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Transcript of Www.geongrid.org Geosciences Network (GEON): Enabling Discoveries in the Earth Sciences Dogan Seber...
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Geosciences Network (GEON): Enabling Discoveries in
the Earth Sciences
Dogan SeberSan Diego Supercomputer CenterUniversity of California, San Diego
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Outline• Cyberinfrastructure and the Geosciences• GEON Cyberinfrastructure• GEON Resources and Access Mechanisms• Impact on Science and Education
• Synthetic seismogram calculation • LiDAR data processing• 3D and 4D visualizations• Discover Our Earth
• Future activities• Open Earth Framework
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Enabling Scientific Discoveries:Pathway to Discovery
Access/Collect
Process Analyze Interpret Discovery
Data Knowledge
How can cyberinfrastructure help?
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What Geoscientists worry about … beyond science questions
• Exponential Increase in Data Volume• Data Storage, Access and Preservation• Data Integration (semantic and syntactic)• Computational Challenges • Advance Visualization (3D/4D)• Archiving and publications of results with
reusable components (reusability)• Improving education and developing a strong
workforce – the next generation of scientists
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Cyberinfrastructure can help!
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Hardware
Integrated Cyberinfrastructure System Source: Dr. Deborah Crawford, Chair, NSF CI Working Committee
Middleware Services
DevelopmentTools & Libraries
Applications• Geosciences• Environmental Sciences• Neurosciences• High Energy Physics … •
Domain-specific Cybertools (software)
Domain-specific Cybertools (software)
Shared Cybertools (software)
Shared Cybertools (software)
Distributed Resources (computation, storage, communication, etc.)
Distributed Resources (computation, storage, communication, etc.)
Ed
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tion a
nd
Tra
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Dis
covery
& In
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on
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GEON’s Vision
Enable new discoveries in the geosciences by developing an easy-to-use integration environment (i.e., GEON Cyberinfrastructure) built using state-of-the-art information technology resources.
GEON’s ChallengeIt is an effort involving multi-disciplinary teams. A variety of Earth scientists representing various disciplines such as seismology, structural geology, paleontology, geochemistry, geology and general geophysics are working with computer scientists to realize the vision.
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GEON Cyberinfrastructure Principles
• An equal partnership • Geoscientists working with IT experts and Computer Scientists
• The “two-tier” approach• Use best practices, including use of commercial tools and open
standards, where applicable…• …while developing advanced technology, and doing CS research
• Create shared “science infrastructure”• Integrated online databases, with advanced search and query engines• Online models, robust tools and applications
• Leverage from and work with other intersecting projects• Much commonality in the technologies, regardless of science
disciplines
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GEON Infrastructure
Mapping Services
ArcIMSWMSWFS
Logging Services
Usage Stats Collection &
Analysis
Data Services
DB
2,
Postg
res
myS
QL
Op
en
DA
P
SR
B
Data Registration Services
Indexing Services
SpatialTemporal
Conceptual
Data Integration Services
Ontology Enabled
Integration
Computational & Modeling Services
Modeling, Analysis Tools
Metadata Services
GEO
NC
ata
log
Oth
ers
Registration GEONsearch GEONworkbenchworkflow, visualization, HPC
Web/Grid Services Interfaces
Physical GridRedHat Linux, ROCKS, OGSI,
Internet, I2
Other Core Services
GridFTPOGSA-DAI
CSF
GEON Portal
MyGEON
Har
dw
are
So
ftw
are
Acc
ess
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Primary GEON Services
• Resource (data, tools, files) Registration => GEONcontribute• Resource Discovery => GEONsearch • Personalized Access => myGEON • Data Integration => GEON Integration Cart • Application Developments => GEONtools
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GEONmiddleware
myOntology.owl myDataset.foo
metadatametadata
User Access (via Portal)User Access (via Portal)
Gazetteer, DLESE, …
Geologic Age, Chronos, …
external services
GEONsearchGEONsearch
Search condition(s)spatial temporal concept
LogLog
GEONworkbench GEONworkbench
GEON Workspace
(user)
User actionsadd delete manipulate
GEON Catalog
ResourceRegistrationResourceRegistration
SRB
Client Access (via Web Services)Client Access (via Web Services)
Other distributed apps Kepler, DLESE, …
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Access -- GEON Web Site and the Portal
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GEON Resource Registration System
• Hosted registration: Contributor provides a full copy of the resource to the GEON network, and the network maintains the resource and archives it
• Non-hosted registration: Users provide access to a resource, but GEON does not keep a copy, and accesses the resource remotely. (e.g., RDBMS). Full functionalities are available in the integration area.
