Pacific Rim Application and Grid Middleware Assembly - PRAGMA: An Overview of Past and Future Catalyzing Global Team Science PRIME, PRIUS, GLEON Peter Arzberger Philip Papadopoulos, Mason Katz Gabriele Wienhausen, Linda Feldman Tim Kratz, Fang-Pang Lin And many more The Minority-Serving Institutions Cyberinfrastructure Institute MSICI2 26 June 2006

Why Bother with International Activities? In the 21st century advances in science and engineering (S&E) will, to a large measure, determine economic growth, quality of life, and the health of our planet. The conduct of science, intrinsically global, has become increasingly important to addressing critical global issues…Our participation in international S&E collaborations and partnerships is increasingly important as a means of keeping abreast of important new insights and discoveries in science and engineering [NSB 2000] What nations don’t know can hurt them. The stakes involved in study abroad are that simple, that straightforward, and that important. For their own future and that of the nation, college graduates today must be internationally competent. [Lincoln Report 2005] 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. [Annual Report IIE 2005, and “About”)

e-science’s New Frontier: Merging of Science and Information Technology – PRAGMA’s Activities Previously Unobtainable Observations and Understanding Enabling Technology Advance science Science Drivers Focus development Persistent Infrastructure Broaden impact Education & Capacity Building Develop human resources Sustained Collaboration Build teams and trust

PRAGMA’s Founding Motivations 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 Science is an intrinsically global activity

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 Goals PRAGMA Working closely with established activities that promote grid activities or the underlying infrastructure, both in the Pacific Rim and globally.

PRAGMA’s Role in the Community Constructed conduit of technology, ideas, information, people –Multi-directional flow among institutions and communities of software, approaches Developed framework for collaboration –Catalytic in forming teams –Foundation for continued and greater work Built trust among members –Interoperability essential among people –Sharing of resources, ideas, and people resulted Result: many unplanned successes

Collaborative Framework for Success SARS: Grid Community Pulls together to Battle SARS GLEON: Launching 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, Osaka PRIUS : Osaka University, international internships and “PRAGMA Classes” KRocks: Localization of Rocks in Korea Successes that happened because PRAGMA exists

Conduit for Success Telescience: Sharing and Contributing Technology Multi-way Dissemination, Integration, and Synthesis of Software: –Rocks Rolls of SCE, Gfarm, Ninf-g –Ninf-G into NMI 8.0 (and soon Naregi CA) –iGAP/Gfarm, GAMESS/Nimrod 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) –Joint papers Issues and Methods for Building a Multi-Application International Grid Resource (6 institutions on author list); Applications Assisted in RPC standards at GGF, and launching of International Grid Trust Federation (Lead by AIST) Outcomes through on-going meetings

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

PRAGMA Grid Testbed AIST, Japan CNIC, China KISTI, Korea ASCC, Taiwan NCHC, Taiwan UoHyd, India MU, Australia BII, Singapore KU, Thailand USM, Malaysia NCSA, USA SDSC, USA CICESE, Mexico UNAM, Mexico UChile, Chile TITECH, Japan QUT, Australia UZurich, Switzerland JLU, China NGO, Singapore MIMOS, Malaysia OSAKAU, Japan IOIT-HCM, Vietnam Source: Cindy Zheng

PRAGMA Grid resources

Applications grid.net Real science, multiple applications –Resource sharing Mpich-g2 Reservation and meta-scheduling –TDDFT: quantum-chemistry, AIST, Japan –Savannah: climate Model, MU, Australia –QM-MD: quantum-mechanic, AIST, Japan –iGAP: bioinformatic, UCSD, USA –Gamess-APBS: organic chemistry, UZurich, Switzerland –Siesta: molecular simulation, UZurich, Switzerland –Amber: molecular simulation, USM, Malaysia –FMO: quantum-mechanics, AIST, Japan –HPM: Genomics, IOIT-HCM, Vietnam –(GEON, Sensor, … )

SCMSWeb Web-based monitoring system for clusters and grid –System usage –Performance metrics Reliability –Grid service monitoring –Spot problems at a glance

How We Operate status/work.htm status/work.htm

Software Layers Globus 2, 3, 4 GT4 pre-WS, 9 sites GT4 WS, 1 Moving requirements

PRAGMA Testbed Software Layers

iGAP Genome annotation pipeline Use CSF/Gfarm Driver: Wilfred Li (SDSC), Osamu Tatebe (AIST), Xiaohui Wei (JLU) 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

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 v8 first experience for NMI to include non-U.S. software. Evaluate and improve Ninf-G2 through the PRAGMA routine-basis experiments

