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


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


Enabling Scientific Discoveries:Pathway to Discovery

Access/Collect

Process Analyze Interpret Discovery

Data Knowledge

How can cyberinfrastructure help?


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


Cyberinfrastructure can help!


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.)

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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.


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


GEON Infrastructure

Mapping Services

ArcIMSWMSWFS

Logging Services

Usage Stats Collection &

Analysis

Data Services

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Data Registration Services

Indexing Services

SpatialTemporal

Conceptual

Data Integration Services

Ontology Enabled

Integration

Computational & Modeling Services

Modeling, Analysis Tools

Metadata Services

GEO

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log

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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

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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


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, …


Access -- GEON Web Site and the Portal


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


Resource Discovery in GEON

A Search Engine for Users• Metadata based search• Spatial coverage based search• Temporal coverage based search• Concept based search


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.


Data integration in myWorkbech


myProjects


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


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


IRIS•Earthquakes•Stations•Waveform

Digital Libraries/GEON Data Grid

Earth model

Earth modelEarth

model

HPCHPCCentersCenters

NCSANCSA SDSCSDSC

SYNSEISe3d

SYNSEIS Components --


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


SYNSEIS Portlet

www.geongrid.orgwww.geongrid.orgwww.geongrid.orgSubsurface

Model

Earthquake parameters

Seismic attenuation

Etc.

Observation

SimulationAnalyses and Integration

GEON SYNSEIS INTEGRATION PLATFORME

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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


LiDAR Data Analysis


D. Harding, NASA

Point Cloudx, y, z, …

Example: LiDAR Workflow

Courtesy: Chris Crosby, ASU

Survey

Analyze / “Do Science”

Interpolate / Grid


Example Outputs


PaleoIntegration


3D/4D Visualization - GEON IDV


Visualization - Integration

Yellowstone (Smith and others) and the geodynamics of the mantle (McNamara)


170 ma 90 ma 10 ma

4D Visualization Images from the GEON IDV

Geodynamics-McNamara

Paleomagnetics-Schettino,Scotese

Paleogeography-Blakely


GEON Network: USA NodesGEON Network: USA Nodes

Partner Projects

Chronos

CUAHSI

Partner services

USGS

GeologicalSurvey ofCanada

ESRI

PoP node

5-node cluster

4 Tb


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


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


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)


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


Cyberinfrastructure and Earth Science Education


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


• 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.


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.


http://www.DiscoverOurEarth.org/


Teacher’s Guide

• Provide supportive material for teachers(Lesson Plans)

• Links to students pages, activities and web tools


Student Pages

• Provide supportive material for students.

• Include interactive, discovery-based activities for students.


Web Tools

• Interactive Mapping Tools

• Virtual Experiments

• 3D Graphics


Interactive Mapping Tools

• The Quick Use Earth Study Tool (QUEST) is an interactive web mapping tool designed for students.


Virtual Experiments

• Interactive experiments allow students to test their own ideas.

Experiments:- Continental Drift- Isostasy- Viscosity.


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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