PRAGMA: A collaborative framework for global team science and education

PRIMEGLEON

Peter Arzberger1 November 2005Shenzhen, China

We Are Living Through A Fundamental GlobalChange—How Can We Glimpse the Future?

[The Internet] has created a [global] platform where intellectual work, intellectual capital,

could be delivered from anywhere. It could be disaggregated, delivered, distributed, produced, and

put back together again…

The playing field is being leveled.”

Nandan Nilekani, CEO Infosys (Bangalore, India)

Slide Source:Larry Smarr

“The World is Flat”*

• Fundamental changes are underway in how:– Researchers interact with each other and with resources– Resources are distributed and accessed on the network– Science and education are conducted

• This is leading to new– Research and educational paradigms– Discoveries and innovations– Networks of people

• Multidisciplinary, multi-institutional, international

• Many scientific problems are global – Demanding global approaches– Providing future opportunities for creating previously

unobtainable observations and understanding

* Thomas Friedman

M.Brown

Trends Enabling Scientific Research

Cyberinfrastructureand e-science: Bringing Resources to Researchers

Human

Interfaces for visualization

and collaborations

Digital collectionsfor

knowledge management

Compute resources for modeling, simulation,

data analysis Instruments for

observationsGlobal

Connectivity

e-science’s New Frontier: Merging of Science and Information Technology

PreviouslyUnobtainable

Observations andUnderstanding Enabling

Technology

• Advance science

Science Drivers

• Focus development

PersistentInfrastructure

• Broaden impact

Education & Capacity

Building

• Develop human resources

Sustained Collaboration

• Build teams andtrust

PRAGMA’s Founding Motivations

• Science is an intrinsically global activity

• The grid is transforming e-science:computing, data *, and collaboration

• The problem remains that the grid is too hard to use on a routine basis

• Middleware software and people need to interoperate

http://www.pragma-grid.net

Establish sustained collaborations and

Advance the use of the grid technologies for applications

among a community of investigators working with leading institutions around the Pacific

Rim

Overarching GoalsPRAGMA

Working closely with established activities thatpromote grid activities or the underlying infrastructure,

both in the Pacific Rim and globally.

Key Attributes of PRAGMA Successes (Intangible but Critical)

• Constructed conduit of technology, ideas, information, people– Multi-directional flow among institutions and

communities of software, approaches• Developed framework for collaboration

– Foundation for continued and greater work• Built trust among members

– Interoperability is essential among people– Sharing (resources, ideas, people) resulted

Results: many unplanned, tangible successes

www.uohyd.ernet.in/pragma9www.prama-grid.org

Highlighted Successes Unanticipated

• SARS: Grid Community Pulls together to Battle SARS

• GLEON: Launching a new community effort– Building on EcoGrid in Taiwan

• Expanding Reach of Projects– Optiputer; NEESit; iGEON; IVOA

• PRIME: Creating opportunities for undergraduate students– Reciprocal Projects from Jilin

• PRIUS: Osaka University, international internships and “PRAGMA Classes”

• KRocks: Localization of Rocks in KoreaSuccesses that happened because PRAGMA exists

Highlighted Successes - Anticipated• Telescience: Sharing and Contributing Technology• Multi-way Dissemination and Integration of Software:

– Ninf-G into NMI (and Naregi CA)– iGAP/Gfarm, GAMESS/Nimrod– Rocks Rolls of SCE, Gfarm, Ninf-g

• Creation of Laboratory for Routine Use Experiments– Grew from 8 sites to 19 sites; Multiple, persistent experiments– Use and co-development of SCMSWeb and other software in

PRAGMA (e.g. CICESE porting SCMSWeb to solaris system; CNIC porting it to Itanium) and use of MOGAS (Grid Acct System – from PRAGMA 8)

– Active dissemination of iNLANR AMP network– Joint paper (Resource Working Group rose to challenge) Issues

and Methods for Building a Multi-Application International Grid Resource

• Assisted in RPC standards at GGF, and launching of International Grid Trust Federation

