GEON: A Cyberinfrastructure Facility to
Advance Research and Education
Dogan Seber
San Diego Supercomputer Center
University of California, San Diego
www.geongrid.org
Acknowledgements
Chaitan Baru
Sandeep Chandra
Efrat Frank
Kai Lin
Ashraf Memon
Choonhan Youn
www.geongrid.org
Outline:
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Cyberinfrastructure and the Geosciences
GEON Cyberinfrastructure
GEON Services and Access Mechanisms
Impact on Science and Education
• Synthetic seismogram calculation
• LiDAR data processing
• 3D and 4D visualizations
• Future activities
www.geongrid.org
Enabling Scientific Discoveries:
Pathway to Discovery
Data
Access
Knowledge
Process
Analyze
Interpret
Discovery
How does cyberinfrastructure help?
www.geongrid.org
GEON’s Vision
• Enable new discoveries in the geosciences by
utilizing an easy-to-use integration environment
built using state-of-the-art information technology
resources.
The end product is a system that :
Enables new interdisciplinary research and encourages resource sharing
Stores and seamlessly integrates distributed data sets, software, and tools
Allows users to make searches to discover data and information
not only by name, but also by concepts.
Provides high-end computational resources
Provides a customizable analysis and research environment (workflow)
Is a rich resource for teachers and learners
www.geongrid.org
GEON Project
 NSF Large ITR project – collaborative effort
 GEON is creating an IT infrastructure to
“enable” interdisciplinary geoscience
research for the entire community
 Project started in October 1, 2002 (after three
years of preparation) and will continue until
September 30, 2007
www.geongrid.org
GEON Cyberinfrastructure Principles
• An equal partnership
• IT works in close conjunction with science
• CI: Support the “day to day” conduct of science (escience), in addition to “hero” computations
• 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
www.geongrid.org
GEON Cyberinfrastructure
GEON Portal
Web/Grid Services Interfaces
Registration
GEONsearch
Data Registration Services
GEONworkbench
workflow, visualization, HPC
Data Integration Services
Mapping Services
ArcIMS
WMS
WFS
Ontology
Enabled
Integration
Spatial
Temporal
Conceptual
Metadata Services
GEON
Catalog
Indexing Services
Others
Postgres
SRB
OpenDAP
mySQL
DB2,
Data Services
Physical Grid
MyGEON
Computational &
Modeling Services
Modeling,
Analysis Tools
Logging Services
Other Core Services
Usage Stats
Collection &
Analysis
GridFTP
OGSA-DAI
CSF
RedHat Linux, ROCKS, OGSI, www.geongrid.org
Internet, I2
GEON Nodes
Geological
Survey of
Canada
Chronos
USGS
ESRI
CUAHSI
PoP node
5-node cluster
Partner Projects
4 Tb
Partner services
www.geongrid.org
Node Deployment Architecture
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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
www.geongrid.org
GEON Software Stack
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Base OS
• Rocks: highly programmatic software configuration
GEONGrid Software Stack Version 1.0
management
Development
GridSphere Portal
• Globus 4.0.2
• Web Services (Jakarta-tomcat-5.0.28, axis-1.1, ant-1.6,
GRASS (GDAL, NetCDF, Tiff)
GMT
jdk1.4.2)
• GridSphere 2.0.2 Portal Framework
PBS
Condor
NWS INCA/GRASP
Database
OGSA-DAI NMI Globus OGSA
Axis
• Postgres 8.0.3
• PostGIS 1.0.2 (Geos, Proj)
Tomcat
Postgres
PostGIS Geos Proj
GIS/Mapping
• Grass 6.0.2, GMT
Ant
Samba
JDK
Tripwire
Security
• Tripwire, chkrootkit
Rocks 4.2.1 based on
RedHat Enterprise Linux
System Monitoring
• INCA Testing and Monitoring framework (Teragrid)
• With GRASP benchmarks
• Network Weather Service (NWS)
• Ganglia
Job Submission and Monitoring
www.geongrid.org
• Condor, PBS
GEON Cyberinfrastructure
GEON Portal
Web/Grid Services Interfaces
Registration
GEONsearch
Resource/data Registration
Services
GEONworkbench
workflow, visualization, HPC
Data Integration Services
Mapping Services
ArcIMS
WMS
WFS
Ontology
Enabled
Integration
Spatial
Temporal
Conceptual
Metadata Services
GEON
Catalog
Indexing Services
Others
Postgres
SRB
OpenDAP
mySQL
DB2,
Data Services
Physical Grid
MyGEON
Computational &
Modeling Services
Modeling,
Analysis Tools
Logging Services
Other Core Services
Usage Stats
Collection &
Analysis
GridFTP
OGSA-DAI
CSF
RedHat Linux, ROCKS, OGSI, www.geongrid.org
Internet, I2
User Entry Points:
GEON Web Site and the Portal
Portal Framework: gridsphere;
JSR168 compliant
www.geongrid.org
(www.gridsphere.org)
Security Infrastructure
• Portal users need access to various Grid-enabled
resources for job submission, data management,
instrument control, etc.
