-operations
• PRAGMA->TeraGrid (October, 2006 – on-going)
– PRAGMA member runs application across both grids
– QM/MD/Ninf-G (AIST, Japan)
– Manual reservation, 7 sites in PRAGMA, 3 sites in TeraGrid
• OSG<->PRAGMA (January, 2007 – on-going)
– Members from both grids run applications across both grids
– Applications:
• OSG
– GISolve
– spatial Interpolation
– UIowa, USA
• PRAGMA
– FMO/Ninf-G
– quantum Chemistry
– AIST, Japan
OSG All Hands, 3/5/2007
OSG-PRAGMA Interoperation Experiment
http://goc.pragma-grid.net/wiki/index.php/OSG-PRAGMA_Grid_Interoperation_Experiments
Resources
Learned
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OSG
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FermilabGrid
Jan 4, 2007, identify who and how
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Coordinator, application drivers,
resource supporters
Wiki, application, requirements
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Jan 25, 2007, initial VTC
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Goals, Q/A exchange
Start working
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Email immediately issues, solutions
Weekly status, email, wiki
Status
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Feb 26 - March 1, started application
runs successfully
OSG All Hands, 3/5/2007
Job submission
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SDSC, USA
NECTEC, Thailand
NGO, Singapore
ThaiGrid, Thailand
Process
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PRAGMA
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Differences in grid environment effect users
and applications
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Security policy
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Change RSL parameter
Remove inter-node parallel execution
Take work to setup access
Account on gatekeeper node
Large scale calculations are possible
Middleware fault tolerance and flexible
resource management is important
A set of jobs are processed
on the VO, collected, and
updated for the next iteration.
PRIME
http://prime.ucsd.edu
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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
• 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
OSG All Hands, 3/5/2007
PRIME Class 2006
PRIME 2006 (Thrid Year)
Host Institutions and Projects at a Glance
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CNIC, China
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MU, Australia
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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
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Prime Students 2006
Hosted by CNIC, China
At Lao She Tea House
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
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Virtual Screening of Avian Influenza H5N1
Neuraminidase and Hemagglutinin proteins
against two libraries of ligands
High-resolution astronomial visualization and
visual collaboration environment
implementing image-processing software for
neural networks
– Develop software tools for earthquake
experiments, monitoring and analysis
PRIUS - 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
Doc
Long Abroad Internship:
Provide skill building chances
M2
M1
liquidity in human resource
Short Abroad Internship:
Offer trial opportunities
Research Part
Educational Part
Lecture course:
Stimulate students’ ambitious
OSG All Hands, 3/5/2007
Source: Susumu Date, Osaka University
PRIUS
(First Year)
• Internship abroad
– UCSD, USA
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10 International instructors
– All from PRAGMA members
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UCSD, USA
NCHC, Taiwan
NTU, Singapore
QUT, MU, Australia
– Grid computing/applications
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Grid and web services
Clustering tools
Optical network computing
Grid accounting systems
Biomedical grid applications
Economic and social impact of
cyberinfrastructure
– Interaction with students
OSG All Hands, 3/5/2007
• 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
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
OSG All Hands, 3/5/2007
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PRAGMA is supported by the National
Science Foundation (Grant No. INT0216895, INT-0314015, OCI -0627026),
and member institutions
PRIME is supported by the National
Science Foundation under NSF INT
04007508
Thank You
http://www.pragma-grid.net
http://goc.pragma-grid.net
OSG All Hands, 3/5/2007