Developing Standards-Developing Standards-Based Analysis and Based Analysis and Visualization ToolsVisualization Tools

Rich SignellRich SignellUSGS USGS

Sachin BhateSachin BhateMiss. State UniversityMiss. State University

John EvansJohn EvansRutgers UniversityRutgers University

Krish NarasimhanLMCO

Standardize the Standardize the Interface!Interface!

Climate and Forecast (CF) Climate and Forecast (CF) Metadata ConventionsMetadata Conventions

Groups adopting CF:

GO-ESSP: Global Organization for Earth System Science Portal

IOOS: Integrated Ocean Observing System

ESMF: Earth System Modeling Framework

OGC: Open Geospatial Consortium

CF-Compliant ROMS 2.2 CF-Compliant ROMS 2.2 History FileHistory File

CF Conventions IICF Conventions II

UnidataCommon Data

Model(CF)

HDFXMDF

NetCDFCF

TBD

JAVAAPI

CAPI

FORTRAN API

Viewer

CF-CompatibleFORMATS

CF-APIS

CF Applications

CF Conventions

ModelAnalysisTool

NetCDF-Java

Unidata’s “NetCDF” Java Unidata’s “NetCDF” Java LibraryLibrary

NetCDF Files, OpenDAP, HDF5, GRIB, NcML, and more.

Generic visualization tools Generic visualization tools via standards: IDVvia standards: IDV

from Hawaii

from Woods Hole

IDV: Hurricane KatrinaIDV: Hurricane Katrina

IDV DemoIDV Demo

Matlab/NetCDFMatlab/NetCDF

Matlab and CFMatlab and CF

Matlab can access Java routines!Matlab can access Java routines! Could we do away with machine-Could we do away with machine-

dependent “mex” interface by using dependent “mex” interface by using NetCDF-Java? Maybe. Not a one-to-one NetCDF-Java? Maybe. Not a one-to-one correspondence between NetCDF-Java & correspondence between NetCDF-Java & C/Fortran Interface.C/Fortran Interface.

SNCTOOLS reading tools (e.g. nc_varget, SNCTOOLS reading tools (e.g. nc_varget, nc_attget) now work with Java, but nc_attget) now work with Java, but writing still requires mexnc.writing still requires mexnc.

RSLICE can run on Java!RSLICE can run on Java!

…and so could any other read-only viz or analysis tool.ROMS_GUI?

Matlab/NetCDFMatlab/NetCDF

Question: Can we use NetCDF Java to avoid Question: Can we use NetCDF Java to avoid re-coding CF-logic into Matlab routines? re-coding CF-logic into Matlab routines?

Answer: Yes!Answer: Yes!

CFtime.m (traditional)CFtime.m (traditional)

CFtime.m (with NetCDF Java)CFtime.m (with NetCDF Java)

Matlab DemoMatlab Demo

NOPP Program TasksNOPP Program Tasks

T1. Science and Technical Management T1. Science and Technical Management and Reviewand Review

T2. Model Development and CouplingT2. Model Development and Coupling

T3. Software Tool Development T3. Software Tool Development (Sachin Kumar-Bhate: 3 man years)(Sachin Kumar-Bhate: 3 man years)

T4. Algorithm DevelopmentT4. Algorithm Development

T5. Community EngagementT5. Community Engagement

T6. ApplicationsT6. Applications

The Way ForwardThe Way Forward

Work with CF Conventions Group, IOOS Work with CF Conventions Group, IOOS MAST, and ESMF Developers to ensure that MAST, and ESMF Developers to ensure that developing CF Standards meet ocean developing CF Standards meet ocean community (including ROMS) needscommunity (including ROMS) needs

Build a CF toolbox for Matlab, using NetCDF-Build a CF toolbox for Matlab, using NetCDF-JavaJava

Build a CF toolbox for Python, using CF-Lib Build a CF toolbox for Python, using CF-Lib (C)(C)

Build and support analysis and visualization Build and support analysis and visualization tools that work with CF standards (e.g. IDV)tools that work with CF standards (e.g. IDV)

Listen to the Community!Listen to the Community! Standardize the Interface!Standardize the Interface!

NRL SSC Role in the NRL SSC Role in the Battlespace Environments Battlespace Environments

InstituteInstituteRick Allard, Tim CampbellRick Allard, Tim Campbell

Build ESMF interfaces within existing scalable ocean models (HYCOM, NCOM, SWAN and ADCIRC)

Provide the necessary components for applications with atmospheric, ocean, ice, and riverine models.

Develop coupled applications to support operational Navy:•HYCOM-CICE (ocean, ice)

•SWAN-ADCIRC (wave, circulation)•ADCIRC-WASH123D (circulation, riverine, watershed)•COAMPS-NCOM (atmosphere, ocean)

nc=netcdf(‘fem.nc’);nc=netcdf(‘fem.nc’);

lon=nc{‘lon’}(:);lon=nc{‘lon’}(:);

lat=nc{‘lat’}(:);lat=nc{‘lat’}(:);

ele=nc{‘ele’}(:);ele=nc{‘ele’}(:);

salt=nc{‘salt’}(1,1,:);salt=nc{‘salt’}(1,1,:);

trisurf(ele,lon,lat,salt)trisurf(ele,lon,lat,salt)

[t,b,jday,u]=[t,b,jday,u]=CFtimeCFtime(nc,’ti(nc,’time’)me’)

title([‘Salt title([‘Salt ‘,datestr(jday(1))])‘,datestr(jday(1))])

Simple Matlab AccessSimple Matlab Access

CFtime.m (with API)CFtime.m (with API)

ERDC’s XMDFERDC’s XMDF

104 pages

Matthew Piggott (Imperial College, UK)