• Standard security mechanism is GSI (Grid
Security Infrastructure). Typically involves:
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Creation of credentials for a new user
Storage of a proxy in MyProxy by user
Retrieval of proxy upon user login to portal
Configuration of resources to accept credentials
www.geongrid.org
GAMA: Grid Account Management
Architecture
• Install command-line security infrastructure on a dedicated,
locked-down machine (GAMA server)
• Wrap tools as Web Services on GAMA server
• Construct GridSphere portlets and services for submitting and
managing account requests from users on a portal server
• Configure GridSphere to automatically retrieve a proxy from the
GAMA server when a user logs on to the portal
www.geongrid.org
GEON Cyberinfrastructure
GEON Portal
Web/Grid Services Interfaces
Registration
GEONsearch
Resource/data Registration
Services
GEONworkbench
workflow, visualization, HPC
Data Integration Services
Mapping Services
ArcIMS
WMS
WFS
Ontology
Enabled
Integration
Spatial
Temporal
Conceptual
Metadata Services
GEON
Catalog
Indexing Services
Others
Postgres
SRB
OpenDAP
mySQL
DB2,
Data Services
Physical Grid
MyGEON
Computational &
Modeling Services
Modeling,
Analysis Tools
Logging Services
Other Core Services
Usage Stats
Collection &
Analysis
GridFTP
OGSA-DAI
CSF
RedHat Linux, ROCKS, OGSI, www.geongrid.org
Internet, I2
Primary GEON Services*
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Resource Registration - GEONcontribute
Resource Discovery -- GEONsearch
Data Integration -- GEON Integration Cart
Personalized Access -- myGEON
Applications -- GEONtools
* All services accessible via the portal, some available as “remote services”
to other client applications.
System Architecture
User View
www.geongrid.org
Other distributed apps
Kepler, DLESE, …
Client Access (via Web Services)
User Access (via Portal)
myOntology.owl
metadata
myDataset.foo
metadata
ResourceRegistration
GEON
Catalog
Search condition(s)
spatial temporal concept
GEONsearch
User actions
add delete manipulate
GEONworkbench
GEON
Workspace
(user)
SRB
Log
GEONmiddleware
external services
Gazetteer,
DLESE, …
Geologic Age,
Chronos, …
www.geongrid.org
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
www.geongrid.org
www.geongrid.org
Other distributed apps
Kepler, DLESE, …
Client Access (via Web Services)
User Access (via Portal)
myOntology.owl
metadata
myDataset.foo
metadata
ResourceRegistration
GEON
Catalog
Search condition(s)
spatial temporal concept
GEONsearch
User actions
add delete manipulate
GEONworkbench
GEON
Workspace
(user)
SRB
Log
GEONmiddleware
external services
Gazetteer,
DLESE, …
Geologic Age,
Chronos, …
www.geongrid.org
Resource Discovery in GEON
A Search Engine for Users
• Metadata based search
• Spatial coverage based search
• Temporal coverage based search
• Concept based search
www.geongrid.org
GEON Basic Search
www.geongrid.org
GEON Advanced Search
www.geongrid.org
www.geongrid.org
www.geongrid.org
www.geongrid.org
Resource Usage Statistics
www.geongrid.org
GEON Semantic Mediator
Oracle
DB2
SQL
Server
MySQL
PostgreSQL
PostGIS
Query Execution
Query
Optimization
Query
Planning
Internal Database
SQL Parser
Spatial SQL against federal schemas
Mediator JDBC Driver
SOQL
GUI
Portal or Application
Semantic Query Rewriter
SOQL
Parser
Ontology
Reasoner
ODAL Processor
OWL
SOQL Processor
www.geongrid.org
ODAL
Other distributed apps
Kepler, DLESE, …
Client Access (via Web Services)