Outcomes through on-going meetings

PRAGMA Grid TestbedPRAGMA Grid Testbed

AIST, JapanCNIC, China

KISTI, Korea

ASCC, Taiwan

NCHC, TaiwanUoHyd, India

MU, AustraliaBII, Singapore

KU, Thailand

USM, Malaysia

NCSA, USA

SDSC, USA

CICESE, Mexico

UNAM, Mexico

UChile, Chile

TITECH, Japan

UMC, USA

UZurich, Switzerland

GUCAS, China

http://pragma-goc.rocksclusters.org

PRAGMA Grid resourceshttp://pragma-goc.rocksclusters.org/pragma-doc/resources.html

AIST, JapanCNIC, China

KISTI, Korea

UoHyd, India

MU, Australia

NCSA, USA

UChile, Chile

TITECH, Japan

PRAGMA Grid Testbed12 countries, 19 clusters, 550 CPUs, 900GB memory

RoutineRoutine--basisbasisexperimentsexperiments

KU, Thailand

USM, Malaysia

BII, Singapore

UNAM, Mexico

NCHC, Taiwan

ASCC, TaiwanCICESE, Mexico

SDSC, USA

TDDFT

Savannah Study

QM/MD

BioGridSCMSWeb

Source: Cindy Zheng

Grid-enabling Applications• Ocean science (CICESE, Mexico)

– IGrid05 demoRaul Hazas, Luis Farfán, Salvador Castaneda,

Julian Delgado• GAMESS/APBS (UZurich, Switzerland)

Kim Baldridge, Celine Amoreira• FLARM, Drug-design (CNIC, China)

Bin Shen, Kevin Dong• San Andreas Fault simulation (iGEON)

Mian Liu (UMC), Huai Zhang (GUCAS)

SCMSWebhttp://pragma-goc.rocksclusters.org/scmsweb/

• Grid monitoring system• Development lead: KU: Putchong Uthayopas, Somsak

Sriprayoonsakul, Sugree Phatanapherom• Collaborations:

– Solaris porting at CICESE: Raul Hazas, Areli Garcia– IA64 porting at CNIC: Kevin Dong

• Deployed on 15 sites:– AIST: Yoshio Tanaka, Yusuke Tanimura– ASCC: Hurng-Chun Lee, Mike Chiang– BII: Stephen Wong, Damien Leong Wye Kit– CICESE: Raul Hazas, Salvador Castaneda, Julian Delgado– CNIC: Kai Nan, Kevin Dong– KISTI: Jysoo Lee, Jae-Hyuck Kwak– KU: Sugree Phatanapherom, Somsak Sriprayoonsakul– NCHC: Weicheng Huang, Chien-Lin Huang– NCSA: Radha Nandkumar, Tom Roney– SDSC: Mason Katz, Cindy Zheng– TITECH: Satoshi Matsuoka, Hitoshi Aoki– UChile: Alejandro Jofre, Juan Carlos Maureira– UNAM: Jose Luis Gordillo Ruiz, Eduardo Murrieta Leon– UoHyd: Arun Agarwal, Rajeev Wankar, Neelakanta Reddy– USM(hawk): Habibah Wahab, Suhaini Ahmad

Ninf-G/NMI/Rocks Integration• Ninf-G-2.4/NMI

– Lead integrators: • Yoshio Tanaka (AIST)• Mats Rynge (NMI)

• Ninf-G 2.4 Rocks Roll – Lead integrators:

• Mason Katz (SDSC)• Yoshio Tanaka (AIST)

Ninf-G v2.4.0 released in NMI v8first experience for NMI to include non-U.S. software.

