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Cyberinfrastructure, E-Science and the San Diego Supercomputer Center

Cyberinfrastructure, E-Science and the San Diego Supercomputer Center

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Cyberinfrastructure, E-Science and the San Diego Supercomputer Center

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  1. Cyberinfrastructure, E-Science and the San Diego Supercomputer Center Chaitan Baru San Diego Supercomputer Center California Institute for Telecommunications and Information Technology University of California, San Diego

  2. Acknowledgements • US National Science Foundation • Sponsors of GEON, and GEON international activities • The University of Auckland • Local hosts

  3. Cyberinfrastructure and E-science • Cyberinfrastructure: • “…The comprehensive infrastructure needed to capitalize on dramatic advances in information technology…” • “…essential to support the frontiers of research and education in this field…” • From NSF’s Cyberinfrastructure Vision for 21st Century Discovery,, July 20, 2006 • “E-Science”- thescience enterprise enabled by the use of such cyberinfrastructure • “Science increasingly performed through distributed global collaborations enabled by the Internet, using very large data collections, terascale computing resources and high performance visualizations.” • From Oxford e-Science Center, public/general/definitions.xml

  4. SDSC’s Support for CI and e-Science • Production Services • For nationally allocated supercomputer platforms, as well as computational platforms and storage systems for other projects • User Services • For nationally allocated supercomputers • Research and Development Collaborations • In support of computational science and informatics in a wide variety of science, engineering, humanities, and other disciplines • To develop common cyberinfrastructure (software) components • R&D constitutes >50% of SDSC’s activities • In funding as well as staffing

  5. Integrated Cyberinfrastructure SystemSource: Dr. Deborah Crawford, Chair, NSF CI Working Committee Domain-specific Cybertools (software) Shared Cybertools (software) Distributed Resources (computation, storage, communication, etc.) • Applications • Geosciences • Environmental Sciences • Neurosciences • High Energy Physics … Education and Training DevelopmentTools & Libraries Discovery & Innovation Middleware Services Hardware

  6. TeraGrid Network Grid Infrastructure Group (UChicago) UW PSC UC/ANL NCAR PU NCSA UNC/RENCI IU Caltech ORNL U Tenn. USC/ISI SDSC LSU TACC Resource Provider (RP) Software Integration Partner

  7. TeraGrid Science Gateways • Provide entry points into TeraGrid for community-specific tools • Community-led initiative for the TeraGrid • URL •

  8. Computational Science and Informatics: And the CS/IT context • Computational physics and chemistry • Born at the time of Fortran, file-based systems, and expensive supercomputers, Internet, ftp, and HTML • Bioinformatics • Born at the time of Relational Database Management Systems (RDBMS), microprocessors, client-server computing, the Web, 3-tier architectures, CORBA, XML • Geoinformatics • Being born at the time of Web2.0, Google, mySpace, YouTube, mashups, social networking, and ontologies… Ref: Caring and Sharing of e-Science Data, C. Baru, Commentary, International Journal of Digital Libraries, October 2007

  9. Community Cyberinfrastructure Projects Your Specific Tools & User Apps. Shared Tools ScienceDomains Friendly Work-Facilitating Portals Authentication - Authorization - Auditing - Workflows - Visualization - Analysis DevelopmentTools & Libraries Ecological Observatories (NEON) High Enegy Physics (GriPhyN) Ocean Observing (OOI) Biomedical Informatics (BIRN) Geosciences (GEON) Earthquake Engineering (NEES) Middleware Services Hardware Distributed Computing, Instruments and Data Resources Adapted from: Mark Ellisman UC San Diego

