PRAGMA: A Collaborative Framework for Advancing Grid Technologies

1. 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

2. 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

3. 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

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

5. PRAGMA Grid Testbed JLU China UZurich Switzerland CNIC GUCAS China AIST OsakaU UTsukuba TITech Japan NCSA USA AIST KISTI Korea BU USA UUtah USA SDSC USA SDSC NECTEC ThaiGrid Thailand NECTEC ThaiGrid ASGC NCHC Taiwan UMC USA CICESE Mexico UoHyd India CUHK HongKong UNAM Mexico MIMOS USM Malaysia IOIT-HCM Vietnam ASURC Costa Rica APAC QUT Australia BII IHPC NGO Singapore UCN Chile NGO BESTGrid New Zealand UChile Chile MU Australia 31 Clusters from 27 institutions in 14 countries/regions (+8 in preparation) 5 gfarm sites

6. Applications and Middlewarehttp://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)

7. Application/Middleware Collaborationshttp://wiki.pragma-grid.nethttp://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

8. 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

9. Source: Elaine Liu, PRIME 2006 TDW/OptIPuter Example Viewing @ UCSD Controlling @ CNIC

10. 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

11. 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

12. 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

13. 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

14. Collaborate in Publishing Research Results Some published papers in 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-grid-promoting-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. • …

15. 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)

16. Peer-grid Interoperation Experimentshttp://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

17. OSG-PRAGMA Interoperation Experimenthttp://goc.pragma-grid.net/wiki/index.php/OSG-PRAGMA_Grid_Interoperation_Experiments Learned • Differences in grid environment effect users and applications • Job submission • Change RSL parameter • Remove inter-node parallel execution • Security policy • Take work to setup access • Account on gatekeeper node • Large scale calculations are possible • Middleware fault tolerance and flexible resource management is important Resources • OSG • FermilabGrid • PRAGMA • SDSC, USA • NECTEC, Thailand • NGO, Singapore • ThaiGrid, Thailand Process • Jan 4, 2007, identify who and how • Coordinator, application drivers, resource supporters • Wiki, application, requirements • Jan 25, 2007, initial VTC • Goals, Q/A exchange • Start working • Email immediately issues, solutions • Weekly status, email, wiki Status • Feb 26 - March 1, started application runs successfully A set of jobs are processed on the VO, collected, and updated for the next iteration.

18. PRIME http://prime.ucsd.edu • 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 PRIME Class 2006

19. PRIME 2006 (Thrid Year)Host Institutions and Projects at a Glance • 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 Prime Students 2006 Hosted by CNIC, China At Lao She Tea House

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

21. 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 PRIUS (First Year)

22. 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

23. 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 Thank You http://www.pragma-grid.net http://goc.pragma-grid.net