GRID TECHNOLOGIES Portals Middleware Graphics Computational Chemistry Engine Data Analysis Tools Hardware ENABLING NEW SCIENCE Exploiting grid technology & hybrid computational methods PARAMETER SEARCH 4 variables 15,876 points Refineable hypersurface ICCS’03 PRAGMA 4 Monash, Australia HPCC, Japan CRAY, Japan SDSC, USA UCSD, USA CPE, Thailand KISTI, Korea GEOGRAPHIC DISTRIBUTION OF JOBS DURING EXECUTION Source: Wibke Sudholt, Kim Baldridge, David Abramson, Colin Enticott, Slavisa Garic GAMESS and Nimrod/G

The PRAGMA Steering Committee

Working Groups: Organize PRAGMA Efforts Resources –Mason Katz, SDSC –Yoshio Tanaka, AIST Biological Sciences –Karpjoo Jeong, Konkuk U/KISTI Telescience –Shinji Shimojo, Osaka –Fang-Pang Lin, NCHC Data Computing –Osamu Tatebe, AIST

Some Members and Participants Resource Group Album: Total 85 Pictures – and another album

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

Annual Reports Prepare for SCxy Highlight Accomplishments Promote PRIME and PRIUS Describe Working Group Progress Summarize Individual Institution Contributions Give Additional Information, e.g. Publications, Sponsors

CCGrid - Singapore 16 – 19 May 2006 Abramson D, Lynch A, Takemiya H, Tanimura Y, Date S, Nakamura H, Jeong K, Lee H, Wang C, Shih HL, Molina T, Baldridge K, Li, W, Arzberger P. Deploying Scientific Application on the PRAGMA Grid Testbed: Ways, Means and Lessons. CCgrid 2006 Lee B-S, Tang M, Zhang J, Soon OY, Zheng C, Arzberger P. Analysis of Jobs on a Multi-Organizational Grid Test-bed. CCGrid Zheng C, Abramson D, Arzberger P, Ayuub S, Enticott C, Garic S, Katz M, Kwak J, Papadopoulos P, Phatanapherom S, Sriprayoonsakul S, Tanaka Y, Tanimura Y, Tatebe O, Uthayopas P. The PRAGMA Testbed: Building a Multi-Application International Grid CCGrid

Articles On Infrastructure in Australia India’s Grid Initiative Cyber Science Initiative in Japan CI in Korea Taiwan CI for Knowledge Innovation Brazil South Africa PRAGMA Guest Editor: Radha Nandkumar

CCGrid - Singapore 16 – 19 May 2006 Abramson D, Lynch A, Takemiya H, Tanimura Y, Date S, Nakamura H, Jeong K, Hwang S, Zhu J, Lu ZH, Amoreira C, Baldridge K, Lee H, Wang C, Shih HL, Molina T, Li, W, Arzberger P. Deploying Scientific Application on the PRAGMA Grid Testbed: Ways, Means and Lessons. CCgrid 2006 Lee B-S, Tang M, Zhang J, Soon OY, Zheng C, Arzberger P. Analysis of Jobs on a Multi-Organizational Grid Test-bed. CCGrid Huang W, Huang C-L, Wu, C-H., The Development of a Computational Grid Portal. Accepted CCGrid Zheng C, Abramson D, Arzberger P, Ayuub S, Enticott C, Garic S, Katz M, Kwak J, Papadopoulos P, Phatanapherom S, Sriprayoonsakul S, Tanaka Y, Tanimura Y, Tatebe O, Uthayopas P. The PRAGMA Testbed: Building a Multi-Application International Grid CCGrid 2006.

Preparing the Global Workforce

PRIME: Providing Students International Interdisciplinary Research Internships and Cultural Experiences preparing the global workplace of the 21 st century 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

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 SC’05

Background and Motivation of PRIUS Pacific Rim International UniverSity Success of PRAGMA community –Accumulated Expertise and practice of building Highly advanced Grid applications and middleware –Formation of Human network of researchers and scientists in pacific rim Activation of Educational activities – PRIME: Providing UCSD students with an opportunity of experiencing, studying, and learning highly sophisticated technology and cultural background through practical R&D with PRAGMA partners. Maturity of PRAGMA R&D network Stimulating the movement toward the establishment of PRAGMA Educational network

PRIUS: Pacific Rim International UniverSities 12 Oct 05 Exchange among PRAGMA Sites Lectures from PRAMGA members PRAGMA 11 Oct 2006 – to expand PRIUS

Rough Approach of PRIUS Establish a consistent educational program for 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 Part Research Part Source: Susumu Date, Osaka University

Taiwan’s Natural Beauty

Lake Metabolism Website

Wind Speed Precipitation (mm/5 minutes) Typhoon causes water column mixing Mixing event Source: Tim Kratz

From Cole, J. J., N. F. Caraco, G. W. Kling, and T. K. Kratz Carbon dioxide supersaturation in the surface waters of lakes. Science 265: Of 4665 samples from 1835 lakes worldwide, 87% were supersaturated Why? Source: Tim Kratz

Programs -Australia -Canada -China -Finland -Florida -New Zealand -Israel -South Korea -Taiwan -United Kingdom -Wisconsin First meeting: San Diego March 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