  10. Portal-based Science EnvironmentsSupport for resource sharing and collaborations

  11. Common CI Software Elements • NSF Software Development for Cyberinfrastructure (SDCI) Program • ROCKS -- Cluster Management Software • SRB/IRODS -- Collection-based Data Management • Kepler -- Scientific Workflow Software • Open Source DataTurbine -- Streaming Data Middleware • Inca -- Testing and Monitoring Software • Other Common Software • GAMA -- Grid Account Management Architecture • GridSphere -- Portlet-based Portal Infrastructure • RDV -- Realtime Data Viewer • Common Portlets • GEON portlets: Registration, Search, myWorkspace, TeraGrid Gateway • Used in several other CI projects

  12. Observing Systems • An important area for several US agencies, including National Science Foundation • Several agencies support observing system networks, e.g. USGS, NOAA, EPA, DoE, DOD, NASA, DHS, etc • A range of projects • Major research equipment: deployment of coordinated, regional, continental, international-scale instrumentation and sensor networks •  standardized instrumentation and protocols • Cyberinfrastructure: development of IT and software for managing sensor networks; collecting, analyzing, distributing data; data assimilation and execution of forecasting models •  standardized IT infrastructure (interfaces, technology implementations) • Individual investigator, or small group-driven research: • Local (regional) sensor networks, to study specific phenomena • Analysis of collected data • Modeling and data assimilation • …

  13. Observing Systems Efforts • Some NSF Projects • EarthScope: Obtain “snapshot” of the lithospheric structure of the continental US • US Array; Plate Boundary Observatory (PBO); San Andreas Fault Observatory at Depth (SAFOD) • Ocean Observing Initiative: Understand ocean phenomena in the deep ocean and at the coastal margins • Regional Coastal Observatory; Global Observatory • National Ecological Observatory Network (NEON): model and predict the state of the ecosystem of the US • 17 climatic domains across contiguous states + 2 in Alaska + 1 in Hawaii • Long-Term Ecological Research Network (LTER): intensive studies at local and regional scales • >30 LTER sites across US • WATERS: monitor watersheds across US to study hydrologic as well as environmental engineering issues • CLEANER: Environmental engineering-based observatory projects • Hydrologic Information System (HIS): Hydrology-based observing systems projects • NEES, NVO, … • Moore Foundation-funded Projects • CAMERA: Metagenomics and marine microbials • GLEON: Global Lake Observatory Network • TEAM: Tropical Ecological Assessment and Monitoring Network

  14. Cyberinfrastructure (CI) Components in Observing Systems • “Embedded CI” • Software for managing instruments, dataloggers, and data in sensor networks, including metadata generation • “Cyberdashboard” for management of instruments/sensor networks • Data Management • of data streams (with metadata) from dataloggers (in the field) to data repositories, to data archives • “Cyberdashboard” to keep track of data collection protocols • Analysis and Computation • Support for model runs, data assimilation, data analysis, data mining, including periodic reprocessing of archived data • Data Access • Authenticated access to a range of data products, from raw to highly derived, including the ability to “push” data to client applications

  15. NSF Ocean Observing Initiative (OOI) Courtesy: John Orcutt, Scripps Institution of Oceanography, University of California, San Diego

  16. OOI - Coastal Scale Observatory Courtesy: John Orcutt, Scripps Institution of Oceanography, University of California, San Diego

  17. OOI - Regional Courtesy: John Orcutt, Scripps Institution of Oceanography, University of California, San Diego

  18. OOI - Global Node Courtesy: John Orcutt, Scripps Institution of Oceanography, University of California, San Diego

  19. OOI - From Construction to Operations Courtesy: John Orcutt, SIO Matt Arrott, Calit2, University of California, San Diego

  20. OOI - Conceptual View of the Cyberinfrastructure

  21. NEON Cyberinfrastructure NEON Domains

  22. The NEON “Single String” Testbed NEON Single String Testbed (SSTB) James Reserve, CA SDSC, San Diego

  23. MoveBankFor Animal Tracking and Photo Monitoring Data • A data repository • A live data pipeline • Online mapping and analysis tools • An educational tool • A community of collaborators • • NSF BD&I: 0756920 PIs: Roland Kays (NY History Museum), Martin Wikelski (Princeton), Tony Fountain (SDSC, UCSD), Sameer Tilak (SDSC, UCSD)