Evaluate and improve Ninf-G2 through the PRAGMA routine-basis experiments

PRAGMA: Collaborative Overview 2005- 2006

• Points of Contact• Table of Content• Overview of last years

progress• Accomplishments• PRIME and PRIUS• Working Groups• Institutional Members• Publications• Past and future meetings

2005 Accomplishments• iGRID 2005 (18 or 49

demos by PRAGMA members)

• GLEON• Computational Chemistry• iGAP-Gfarm (active

collaboration – many institutions)

• Testbed and GOC• International AMP mesh –

all testbed sites• Multi-way software

dissemination– E.g. NinfG and NMI

PRAGMA at iGRID200518 of 49 demos

• 13 Institutions– APAC: Australia Partnership for Advanced Computing– CMC: Cybermedia Center, Osaka– CNIC, CAS: Computer Network Information Center, Chinese Academy

of Sciences– GTRC/AIST: Grid Technology Research Center, National Institute for

Advanced Industrial Science and Technology– KISTI: Korea Institute for Science and Technology Information– NCHC: National Center for High-performance Computing– NCSA: National Center for Supercomputing Applications– PNWGP: Pacific Northwest Gigapop– Starlight– Titech: Tokyo Institute of Technology– UCSD and Calit2: University of California and California Institute for

Telecommunications and Information Technology– CICESE: Centro de Investigacion Cientifica y de Educacion Superior de

Ensenada– WestGrid: Western Canada Research Grid

PRAGMA at SC05

• Many Members Present– Booths (10): AIST, CCS/Tsukuba, CMC/Osaka, KISTI, NCHC,

NCSA, PNWGP, SDSC, UCSD, NBCR (NIH)– Others (3): Monash, Starlight, TransPAC

• Joint Presentation at NCHC stage– Wed 14 Nov, 3 – 5 pm

• Other PRAGMA presentations– NCHC Booth Thursday 10 to 11 am– NCSA Booth Tuesday 2:30 pm– SDSC Stage: TBD

• Pacific Northwest Gigapop: – Host PRAGMA reception on Wed 16 November

List of Demonstration• Long-run of the Hybrid QM/MD simulation on the PRAGMA Grid Testbed,

AIST• Gfarm Grid file system, AIST• High-performance KEKB/Belle data analysis using Gfarm file system, AIST• Bioinformatics applications inside Gfarm using metaschedulers and local

batch schedulers, KISTI• NCHC's Grid Portal, NCHC• NCHC's Flood Mitigation Grid, NCHC• CFD Portal on e-Science Environment, NCHC• iGRID, Gfarm, SDSC, AIST• High bandwidth application over a dedicated high-bandwidth, long-pathway

circuit, PNWGP, Pacific Wave, EVL, others• High-definition video conference including groups from Japan, Korea,

Australia, Canada, Michigan, Wisconsin, Pennsylvania, PNWGP and others• High-definition video production including video/audio capture; distribution

to Storage Resource Broker (SRB) locations; and real-time collaborative editing, PNWGP and others

• OptIPuter, UCSD• Telescience, NCRR

The PRAGMA Steering Committee

http://www.pragma-grid.net/steering_committee.htm

Steering CommitteeCame into effect 25 Feb 2003

• John O’Callahan, David Abramson, Bernard Pailthorpe: APAC

• Santosh Mishra: BII

• Baoping Yan, Kai Nan: CAS/CNIC

• Satoshi Matsuoka: TITech/GSICC

• Satoshi Sekiguchi, Yoshio Tanaka: AIST

• Jysoo Lee, Kum-Won Cho: KISTI

• Whey-Fone Tsai, Fang-Pang Lin: NCHC

• Shinji Shimojo, Sumumu Date: Osaka University

• Piyawut Srichaikul, Chalermpol Charnsripinyo : NECTEC

• Maxine Brown: StarTap

• Rick McMullen, Jim Williams: TransPAC

• Ahmad YusoffHassan, Habibah Wahab: U SainsMalaysia

• Arun Agarwal: U Hyderabad

• Philip Papadopoulos, Peter Arzberger: UCSD/SDSC/Calit2/CRBS/NLANR

PRAGMA Future Meetings

• PRAGMA 10– QPSF, JCU, APAC, Townsville, Australia 26 – 28 March 2006– Bringing the Grid to coastal zones; Held in conjunction with