UnstructuredUnstructuredAdaptive GridAdaptive Grid Imperial College Imperial College

Ocean Model (ICOM)Ocean Model (ICOM)

FVCOM using LLNL’s “VisIt”FVCOM using LLNL’s “VisIt”Free software based on VTK w/Java,C+Free software based on VTK w/Java,C+

+,Python interfaces+,Python interfaces

Chen & Cowles, UMASSD

Unstructured Mesh PrioritiesUnstructured Mesh Priorities

CF Conventions (define and adopt)CF Conventions (define and adopt) CF APIs (C in addition to Java)CF APIs (C in addition to Java) CF Reference Applications (e.g. IDV, CF Reference Applications (e.g. IDV,

CDAT, VisIt module)CDAT, VisIt module)

New ESMF-Based ProgramsNew ESMF-Based ProgramsFunding for Science, Adoption, and Core Funding for Science, Adoption, and Core

DevelopmentDevelopment

Modeling, Analysis and Modeling, Analysis and Prediction Program for Prediction Program for Climate Variability and Climate Variability and ChangeChangeSponsor:Sponsor: NASA NASAPartners:Partners:University of Colorado at Boulder, University of Colorado at Boulder, University of Maryland, Duke University of Maryland, Duke University, NASA Goddard Space University, NASA Goddard Space Flight Center, NASA Langley, Flight Center, NASA Langley, NASA Jet Propulsion Laboratory, NASA Jet Propulsion Laboratory, Georgia Institute of Technology, Georgia Institute of Technology, Portland State University, Portland State University, University of North Dakota, Johns University of North Dakota, Johns Hopkins University, Goddard Hopkins University, Goddard Institute for Space Studies, Institute for Space Studies, University of Wisconsin, Harvard University of Wisconsin, Harvard University, moreUniversity, moreThe NASA Modeling, Analysis and The NASA Modeling, Analysis and Prediction Program will develop an Prediction Program will develop an ESMF-based modeling and analysis ESMF-based modeling and analysis environment to study climate environment to study climate variability and change. variability and change.

Battlespace Environments Battlespace Environments InstituteInstituteSponsor:Sponsor: Department of Defense Department of DefensePartners:Partners:DoD Naval Research Laboratory, DoD Naval Research Laboratory, DoD Fleet Numerical, DoD Army DoD Fleet Numerical, DoD Army ERDC, DoD Air Force Air Force ERDC, DoD Air Force Air Force Weather AgencyWeather AgencyThe Battlespace Environments The Battlespace Environments Institute is developing integrated Institute is developing integrated Earth and space forecasting systems Earth and space forecasting systems that use ESMF as a standard for that use ESMF as a standard for component coupling.component coupling.

Integrated Dynamics Integrated Dynamics through Earth’s through Earth’s Atmosphere and Space Atmosphere and Space Weather InitiativesWeather InitiativesSponsors: Sponsors: NASA, NSFNASA, NSFPartners:Partners: University of University of Michigan/SWMF, Boston Michigan/SWMF, Boston University/CISM, University of University/CISM, University of Maryland, NASA Goddard Space Maryland, NASA Goddard Space Flight Center, NOAA CIRESFlight Center, NOAA CIRESESMF developers are working ESMF developers are working with the University of Michigan with the University of Michigan and others to develop the and others to develop the capability to couple together Earth capability to couple together Earth and space software components.and space software components.

Spanning the Gap Between Spanning the Gap Between Models and Datasets:Models and Datasets:Earth System CuratorEarth System CuratorSponsor:Sponsor: NSF NSFPartners:Partners:Princeton University, Georgia Princeton University, Georgia Institute of Technology, Institute of Technology, Massachusetts Institute of Massachusetts Institute of Technology, PCMDI, NOAA GFDL, Technology, PCMDI, NOAA GFDL, NOAA PMEL, DOE ESGNOAA PMEL, DOE ESGThe ESMF team is working with data The ESMF team is working with data specialists to create an end-to-end specialists to create an end-to-end knowledge environment that knowledge environment that encompasses data services and encompasses data services and models.models.

Origins of the CSTMOrigins of the CSTM

““A better understanding is needed of the basic physics A better understanding is needed of the basic physics that control sedimentary processes such as bottom that control sedimentary processes such as bottom roughness, aggregation or flocculation and roughness, aggregation or flocculation and disaggregation, erosion and deposition, and bed disaggregation, erosion and deposition, and bed consolidationconsolidation””

““Wide acceptance of a community sediment transport Wide acceptance of a community sediment transport model would make an effective tool for scientific model would make an effective tool for scientific researchresearch.. …no existing model has the features that would …no existing model has the features that would allow wide access and acceptance by the community: freely allow wide access and acceptance by the community: freely available code; state-of-the-art hydrodynamic and sediment available code; state-of-the-art hydrodynamic and sediment algorithms with modern, modular coding; comprehensive algorithms with modern, modular coding; comprehensive documentation; and demonstrated performance on a suite of documentation; and demonstrated performance on a suite of community defined test cases.”community defined test cases.”

““Coordination of the community modeling effort Coordination of the community modeling effort should be by an impartial organization with long-term should be by an impartial organization with long-term stabilitystability””

Community Sediment Community Sediment Transport Model (CSTM)Transport Model (CSTM)

CSTM Project Contributions CSTM Project Contributions

Suspended and bed load sediment transportSuspended and bed load sediment transport Multiple sediment classesMultiple sediment classes Bed framework & stratigraphyBed framework & stratigraphy New wave/current bottom New wave/current bottom

boundary layer boundary layer Monotonic advection Monotonic advection Umlauf & Burchard GLS mixing Umlauf & Burchard GLS mixing Test casesTest cases Wetting/dryingWetting/drying Nearshore processesNearshore processes