Overview of PRAGMA
View to the Future
Examples of Team Science and
Global Engagement in Asia Pacific and South Asia
Peter Arzberger
Philip Papadopoulos
Mason Katz
Cindy Zheng
Enhancing Research and Education
Connectivity to and within South Asia
26 April 2007
Spring Internet2 Meeting
Some Perspectives: Do they apply to you?
• “…The conduct of science,
Spread of Infectious Diseases
intrinsically global, has become
Health of Oceans
increasingly important to
Health of Coral Reefs
addressing critical global
Impacts of Global Warming
issues… .” [NSB 2000]
Role of Lakes in Carbon Cycling
• “ It is imperative that the ACP
[Advanced Cyberinfrastructure
Avoid Replay of Cluster Divergence
Program] interoperate with
Grids Support Global Science
cyberinfrastructure being
developed and deployed in other Tools Developed Across Globe
countries.” [Atkins et.al. 2003 ]
• “What nations don’t know can hurt
them. The stakes involved in
study abroad are that simple, that People Make Collaborations
straightforward, and that important.
… college graduates today must
be internationally competent.”
Delivered by Philip Papadopoulos,
[Lincoln Report 2005]
NSF Global Engagement Workshop
e-science’s Team Science:
Merging of Science and Information Technology
Education
& Capacity
Building
Sustained
Collaboration
• Build teams and
trust
• Many meetings
Science
Drivers
Previously
Unobtainable
Observations and
Understanding
• Develop human resources
• Students and postdocs
Enabling
Technology
• Advance science
• Focus development
Persistent
• Stream Data
• Source, movement,
Infrastructure
• Dist. Files System
fate of carbon in lakes
• Web Services
• Role of Savannah Burns • Broaden impact
• Cross-site query
• Software, data
on Monsoons
• Collaborative Tools
• Active sites of infectious • Lambda Grids
• Wireless sensor network • Many more
agents
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
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
Multiway Dissemination
Key Middleware
Outcomes
Improved middleware
Broader Use
New Collaborations
Transfer Tech.
Standards
Publications
New Knowledge
Data Access
Education
Applications and Middleware
http://goc.pragma-grid.net/applications/default.html
•
•
•
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)
Source: Cindy Zheng
PRAGMA Grid Testbed
CNIC
CNIC
GUCAS
China
UZurich
Switzerland
JLU
China
LZU
China
UoHyd
India
CUHK
HongKong
NECTEC
NECTEC
ThaiGrid
ThaiGrid
Thailand
MIMOS
USM
Malaysia
AIST
AIST
OsakaU
UTsukuba
TITech
Japan
KISTI
Korea
ASGC
NCHC
Taiwan
IOIT-HCM
Vietnam
BII
IHPC
NGO
NGO
Singapore
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
32 Clusters from 29 institutions in 14 countries/regions (+ 7 in preparation) 7 gfarm sites
Source Cindy Zheng
BU
USA
Savannah Burn:
How tightly linked are burning, vegetation, and rainfall?
• PRAGMA Testbed ran CSIRO
climate model called CCAM in
combination with Nimrod/G tool set.
• Executed on a maximum of 90
processors (out of a maximum 159)
across 7 PRAGMA grid resources
located in Australia, Japan, Korea,
Taiwan, Thailand and the U.S.
• David Abramson, Amanda Lynch
Validation of Cyberinfrastructure Investments
by the Savannah Burn experiment
•
Science Resulted: The hypothesis that burning the
Savannah can affect the strength and timing of the
monsoon was confirmed.
Testbed Exercised: The testbed operated for 170 days,
and delivered over 1.25 million processor hours!
Importantly, we were able to do a live upgrade of a
number of the cyberinfrastructure components during the
period.
Middleware Improved: Improved Nimrod's ability to
schedule computations by incorporating both data location
and transport delays.
•
•
–
–
•
Allowing it to make a better choice of resources, improving the
performance of the system as well as its fault tolerance.
We also enhanced Nimrod's ability to handle faults in the Grid
testbed.
Policy Impacted: The experiment shipped some 1.6TB of
data across national and international networks. This
exposed some interesting features of Australia’s network
charging policy, and will lead to lasting improvements.