GLEON and Coral Reef • PRAGMA 11

– Osaka University, Japan, approx. 15 – 17 October 2006– Preparing Future Generations; in conjunction with PRIUS

program• PRAGMA 12

– NECTEC, Kasetsart University, Thailand, Spring 2007– Advancing Collaborations with ThaiGrid

• PRAGMA 13– NCSA, Illinois, USA, Fall 2007– PRAGMA Engagements in Cyberenvironments

• PRAGMA 14– NCHC, Taiwan, Spring 2008– Living Grids; Held in conjunction with Taiwan Grid Activities

Criteria for Membership

• Active Participation

Taiwan’s Natural Beauty

EnvironmentalObservatoriesDistributed

Infrastructure

Transformative in understanding complexity of natural and human environments

Liz Blood

NSF

EO

S

Geographically distributed infrastructure connected via cyberinfrastructure into national observatory network

Apply emerging technologies (sensor, analytical, communication, and information) to investigate the structure, dynamics, and evolution of systems in the United States and forecast change.

New collaborative environments (simulation, computation, visualization, and knowledge systems) are needed to facilitate the integration of research, education, and dialog across a wide range of biological, geophysical, and social sciences.

Data repositories and facilities for synthesis and prediction

Characteristics

Liz Blood

Sensor networks allow high frequency observations over broad spatial extents

Frequency of measurement

Spatial extent

Annual

100 km

Monthly Weekly Daily Hourly Min. Sec.

10 km

1 km

100 m

10 m

1 m

10 cm

Existing Sensor Networks

random selection from Ecology 2003

Source: John Porter et al., Bioscience, in review

Lake Metabolism Website

http://lakemetabolism.org

12

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22-Aug 23-Aug 24-Aug 25-Aug 26-Aug 27-Aug 28-Aug

Date

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(mm

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5 m

inut

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Surface0.5 meters1 meter1.5 meters2 meters2.5 meters3 metersPrecipitation

Typhoon

Yuan Yang Lake, Taiwan – August 2004

Part of a growing global lake observatory network - http://lakemetabolism.org

An example of episodic events and threshold dynamicsAccess can be difficult

during the most interesting times

Photo by Peter Arzberger, October 2004

Used by N

SF Director Feb 2005

Vision and Driving Rationale for GLEON

• A global network of hundreds of instrumented lakes, data, researchers, students,

• Predict lake ecosystems response to natural and anthropogenic mediated events – Through improved data inputs to simulation

models– To better plan and preserve freshwater

resources on the planet

What is the “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

Source: T. Kratz

Programs-Australia-Canada-China-Finland-Florida-New Zealand-Israel-South Korea-Taiwan-United Kingdom-Wisconsin

First meeting:San DiegoMarch 7-9, 2005

Source: T. Kratz

Steering Committee-Peter Arzberger, UCSD, USA-David Hamiltion, University of Waikato,

New Zealand-Tim Kratz, University of Wisconsin, USA-Fang-Pang Lin, NCHC, Taiwan

Why develop such a network?

• Lakes are globally important– Sources of drinking water, irrigation, recreation, aesthetics, etc.– Hotspots of biogeochemical cycling– Millenium Assessment shows water resource use is currently not

sustainable globally– Quality of water resources will determine quality of life

• Need to understand lake dynamics at local, regional, continental, and global scales – Effect of large-scale climatic forcing such as El Nino, North Atlantic

Oscillation etc.– Carbon dynamics of lakes and role in global carbon balance– Effect of chronic and episodic events (land use change, climate

change, typhoons, etc.)– Coupling of physical-biological processes in lakes

Source: T. Kratz

Why develop such a network?• Science

– Global e-science becoming increasingly possible

– Developments in sensors and sensor networks allow some key measurements to be automated