  24. MoveBankCurrent Activities • Designing Data System • Requirements analysis • Schema definitions for camera trap and tracking data (trajectories) • Extending DataTurbine streaming data system for animal tracking and photo monitoring • Integration of cameras to data acquisition system • Event detection and notification system design • Building a knowledge base of best practices • Networking with other animal tracking communities and researchers to build collaborations

  25. Moore Observing Systems Projects • Some projects funded by Gordon and Betty Moore Foundation at UCSD • CAMERA: Metagenomics project • Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (Craig Venter, Larry Smarr) • Provide access to metagenomics databases collected from ocean water samples from around the world • OceanLife: Biodiversity in seamounts • Karen Stocks & Amarnath Gupta, SDSC • Integrated information source for seamount biodiversity • GLEON: Global Lake Ecological Observatory Network • Peter Arzberger, Calit2/UCSD, Tony Fountain, SDSC • Tim Kratz, Paul Hanson, U.Wisc • Cyberinfrastructure for TEAM • Tropical Ecology Assessment and Monitoring

  26. Source: Paul Hanson, U.Wisc Courtesy: Peter Arzberger, Calit2/UCSD

  27. GLEON’s Mission Facilitate interaction and build collaborations among an international, multidisciplinary community of researchers focused on understanding, predicting, and communicating the impact of natural and anthropogenic influences on lake ecosystems by developing, deploying, and using networks of emerging observational system technologies and associated cyberinfrastructure. Source: Tim Kratz, U.Wisc

  28. 19 countries participating • More than 120 scientists • Most sites are developing Source: Paul Hanson, U.Wisc

  29. 3 Networks People Data Lake observatories Source: Paul Hanson

  30. Tropical Ecology Assessment and Monitoring (TEAM) Network • Conservation International project • PI: Sandy Andelman, Vice President, Conservation International • Funded by Gordon and Betty Moore Foundation • Monitor wildland plots in tropical regions • Current sites: Brazil (3), Costa Rica, Suriname • Upcoming site: Madagascar • Cyberinfrastructure provided by SDSC

  31. TEAM Cyberinfrastructure Goals • Provide secure, reliable access to near real-time data from all TEAM sites • Facilitate timely, efficient, consistent data entry • By assisting with adherence to site-specific protocols • Providing up-to-date status of data entry • Providing ready visualizations of cross-site, network-level data • Manage a variety of different data types • Field collections, sensor data, museum collections, remote sensing data • Sensor data includes images and acoustic data • Provide customized portals (portlets) • E.g. site-specific information (with multi-lingual support), and project specific data and tools • CI goals are similar to those of other environmental observatory projects, e.g. NEON…

  32. TEAM Initial Implementation • Local PoP node: • E.g. at a site in a given country, or • One PoP node for a country • Future capability

  33. TEAM Portal and Data Management • Portal based on • Drupal: for content management • GridSphere: for sharing and collaboration of data and tools • Support different data types • Observational data • Climate data; Photos / images • Spatial (GIS) data • Different layers, e.g. including socioeconomic data • Museum collections • E.g. MetaCat, EcoGrid • Acoustic data • Algorithms for classifying acoustic data • Remote sensing data • Landsat, MODIS, ASTER, LiDAR

  34. CUAHSI Hydrologic Information System (HIS) • Hydrology Data Portal • Digital Watershed • Hydrologic Analysis (Source: David Maidment, UT Austin)

  35. HIS Service Oriented Architecture Web portal Interface (HDAS) Information input, display, query and output services Preliminary data exploration and discovery. See what is available and perform exploratory analyses 3rd party servers Web services interface e.g. USGS, NCDC GIS Matlab Observatory servers Workgroup HIS IDL SDSC HIS servers Splus, R D2K, I2K Programming (Fortran, C, VB) Downloads Uploads HTML -XML Data access through web services WaterOneFlow Web Services WSDL - SOAP Data storage through web services