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
–
–
–
–
Gfarm-fuse (AIST, Japan)
GEON data network
GLEON sensor network
OptIPuter - High performance networked TDW,
Telescience
Source: Cindy Zheng
Grid Interoperation Experiments
http://goc.pragma-grid.net/wiki/index.php/Main_Page#Grid_Inter-operations
• OGF – Grid Interoperation Now (GIN), 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)
• Peer-grid interoperation experiments
– 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
OSG - Spatial Interpolation (UIowa, USA)
PRAGMA - FMO/Ninf-G (AIST, Japan)
OSG - FermilabGrid
PRAGMA – SDSC, USA; NECTEC, Thailand; NGO,
Singapore; ThaiGrid, Thailand
Source: Cindy Zheng
PRAGMA Highlights of 2006 - 2007
• Simulating the Australian Monsoon and the
Effect of Wildfires
• PRAGMA Biosciences Portal
• PRAGMA Leads Application Experiment of Grid
Interoperation in GIN Testbed
• PRAGMA Establishes Certificate Authority (CA)
Using Naregi-CA Software
• Expanding the Collaboration Grid
• Building Communities, Catalyzing
Collaborations
• PRIME and PRIUS
• More accomplishments in the Working Group
sections
Collaborate in Publishing Research Results
Some Publications 2006
•
•
•
•
•
•
•
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-gridpromoting-collaborativee-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
Multi-Organizational 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
Services-Based 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.
PRIME: Providing Students International Interdisciplinary Research
Internships and Cultural Experiences
preparing the global workplace of the 21st century
PRIME Class 2006
•Computer Network
Information Center (CNIC),
Chinese Academy of
Sciences
•Cybermedia Center (CMC),
Osaka University, Japan
•Monash University, Australia
•National Center for Highperformance Computing
(NCHC), Taiwan
• Built on top of PRAGMA people network
– Dual Mentors; Pre/post research apprenticeship
– Cultural competency preparation
• What’s Up with Culture
– Professional development seminars
• A Pilot Project for Global Engagement
prime.ucsd.edu
Educational Network linking
13 organizations
Fostering of Globally-Leading
Researchers
in 7 countries centered around the Pacific Rim
in Integrated Science (PRIUS)
Ａｃｈｉｅｖｅｍｅｎｔ ２００６（２００５)：
# of PRIUS-Invited lecturers
# of Internship Students
“Studies on International Integrated Science I, II”
１３ （６）
４ （１）
University of Illinois,
Chicago
Harbin Institute of Technology
University of California,
San Diego
rsity of Zurich, Irchel
National Center for
High-performance Computing
University of Malaysia
Nanyang Technological
University
Queensland University of Technology
QM/MM simulation
Using OPAL OP
Bioscience GridPortal
University of Melbourne
Invited Lecturer
Security Monitoring System
Based on MOGAS
PRIUS URL: http://prius.ist.osaka-u.ac.jp
Internship
Student
University of Canterbury
Augment Reality toolkit
Towards a Global
Lake Ecological
Access can be difficult
during the
most
Observatory
Network
interesting times
20
18
Photo by Peter Arzberger, October 2004
16
20
18
16
14
12
10
8
6
14
4
2
12
22-Aug
(mm per 5 minute interval)
Surface
0.5 meters
1 meter
1.5 meters
2 meters
2.5 meters
3 meters
Precipitation
Precipitation
Water Temperature (°C)
22
0
23-Aug
24-Aug
25-Aug
26-Aug
27-Aug
28-Aug
Date
Source: Tim Kratz
Yuan Yang Lake, Taiwan ; photo by Matt Van de Bogert
Collaboration in Environmental Science
Global Lake Ecological Observatory Network
• 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
GLEON
People & Groups
TEAM SCIENCE
15
MEETINGS
San Diego March 05
Townsville March 06
Hsinchu October 06
Lammi March 07
Montreal August 07
GLEON
Existing sites = yellow
New sites (RCN) = red
Research Coordination Network (NSF award, PI: P Hanson):
• Includes a series of key science questions
• Architectural design of coordinated global sensor network
• Broaden involvement at all levels; new partners, outreach
and education
Lessons Learned in Building e-Communities
• Repeated structured interactions (workshops) to build
the community
– More often at first, twice/year now
– Unstructured/Spontaneous interactions. It was several years
before these started
• Group focuses on enabling science outcomes
• Technology builders give tutorials on capabilities
• Science + Technologists work side-by-side
– Infrastructure/Requirements evolves naturally
– Not “Build it and they will come”
– Not “Gather requirements, Get stakeholder Buy In”
• Culture of openness and sharing of know-how and
software
• Continue to experiment: Applications, Technologies,
Meetings (structure, types), People (and students)
• Baby steps; and more baby steps (Learn by doing)
• Break bread together
• Stay PRAGMAtic
Every Presentation Is an Invitation to Collaboration:
Some Ideas
• Involvement in PRAGMA Grid
or other activities
–
–
–
–
Biosciences - Avian Flu; Metagenomics
Geosciences
GLEON (or CREON)
Telesciences and
Tile Display Walls – NEEDS NETWORKING
• PRAGMA Institute for South Asia
– NCHC (Taiwan) has annual workshop for Southeast Asia
– U of Hyderabad is willing to host a PRAGMA Institute for this
region!