Scalable instrumentation and cyberfrastructure is critical We can do this scale now Source: Tim Kratz

Problematic, but possible with today’s cyberinfrastructure Source: Tim Kratz

Scale needed to answer regional/continental questions Not currently possible Source: Tim Kratz

New Paradigm: Global Team Science U.Waikato D.Hamilton Models NCHC F.P.Lin Maintain YYL Parallelize Codes U.Wisconsin T.Kratz Maintain Trout Bog Lake Metabolism UCSD F.Vernon, S.Peltier, T.Fountain P.Arzberger ROADNet, Telescience Moore Fnd, PRAGMA NIGLAS B.Q Qin Maintain Taihu Physical Limnology Kangwon U B.Kim Maintain Soyang Public Policy

e-science’s New Frontier: Merging of Science and Information Technology – PRAGMA’s and GLEON’s Activities Previously Unobtainable Observations and Understanding Enabling Technology Advance science Science Drivers Focus development Persistent Infrastructure Broaden impact Education & Capacity Building Develop human resources Sustained Collaboration Build teams and trust Bioscience Chemistry Envir.Sci. Geosciences Lakes (GLEON) Others Ninf-G Gfarm Nimrod SCMCWeb MOGAS KRocks Others (Web service) Testbed Links to resources PRAGMA & GLEON Framework PRIME PRIUS Others

International Education Matters Globalization is driving demand for an internationally competent workforce. Our nation's trade with Asia, now concentrated in California, has exceeded Europe since 1979 and is expected to approach $1 trillion a year this decade. The majority of future growth for industries of all sizes is in overseas markets; today one in six new jobs created flows from international trade. Access to good jobs will require new skills and competencies. Future careers in business, government, health care, law enforcement, and other good jobs will all require global knowledge and skills. Unfortunately, minorities are underrepresented in international careers and must be exposed to global content earlier in their education. Solving new national and human security challenges, including terrorism and HIV/AIDS, and the ongoing problems of poverty and environmental degradation, will require increased knowledge of other world regions, cultures and languages. Increased diversity in our nation's classrooms, workplaces, and communities, including new immigrants from many different parts of Asia and Latin America, requires greater understanding of the myriad cultures and histories students bring to school.

Acknowledgements PRAGMA –Philip Papadopoulos (UCSD) –Mason Katz, Wilfred Li, Kim Baldridge, Tomas Molina, Cindy Zheng –Fang-Pang Lin (NCHC) –And many others at all 28 institutions, in particular the Steering Committee GLEON –Tim Kratz (U WI) –David Hamilton (U Waikato) –Fang-Pang Lin (NCHC) –And others at 10 other sites CREON –Sally Holbrook (UCSB) –Stuart Kininmonth (AIMS) PRIME –Gabriele Wienhausen –Linda Feldman –All Host sites and students PRIUS –Shinji Shimojo (Osaka) –Susumu Date (Osaka) CAMERA –Larry Smarr NSF –Bill Chang –Many others Gordon and Betty Moore Foundation National Institutes of Health

Additional Slides

e-science’s New Frontier: New Directions and Activities for PRAGMA Previously Unobtainable Observations and Understanding Enabling Technology Advance science Science Drivers Focus development Persistent Infrastructure Broaden impact Education & Capacity Building Develop human resources Sustained Collaboration Build teams and trust Geosciences Metaproteomics driver Real-time sensing Access to microscope Coupling chem codes OptIPuter Collab. Env. GOC Gateways Globus Planet Lab Links to production resources (TeraGrid, others) Middleware interactions UK, Netherlands (Switzerland) Grids in China SE Asia, NZ Central/S. Am. Training

e-science’s New Frontier: Merging of Science and Information Technology – PRAGMA’s Activities Previously Unobtainable Observations and Understanding Enabling Technology Advance science Science Drivers Focus development Persistent Infrastructure Broaden impact Education & Capacity Building Develop human resources Sustained Collaboration Build teams and trust Bioscience Chemistry Envir.Sci. Geosciences Others Ninf-G Gfarm Nimrod SCMCWeb MOGAS KRocks Others (Web service) Testbed, AMP Links to resources PRAGMA Framework PRIME PRIUS Others

e-science’s New Frontier: Merging of Science and Information Technology – PRAGMA’s Activities Previously Unobtainable Observations and Understanding Enabling Technology Advance science Science Drivers Focus development Persistent Infrastructure Broaden impact Education & Capacity Building Develop human resources Sustained Collaboration Build teams and trust

e-science’s Team Science: Merging of Science and Information Technology Previously Unobtainable Observations and Understanding Enabling Technology Advance science Parameter Sweep Dist.Data Files Web Services Cross-site query Collaborative Tools Many more Science Drivers Focus development Chemistry Biology Lakes Geosciences Many more Persistent Infrastructure Broaden impact Lambda Grids Wireless sensor network Education & Capacity Building Develop human resources Students and postdocs Sustained Collaboration Build teams and trust Many meetings