  36. WaterML and CUAHSI HIS Mediation • Develop WaterML as an interchange standard for hydrologic data • HIS serves as a mediator across multiple agency and individual PI data • Provides identifiers for sites, variables, etc. across observation networks • Manages and publishes controlled vocabularies, and provides vocabulary/ontology management and update tools • Provides common structural definitions for data interchange • Provides a sample protocol implementation • Governance framework: a consortium of universities, MOUs with federal agencies, collaboration with key commercial partners, led by renowned hydrologists, and NSF support for core development and test beds

  37. NEESit and the NEES User Community • NEES Equipment Sites (15 large-scale labs) • NEESR Research Grants (>40 NSF projects) • Earthquake Engineering Researchers • Earthquake Engineering Practitioners • K-12 and Undergraduate students

  38. The NEESit System Scientific Collaboration Environment (NEES Portal) Telepresence Video, Data, Audio Archiving Secure Communication Data Repository Structured Metadata Graphical User Interface Phys/Comp. Curated EOT Cyber Accessibility Community Content On-line experiment e-publications Computational Tools High Performance Computing Hybrid Simulation (Phys/Comp.) Visualization Scientific Workflows

  39. NEES Portal: Parallel Computing & TeraGrid Access

  40. Emergency Response Projects • Katrinasafe and Disastersafe • Collaboration between American Red Cross and SDSC during Hurricane Katrina • Continuing now as • Funded by an NSF grant for exploratory research on cyberinfrastructure preparedness • Spatiotemporal analysis of 911 call data • Collaboration with Public Safety Network • Funded by the NSF Digital Government program • UCSD Hazards Initiative

  41. • Outcome of collaboration on Katrinasafe • Site hosted at SDSC

  42. Spatiotemporal Analysis of 9-1-1 Emergency Call Streams • Funded by NSF Digital Government program • Project Goals • Provide situational awareness at a command and decision level (vs operational) • Assist local and State level emergency responses by • Generating immediate and dynamic information about the impact of medium- to large-scale events • Facilitating dynamic resource allocation • Serving as an early warning system of emergency events • Collaboration among • California Office of Emergency Services (OES) • University of California, San Diego • Public Safety Network

  43. Temporal Extent of Collected Data • San Francisco Bay Area: 30 months of data • San Diego County: 16 months of data • Total of 5,301,191 calls

  44. Spatial Extent of Collected Data = landline call = cellular call San Francisco Bay Area, 69 PSAPs San Diego County, 20 PSAPs (Dithered to approx. 300m; One day of 9-1-1 call activity shown)

  45. Call Stream Shows Temporal Regularity Average daily call volume for the San Francisco Combined Emergency Communications Center (CECC) PSAP. Average hourly call volume for the San Francisco Combined Emergency Communications Center (CECC) PSAP.

  46. Daily Call Volume 4th of July Data collection process offline Histogram of daily call volume for the collected data Times series of daily call volume for the collected data (SF)

  47. Animation: Clustering of phone calls

  48. Cessna plane collision in San Diego

  49. Other projects • PRAGMA: Pacific Rim Assembly for Grid Middleware Applications • PI: Dr. Peter Arzeberger, UCSD; Co-PI: Phil Papadopoulos • GEON is a participant in PRAGMA, and co-chairs the PRAGMA Geosciences Working Group • Optic fiber links and Lamba Grid • PI: Prof. Larry Smarr

  50. Technical Interoperability Issues • Authentication • Need a common authentication framework, to provide role-based access to distributed resources • Else, users will be burdended with too many accounts and passwords, one for each site • Information security • Provenance, IP issues • Distributed Data (and Metadata) • Metadata search interoperability • Large archives will remain distributed. Need metadata search interoperability so that a single search can search several metadata catalogs • Caching and replication of frequently used (large) data • “Distributed curation with centralized hosting” could be an option