• Student training– Mutual exchanges– International experience– Access to experts– Interdisciplinary science– PRIME students– UW students

2004UCSD UW

2005: UCSD, Georgia Tech, UWPorter, Arzberger, C. Lin, F. P. Lin, Kratz, et al. (2005)Source: T. Kratz

Scalable instrumentation and cyberfrastructure is critical

lakemetabolism

.org

Source: Tim K

ratz

Problematic, but possible with today’s cyberinfrastructure

Scale needed to answer regional/continental questions

Not currently possible

Addressing the Scaling ChallengeNSF NEON Award

• Collaborative Research: Automating Scaling and Data Processing in a Network of Sensors: Towards a Global Network for Lake Metabolism Research and Education– UCSD, UWI, IU, SUNY-Binghamton

• Automate– Instrument management– QA/QC and Event Detection

• Service Oriented Architecture• Broaden Involvement of Students

Lake Taihu

Boqiang Qin (Jackie Qin)(Nanjing Institute of Geography & Limnology, Chinese

Academy of Sciences)

• Basin area: 36,500 km2 • Farmland area: 13,475 km2 • Lake area: 2338 km2• Retention time: 300 days• M.Depth 1.89 m• Max. Depth 3.0 m • Volume 44x108 m3

• Max.Level 4.81 m a.s.l.• Min.Level 2.02 m a.s.l. • Deposit 1.2-1.8 mm/yr

PhytoplanktonZooplanktonAlkalinityWater stand Air temperature Water temperatureTransparencySSpHConductivity CODMn DO NH4

+-N NO2--N NO3--N TN PO4

3--P TPSiO2Chla

0

916

3

4

25

107

8

11

12

13

120 00

Scientific questions will be addressed in Lake Taihu

The structure and functions of ecosystem, and how the ecosystem interacts with the environment in this large shallow lake, and specifically to address the mechanism of algal bloom and the drives of ecosystem shift between algal domination and macrophyte domination system;The hydrodynamic processes impact on the ecosystem throughout the sediment resuspension, changes in underwater light condition, and nutrient release from sediment;

Taihu is a large shallow and eutrophicated Lake and it needs interdisciplinary research from physical limnology, biogeochemistry and aquatic biology. We hope this lake could be involved in global lake communoities.

Other Lakes

• Qinghai Hu

Largest inland salt-water lake, 3000 meters above sea level, on the path of migratory birds.

GLEON welcomes all scientists and institutions willing to participate

and contribute to the mission of the GLEON network

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

PRIME: Providing Students International Internships and Cultural Experiences

• Hosts– Computer Network Information

Center (CNIC), Chinese Academy of Sciences

– Cybermedia Center (CMC), Osaka University, Japan

– Monash University, Australia– National Center for High-

performance Computing (NCHC), Taiwan

• Sponsors– NSF, Calit2, GEON– Host sites provide

administrative support

PRIME 2005 – Presentations at iGRID 2005• Phylogeny Determined by Incomplete Protein Domain Content,

I.Lee, CNIC• A visualization of network measurements, J.Lee, CNIC• Deployment and Extension of JuxtaView for the Scalable Adaptive

Graphics Environment, C.Cheung, NCHC• Developing the Interface between PDA and Sensors, O Langman,

NCHC* (from U Wisconsin)• Visualizing internet connectivity using Cytoscape, S.Lee, NCHC• Extending EcoGrid Capability, D.Leu, NCHC*• BOINC as a Nimrod Resource for Quantum Chemistry, J.Hwang,

Monash• Computational Grid Tools for Protein-Ligand Docking Studies, L

Berstis, Monash• Modeling Cardiac Rhythm Alternation, J.Nevo, Monash• SNPs, Protein Structure and Disease, D.Bitton, Monash• Computational Cardiac Modeling, D.Dederko, Monash• The Development of A Querying System for Structured Metadata

in a Datagrid Environment, J.Chen, Osaka• Visualization Tools for Bio-molecular Simulation, C.Liang, Osaka• A Bio-molecular Simulation Portal, E.Wang, Osaka

prime.ucsd.edu/presentations

PRIUS: Pacific Rim International UniverSities12 Oct 05

•

• Exchange among PRAGMA Sites

• Lectures from PRAMGA members

Future Site of PRAGMA Meeting –

to expand PRIUS

Rough Approach of PRIUS• Establish a consistent

educational programfor graduate students.