• Public, private, and group registrations• Register ontologies (domain knowledge) and
ontology articulations• Optionally register datasets to ontologies
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Resource Discovery in GEON
A Search Engine for Users• Metadata based search• Spatial coverage based search• Temporal coverage based search• Concept based search
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MyGEON -- myWorkbench
A personalized area to “save” resources of personal interest, integrate a variety of resources together, visualize data sets, archive/monitor computational results and share personal products with other selected individuals and groups.
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Data integration in myWorkbech
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myProjects
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Building CI Tools
• Synthetic Seismogram Calculation ToolCPU intensive grid application
• LiDAR data Analysis Tool Very large databases, and on-demand processing
• Paleo Integration Project Adding the component of time
• IDV (Interactive Data Visualization) Volume visualization
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A portal-based grid application in GEON - SYNSEIS
• SYNSEIS is a SYNthetic SEISmogram calculation tool built as part of the GEON system
• Uses E3D in the background• Enables 2D and 3D seismic waveform
simulations using a service-oriented architecture
• Utilizes both local as well as national computational platforms such as TeraGrid
• Integrated with GEON resources allowing utilization of archival and storage resources
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IRIS•Earthquakes•Stations•Waveform
Digital Libraries/GEON Data Grid
Earth model
Earth modelEarth
model
HPCHPCCentersCenters
NCSANCSA SDSCSDSC
SYNSEISe3d
SYNSEIS Components --
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Web Services
Earth Model Service
Job Submission/Monitoring and File Service
Data Archives Service
HPC ResourcesData Repository
Job Database
JDBC IIOP/CORBAGrid Services
GEONGrid Portal
Map Server
IRISDMC
HTTP
Grid FTP
Synseis Portlet
Macromedia Flash GUI
MyGEON
SYNSEIS Computations
GEONTools
SYNSEIS Architecture
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SYNSEIS Portlet
www.geongrid.orgwww.geongrid.orgwww.geongrid.orgSubsurface
Model
Earthquake parameters
Seismic attenuation
Etc.
Observation
SimulationAnalyses and Integration
GEON SYNSEIS INTEGRATION PLATFORME
art
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cop
e d
ata
GE
ON
po
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PC
En
viro
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cien
tific Disco
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s
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Capabilities Built into SYNSEIS
Interactive User Interface
Real-time access to IRIS DMC database –Event, station, waveform access based on a dynamic map interface. Event selection based on date and location
Ability to define (both graphically or lat-long based) events and station locations
Base map choices of topography, geology, tectonic boundaries, and urban area boundaries
Ability to use sediment thickness and Moho depth data sets seamlessly
Ability to use variable thickness flat-layer models
Ability to build 2D models using an interactive model builder
Run jobs remotely at TG and/or local resources
Ability to obtain waveform propagation movies on the fly
Job monitoring
Job archival mechanisms and resubmissions with revised parameters
Source parameter sweep for multiple simulations
Download capabilities for observed as well as simulated records
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LiDAR Data Analysis
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D. Harding, NASA
Point Cloudx, y, z, …
Example: LiDAR Workflow
Courtesy: Chris Crosby, ASU
Survey
Analyze / “Do Science”
Interpolate / Grid
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Example Outputs
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PaleoIntegration
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3D/4D Visualization - GEON IDV
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Visualization - Integration
Yellowstone (Smith and others) and the geodynamics of the mantle (McNamara)
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170 ma 90 ma 10 ma
4D Visualization Images from the GEON IDV
Geodynamics-McNamara
Paleomagnetics-Schettino,Scotese
Paleogeography-Blakely
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GEON Network: USA NodesGEON Network: USA Nodes