User Access (via Portal)
myOntology.owl
metadata
myDataset.foo
metadata
ResourceRegistration
GEON
Catalog
Search condition(s)
spatial temporal concept
GEONsearch
User actions
add delete manipulate
GEONworkbench
GEON
Workspace
(user)
SRB
Log
GEONmiddleware
external services
Gazetteer,
DLESE, …
Geologic Age,
Chronos, …
www.geongrid.org
www.geongrid.org
GEON tools: TeraGrid Science Gateway
• Synthetic Seismogram Calculation Tool
• LiDAR data Analysis Tool
www.geongrid.org
SYNSEIS: A grid application in GEON
• 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
www.geongrid.org
SYNSEIS Components -IRIS
•Earthquakes
•Stations
•Waveform
SYNSEIS
e3d
HPC
Centers
Digital Libraries/GEON Data Grid
Earth
model
NCSA SDSC
Earth
model
Earth
model
www.geongrid.org
SYNSEIS Architecture
GEONGrid Portal
MyGEON
GEONTools
Synseis Portlet
SYNSEIS Computations
Macromedia Flash GUI
Map Server
Web Services
Earth Model
Service
Job Submission/Monitoring
and File Service
Grid Services
Grid FTP
Data
Repository
JDBC
Data Archives
Service
IIOP/CORBA
HPC Resources
Job Database
www.geongrid.org
IRIS
DMC
SYNSEIS Portlet
www.geongrid.org
GEON SYNSEIS INTEGRATION PLATFORM
EarthScope data
Observation
Analyses and Integration
Earthquake
parameters
Seismic
attenuation
Subsurface
www.geongrid.org
Etc.
Model
Scientific Discoveries
GEON portal and HPC Environment
Simulation
LiDAR Data Analysis
www.geongrid.org
Survey
Example: LiDAR
Workflow
Courtesy: Chris Crosby, ASU
D. Harding,
NASA
Point Cloud
x, y, z, …
Interpolate / Grid
Analyze / “Do Science”
www.geongrid.org
A Three-Tier Architecture
• GOAL: Efficient LiDAR
interpolation and analysis
using GEON infrastructure
and tools
Portal
• GEON Portal
• Kepler Scientific Workflow
System
• GEON Grid
• Use scientific workflows to
glue/combine different
tools and the infrastructure
Grid
www.geongrid.org
LiDAR Processing:
Three Tier Architecture
x,y,z and attribute
Client/
NFS Mounted
Disk
DB2
GEON Portal
Render Map
Map
Parameters
Grass
Functions
ArcSDE
ArcInfo
Parameter
xml
ArcIMS
process
output
Create
Workflow
Description
raw
data
DB2
Spatial
query
submit
Map onto the grid (Pegasus)
Grass surfacing algorithms:
Spline
IDW
Compute Cluster
block mean
Binary grid
…
ASCII grid
Text file
Tiff/Jpeg/Gif
ASCII grid
Download data
KEPLER WORKFLOW
www.geongrid.org
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www.geongrid.org
Example Outputs
www.geongrid.org
Visualization - Integration
Putting it all together. The first step to true integration is to remove the
barriers to accessing and importing the data and then visualization of the
data. Below are some examples of multidimensional data displayed in three
dimensions with the GEON IDV.
Yellowstone (Smith and others) and the geodynamics of the mantle (McNamara)
www.geongrid.org
4D Visualization Images from the GEON IDV
170 ma
90 ma
10 ma
GeodynamicsMcNamara
PaleomagneticsSchettino,
Scotese
PaleogeographyBlakely
www.geongrid.org
i-GEON: International GEON
• GEON has started international collaborations
• GEON nodes now operational in Japan, China,
and India.
• Two international GEON workshops were held
• India, October 2005
• China, July 2006
www.geongrid.org
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 at
http://www.geongrid.org/CSIG04/
http://www.geongrid.org/CSIG05/
http://www.geongrid.org/CSIG06/
2007 Summer Institute is being planned, August 2007
www.geongrid.org
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www.geongrid.org