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Published on October 17, 2007

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Slide1:  Mason Katz mjk@sdsc.edu Pacific Rim Application and Grid Middleware Assembly University of California, San Diego http://www.pragma-grid.net http://goc.pragma-grid.net PRAGMA: Experiences in Grass-Roots / Bottom-up Grid Computing Definition of PRAGMA:  Definition of PRAGMA Founded in 2001 US (UCSD/ SDSC) Korea (KISTI) AIST (Japan) NSF Support Renewed for next 5 years Now > 12 Asia-Pacific Countries. Focus Grid Applications Building International Cross-Cultural Collaborations Application needs define the grid. IT does not define grid Differs from national efforts like Tera-Grid. Slide3:  PRAGMA Grid Testbed 31 Clusters from 27 institutions in 14 countries/regions (+8 in preparation) UZurich Switzerland NECTEC ThaiGrid Thailand UoHyd India MIMOS USM Malaysia CUHK HongKong ASGC NCHC Taiwan IOIT-HCM Vietnam AIST OsakaU UTsukuba TITech Japan BII IHPC NGO Singapore MU Australia APAC QUT Australia KISTI Korea JLU China SDSC USA CICESE Mexico UNAM Mexico UCN Chile UChile Chile UMC USA UUtah USA NCSA USA BU USA ASURC Costa Rica BESTGrid New Zealand CNIC GUCAS China AIST SDSC NGO NECTEC ThaiGrid 5 gfarm sites Overview and Approach Process to Promote Routine Use Team Science:  Overview and Approach Process 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 Routine Grid Use:  Routine Grid Use Force Applications onto the Grid Run applications repeatedly across many resources The “science” is in learning what Grid requirements are. Domain-specific scientific results are great, but not expected. Yet. Savannas Climate Simulation Monash University (Australia) Nimrod Middleware for Grid job management Issues: Resource Fault-Tolerance Data Distribution Specific Routine Use Applications http://goc.pragma-grid.net/applications/default.html:  Specific Routine Use Applications http://goc.pragma-grid.net/applications/default.html Climate simulation Savanna/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) CAMERA Ocean Meta-Genomics (UCSD, USA) Organic chemistry Gamess-APBS/Nimrod (UZurich, Switzerland) Molecular simulation Siesta/Nimrod (UZurich, Switzerland; MU, Australia) Amber/Rsh ( USM, Malaysia) Computer Science Load Balancer (VAST-HCM, Vietnam) GriddLeS (MU, Australia) Application/Middleware Collaborations http://wiki.pragma-grid.net http://goc.pragma-grid.net:  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 Application/Middleware Collaborations http://wiki.pragma-grid.net http://goc.pragma-grid.net Collaborations With Science and Technology Teams:  Grid security NAREGI & APGrid (Japan), GAMA (SDSC, USA) Grid infrastructure Monitoring - SCMSWeb (ThaiGrid, Thailand) Accounting - MOGAS (NTU Singapore) Metascheduling - Community Scheduling Forum (JLU, China) Cyber-environment - CSE-Online (U Utah, USA) Rocks and middleware (SDSC, USA; …) Ninf-G, SCE, Gfarm, Bio, K*Rocks, Condor, … Datagrid, sensor, network Gfarm Grid Filesystem (AIST, Japan) GEON data network GLEON sensor network OptIPuter High performance networked TDW Telescience Collaborations With Science and Technology Teams Example of International Collaborations in Grid Middleware:  Example of International Collaborations in Grid Middleware Source: Elaine Liu, PRIME 2006 China <-> USA Image data at CNIC (Beijing) Remote web view of Tile Display Wall at CalIT2 (San Diego) Image displayed at Remote wall. Collaborations in BioScience:  Collaborations in BioScience Avian Flu Research Project UCSD, CNIC, JLU, 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, Tskuba University (Japan) Community Scheduling Framework 4, JLU (China) With University of Wisconsin, UCSD, PRIME project Lesson Learned: Application Sub-Grids:  Lesson Learned: Application Sub-Grids Heterogeneous environment Minimal requirements Globus (gt2 - gt4) Moving recommendations Zheng C, et al. The PRAGMA Testbed: Building a Multi-Application International Grid. 2005 IEEE/CCGRID International Workshop on Grid Computing, 2006, Singapore Inter-Grid Efforts:  Inter-Grid Efforts GLEON: Global Lake Ecological Observatory Network :  GLEON: Global Lake Ecological Observatory Network A grassroots network of People: lake scientists, engineers, IT 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 cyber-infrastructure With a goal of understanding lake dynamics at local, regional, continental, and global scales Lake Pääjärvi Dec 18,2006 (source: L Arvola) Grid Interoperation Experiments http://goc.pragma-grid.net/wiki/index.php/Main_Page#Grid_Inter-operations:  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 Savanna 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 OSG-PRAGMA Interoperation Experiment http://goc.pragma-grid.net/wiki/index.php/OSG-PRAGMA_Grid_Interoperation_Experiments:  OSG-PRAGMA Interoperation Experiment http://goc.pragma-grid.net/wiki/index.php/OSG-PRAGMA_Grid_Interoperation_Experiments 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. 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 GEON-iGEON-PRAGMA:  GEON-iGEON-PRAGMA 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 www.geongrid.org 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:  PRAGMA and GEON/iGEON collaboration Sharing data, software know-how, interoperate grids Joint PRAGMA/GEON Geoscience workgroup seeded at PRAGMA11 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 Geo Working Group:  Geo Working Group GEOGrid: 1st Global Earth Observation Grid Workshops Meeting March 2007, Bangkok Hosted by AIST, NECTEC Supported by CCOP and GEON CCOP: Coordinating Committee for Geosciences Programs in East and South East Asia GEON: GEOsciences Network PRAGMA Geo Working Group Formed With Leadership Ryosuke Nakamura, AIST Guey-Shin Chang, NARL Ashram Memon, SDSC Sornthep Vannarat, NECTEC With Initial Objectives: Focus on accessing either large data or distributed data Interoperability test between GEON/GEO Grid data-search web-service GOALS:  GOALS This new working group aims at development of a grid testbed to support geosciences and practical applications based on huge datasets of satellite imagery and GIS data, such as disaster prevention or environment monitoring. Student Training:  Student Training PRIME http://prime.ucsd.edu:  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 PRIME Class 2006 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 2006 (Third Year) Host Institutions and Projects at a Glance:  PRIME 2006 (Third 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 Osaka University, 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 PRIUS - Pacific Rim International UniverSity Based at Osaka University:  PRIUS - Pacific Rim International UniverSity Based at Osaka University Establish a consistent educational program for graduate students. On-the-Job-training and education with 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 http://prius.ics.es.osaka-u.ac.jp/en/index.html PRIUS (First Year):  PRIUS (First Year) 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 Future PRAGMA Meetings:  Future PRAGMA Meetings PRAGMA 13 Sep 24-25 2007 Urbana-Champaign, USA NCSA PRAGMA 14 Spring 2008 Hsinchu, Taiwan NCHC PRAGMA 15 Fall 2008 Penang, Malaysia USM Collaborate in Publishing Research Results:  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. … www.pragma-grid.net:  www.pragma-grid.net

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