Partner Projects
Chronos
CUAHSI
Partner services
USGS
GeologicalSurvey ofCanada
ESRI
PoP node
5-node cluster
4 Tb
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GEON Software Stack• Base OS
• Rocks: highly programmatic software configuration management
• Development• Globus 4.0.2• Web Services (Jakarta-tomcat-5.0.28, axis-1.1, ant-1.6,
jdk1.4.2)• GridSphere 2.0.2 Portal Framework
• Database• Postgres 8.0.3 • PostGIS 1.0.2 (Geos, Proj)
• GIS/Mapping• Grass 6.0.2, GMT
• Security• Tripwire, chkrootkit
• System Monitoring• INCA Testing and Monitoring framework (Teragrid)
• With GRASP benchmarks• Network Weather Service (NWS)• Ganglia
• Job Submission and Monitoring• Condor, PBS
GridSphere Portal
GEONGrid Software Stack Version 1.0
Rocks 4.2.1 based on RedHat Enterprise Linux
JDKAnt TripwireSamba
OGSA-DAI OGSA AxisNMI Globus
Tomcat
INCA/GRASPNWSCondorPBS
Postgres PostGIS Geos Proj
GRASS (GDAL, NetCDF, Tiff) GMT
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Node Deployment Architecture
• Hardware Deployment• Each site runs a PoP• Optional cluster and
data resources• Users access
resources through PoP• PoP provides point of
entry• PoP provides access
to global services in GEON
• Developers add services & data hosted on GEON resources• Web services/Grid
services
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i-GEON: International GEON
• GEON nodes operational in Japan, China, and India.
• i-GEON workshops• India, October 2005• China, July 2006• Russia, June 25-26, 2007• India, August 2007 (follow-up workshop)• Australia??, (Dates to be determined)
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GEON Cyberinfrastructure Summer Institute Series
The Cyberinfrastructure Summer Institute for Geoscientists series is designed to introduce geoscientists to commonly-used as well as
emergent information technology (IT) tools. Topics covered include Data Modeling, Web Services, Geographic Information
Systems, introduction to key concepts in Grid Computing, Parallel Programming, and Scientific Workflows.
CSIG 2006, August 2006, San Diego, CA. CSIG 2005, July 2005, San Diego, CA.
CSIG 2004, August 2004, San Diego, CA.
Webcasts of Summer Institutes are available athttp://www.geongrid.org/CSIG04/http://www.geongrid.org/CSIG05/http://www.geongrid.org/CSIG06/
2007 Summer Institute is planned August 13-17, 2007
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Cyberinfrastructure and Earth Science Education
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Using Cyberinfrastructure to Improve the Quality of Education
• Discover Our Earth (DOE)
• Designed as a web-accessible resource for learning
• Includes a build-in evaluation component
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• DOE provides a couple of internet mapping applications and other software tools as well as supportive information that enable discovery-based learning.
• Students access the same data sets as scientists
• Using the web allows us to reach a large audience in a cost effective manner.
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System Design & Development
• Access is provided through three gateways:• Teacher’s guide• Student pages • Web tools.
• This allows users to access the website from multiple perspectives.
• Technology used: GIS, Java, Flash, HTML and VRML.
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http://www.DiscoverOurEarth.org/
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Teacher’s Guide
• Provide supportive material for teachers(Lesson Plans)
• Links to students pages, activities and web tools
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Student Pages
• Provide supportive material for students.
• Include interactive, discovery-based activities for students.
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Web Tools
• Interactive Mapping Tools
• Virtual Experiments
• 3D Graphics
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Interactive Mapping Tools
• The Quick Use Earth Study Tool (QUEST) is an interactive web mapping tool designed for students.
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Virtual Experiments
• Interactive experiments allow students to test their own ideas.
Experiments:- Continental Drift- Isostasy- Viscosity.
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Evaluation
• Undergraduates in introductory level geology classes used the QUEST tool in lab exercises.
• The current evaluation focus is middle and high school teachers and students.
• Usability evaluation for all learners.
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