• Exchange students and researchers
– PRIME / PRIUS
• Participation in PRAGMA Workshops
– Two times per year
Future PRAGMA Workshops
• 20 – 22 March 2007, Bangkok Thailand
– PRAGMA 12 Hosted by NECTEC and Thai
National Grid Center,
– 20 March 2007: GEOGrid Workshop
• 23 – 25 September 2007, UrbanaChampaign Illinois USA
– PRAGMA 13 Hosted by NCSA
• Spring 2008, Hsinchu Taiwan
– PRAGMA 14 Hosted by NCHC
• Fall 2008, Penang Malaysia
– PRAGMA 15 Hosted by USM
www.pragma-grid.net
But Why Get Involved?
• Larger Reasons
– Science is global and collaborative
– Internet and grid designed globally
• Personal or Institutional
–
–
–
–
–
–
Exposure to technologies and developers
Obtain users of software
Gain access to resources
Develop collaborators and contacts
Expose students/staff to new conduct of science
Launch new programs
• Other
– Force improvements in infrastructure
Network Challenges:
How common are these?
• 1. Accessibility (easier in metro city)
• 2. Cost of the Bandwidth (very high)
• 3. Bound on latency (to be decreased)
currently to USA it is < 330msecs.
• 4. Bilateral/multilateral agreements
Global Engagement Examples and Programs
SCIENCE
• GLEON
– Global Ecological Observatory Network
– Grassroots effort to understand lake dynamics
EDUCATION
• PRIME
– Pacific Rim Experiences for Undergraduates
– Prepares globally-enabled workforce
• PRIUS
– Pacific Rim International UniverSity at Osaka University
– Prepares global workforce in context of curriculum
GRID
• PRAGMA
– Pacific Rim Application and Grid Middleware Assembly
– Catalyzes collaborations
SOFTWARE
• OptIPuter:
– Optical networking, Internet Protocol, computer storage,
processing and visualization technologies
– Develops technologies for data intensive computing and
collaborations
•
Acknowledgements
All PRAGMA members
– Slides from Phil Papadopoulos, Cindy Zheng, FangPang Lin, Satoshi Sekiguchi
•
•
•
•
•
•
•
•
•
•
•
•
•
•
Gabriele Wienhausen, UCSD - PRIME
Susumu Date and Shinji Shimojo, Osaka University – PRIUS
Tim Kratz, U Wisconsin; Fang-Pang Lin, NCHC, David Hamilton, U Waikato
– GLEON
Larry Smarr – OptIPuter
Wilfred Li – National Biomedical Computation Resource
Tony Fountain, Tim Kratz, Ken Chiu, Rick McMullen, Sameer Tilak Autoscaling
Bill Chang, NSF for planting the seed and ongoing encouragement
NSF, Gordon and Betty Moore Foundation, TATRC, NIH
PRAGMA is supported by the NSF (Grant No. INT-0216895, INT-0314015, OCI 0627026), the San Diego Supercomputer Center, and the California Institute of
Telecommuncations and Information Technology , The University of California, San
Diego and member institutions
PRIME is Supported by the National Science Foundation under NSF INT 04007508
AutoScaling, NEON 0446802
The OptIPuter receives major funding from the National Science
Foundation, cooperative agreement ANI-0225642 to UCSD
TATRC – for funding of avian flu international collaboration
NBCR – for biomedical infrastructure, funded by NIH
A Final Thought
• “Peace and prosperity
around the world
depend on increasing
the capacity of people
to think and work on a
global and
intercultural basis. As
technology opens
borders, educational
and professional
exchange opens
minds.”[i]
http://www.youtube.com/watch?v=4lY6x0S3IoA
Google: PRIME students youtube
[i] Annual Report IIE 2005, and http://www.iie.org/ “About”