• On-the-Job-Training Education on 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 PartResearch Part

Source: Susumu Date

The activity toward the success of the investment to future PRAGMA

• Osaka university is seeking the best way to send Ph.D students to UCSD now.– This year is an experimental step and Osaka university wants to

investigate the problems and issues in sending master students and Ph.D students to UCSD in our course.

• We will soon build a tiled display in Osaka University in hope that the display accelerates our R&D activities as well as education in PRAGMA

• We are exploring the possibility to expand the framework of PRIME on the advanced PRAGMA R&D framework

– We would like to ask for your help.• Giving a lecture at Osaka University• Accepting students from Osaka University

Source: Susumu Date

Some Penultimate Thoughts

• Community Infrastructure (GEON, GLEON, BIRN, …) requires multidisciplinary and multi-institutional teams

• Both top-down (BIRN, Teragrid) and bottom up (PRAGMA, GLEON) can work

• These projects are ideal platforms for people exchange and education

• All of the successful projects seem to take time to build trust (essential in collaboration)– Software, people, and policies need to work together

• All of these projects require sustained funding models for persistence of the infrastructure and software products.

• International team science is possible now, and will become more common

Summary – CANS 2004• Dream big – build the imagination of those

involved• Start small - build trust• Stay concrete – build infrastructure• Focus on people – build community

• Opportunities: – Networking and Measurements– Testbed: Mutual learning– Applications: Geosciences, Astronomy, Ecology,

Biomedicine, …– Exchange: Undergraduates and Graduates– Participate in Meetings and between meetings

Qinghai Hu or Taihu

Challenges: Some of what could we achieve by CANS 2006

• Geosciences– Geosciences Working Group in PRAGMA– Geosciences application driver on the

PRAGMA testbed/lab• Astronomy

– Move data over Gloriad– Persistently

• Ecology/GLEON– Add new site– Share data

• Education– Exchange students/researchers

• OptIPuter – for Global Team Science– Become a node– Set up a tile display wall for collaboraitons

• Greater participation by Chinese Institutes and Universities– PRAGMA, iNLANR Amp Mesh

U Missouri, GSCASCNIC

IVOA

CNIC, NAO China

CHINA PRIMEPRIUS

iGAPhttp://pragma-goc.rocksclusters.org/applications/igap/igap.html

• Genome annotation pipeline• Use CSF/Gfarm• Driver: Wilfred Li (SDSC)• Ready on 7 sites:

– AIST: Yoshio Tanaka, Yusuke Tanimura– ASCC: Hurng-Chun Lee, Mike Chiang– KISTI: Jysoo Lee, Jae-Hyuck Kwak – NCHC: Weicheng Huang, Chien-Lin Huang– NCSA: Radha Nandkumar, Tom Roney– SDSC: Mason Katz, Cindy Zheng– TITECH: Satoshi Matsuoka, Hitoshi Aoki

Science

• Collaborative

• Interdisciplinary

• International

• Data-driven

e-science’s New Frontier: Merging of Science and Information Technology

PreviouslyUnobtainable

Observations andUnderstanding Enabling

Technology

• Advance science

Science Drivers

• Focus development

PersistentInfrastructure

• Broaden impact

Education & Capacity

Building

• Develop human resources

Sustained Collaboration

• Build teams andtrust

International Collaborations

http://www.pragma-grid.nethttp://gleon.org

http://prime.ucsd.edu

PRAGMA

Thank you

I hope we’ll find areas of collaborationResearch and education

PRIME and PRIUS