A Distributed Approach to A Distributed Approach to Ocean, Atmosphere & Climate Ocean, Atmosphere & Climate

Model Data InteroperabilityModel Data Interoperability

A Distributed Approach to A Distributed Approach to Ocean, Atmosphere & Climate Ocean, Atmosphere & Climate

Model Data InteroperabilityModel Data InteroperabilityRich Signell

USGS Woods Hole, MACOAWST Training Workshop

Woods Hole, MA: Aug 25-28, 2014

Rich SignellUSGS Woods Hole, MA

COAWST Training Workshop

Woods Hole, MA: Aug 25-28, 2014

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US Integrated Ocean Observing System (IOOS®)

IOOSIOOS®® Plan defines: Plan defines:• Global ComponentGlobal Component• Coastal ComponentCoastal Component

17 Federal Agencies17 Federal Agencies 11 Regional Associations 11 Regional Associations

The problem: lots of unique (stovepipe) web sites

The GoMOOS Nowcast/Forecast Circulation Model (University of Maine)

IOOS Core PrinciplesIOOS Core Principles

• Adopt open standards & practices

• Avoid customer-specific stovepipes

• Standardized access services implemented at data providers

• Adopt open standards & practices

• Avoid customer-specific stovepipes

• Standardized access services implemented at data providers

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CustomerCustomer

Web accessWeb accessserviceservice

DataDataProviderProviderObservationsObservations

ModelsModels

Issue: Ocean grids are not regularly spaced!Issue: Ocean grids are not regularly spaced!

Stretched surface and terrain following vertical coordinates

Curvilinear orthogonal horizontal coordinates

NetCDF Climate and Forecast (CF) Conventions provide a solution

NetCDF Climate and Forecast (CF) Conventions provide a solution

Groups using CF:

GO-ESSP: Global Organization for Earth System Science Portal

IOOS: Integrated Ocean Observing System

ESMF: Earth System Modeling Framework

OGC: Open Geospatial Consortium (GALEON: WCS profile)

CF-Compliant ROMS fileCF-Compliant ROMS file

double s_rho(s_rho) ; s_rho:long_name = "S-coordinate at RHO-points" ; s_rho:valid_min = -1. ; s_rho:valid_max = 0. ; s_rho:positive = "up" ; s_rho:standard_name = "ocean_s_coordinate_g1" ; s_rho:formula_terms = "s: s_rho C: Cs_r eta: zeta depth: h depth_c: hc" ; s_rho:field = "s_rho, scalar" ;

float temp(ocean_time, s_rho, eta_rho, xi_rho) ; temp:_FillValue = 1.e+37f ; temp:long_name = "potential temperature" ; temp:units = "Celsius" ; temp:time = "ocean_time" ; temp:coordinates = "lon_rho lat_rho s_rho ocean_time" ;

IOOS Model Data Interoperability DesignIOOS Model Data Interoperability Design

ROMS

ADCIRC

HYCOM

SELFE

NCOM NcML

NcML

NcML

NcML

NcML

Common Data Model

OPeNDAP+CF

WCS

NetCDF Subset

THREDDS Data Server

Standardized (CF-1.6, UGRID-0.9) Virtual Datasets

NonstandardModel Output Data Files

Web Services Matlab

Panoply

IDV

Clients

NetCDF-Java

Libraryor Broker

WMS

ncISO

ArcGIS

NetCDF4-Python

FVCOM

PythonERDDAP

NetCDF-Java

SOS

Geoportal Server

GeoNetwork

GI-CAT

Observed data (buoy, gauge, ADCP, glider)

Godiva2

CKANNcML

GridUgridTimeSeriesProfileTrajectoryTimeSeriesProfile

NonstandardData Files

CatalogServices

WMS Browsing with THREDDS/ncWMSWMS Browsing with THREDDS/ncWMS

Matlab NCTOOLBOXhttps://github.com/nctoolbox

Matlab NCTOOLBOXhttps://github.com/nctoolbox

• Objective: Make it simple to access CF data• Example function:• [t, geo]=nj_tslice(URL,’temp’,1);• t = 22x120x180 single• geo =

– lat: [120x180 single] – lon: [120x180 single]– z: [22x120x180 double]– time: 733582 (matlab datenum)

• nj_tslice works identically for ROMS, POM, ECOM, WRF, Wavewatch3

• URL can be: local NetCDF, remote NetCDF, NcML, OpenDAP Data URL

• Objective: Make it simple to access CF data• Example function:• [t, geo]=nj_tslice(URL,’temp’,1);• t = 22x120x180 single• geo =

– lat: [120x180 single] – lon: [120x180 single]– z: [22x120x180 double]– time: 733582 (matlab datenum)

• nj_tslice works identically for ROMS, POM, ECOM, WRF, Wavewatch3

• URL can be: local NetCDF, remote NetCDF, NcML, OpenDAP Data URL

Comparing Models with Data in MatlabComparing Models with Data in Matlab

Model 1: UMASS-ECOMModel 1: UMASS-ECOM Model 2: UMAINE-POMModel 2: UMAINE-POM Data: SST 2008-Sep-08 07:32Data: SST 2008-Sep-08 07:32

Skidaway modena glider (Sep 11-23)Skidaway modena glider (Sep 11-23)

compare_secoora_model_sections.m(using nc_genslice.m)

compare_secoora_model_sections.m(using nc_genslice.m)

Buoy_comp.mBuoy_comp.m

3D visualization of data with IDV3D visualization of data with IDV

NetCDF Subset Service to CSVNetCDF Subset Service to CSV

CSV Time Series from Subset ServiceCSV Time Series from Subset Service

CSV request is a “RESTful” URL:http://geoport.whoi.edu/thredds/ncss/grid/coawst_4/use/fmrc/coawst_4_use_best.ncd?var=Hwave&latitude=39.5&longitude=-69.5&time_start=2014-08-27T01:00:00Z&time_end=2014-08-28T00:00:00Z&vertCoord=&accept=csv

Accessing the CSV data in ExcelAccessing the CSV data in Excel

Access the CSV data in Python, R, etcAccess the CSV data in Python, R, etc

Iris Python tools from the UK Met OfficeIris Python tools from the UK Met Office

ESPreSSO model (Rutgers)ESPreSSO model (Rutgers)

Global RTOFS (NOAA)Global RTOFS (NOAA)

IOOS Models Notebook on WakariIOOS Models Notebook on Wakari

60 minutes to serving your data60 minutes to serving your data

1. Install Sun/Oracle Java (10 min)2. Install/configure Tomcat (15 min)3. Install/configure the Thredds Data

Server (15 min)4.Put NetCDF (or HDF4, Grib1, Grib2,

HDF5 files) in a directory (5 min)5.Add NcML (XML) files for CF

compliance and aggregation (15 min)

Adding data to THREDDSAdding data to THREDDS

rsignell@gam:/usgs/data0/bbleh/tidal$ ls *wide*…his_bbleh_wide_0048.nc his_bbleh_wide_0100.nc his_bbleh_wide_0152.nchis_bbleh_wide_0049.nc his_bbleh_wide_0101.nc his_bbleh_wide_0153.nchis_bbleh_wide_0050.nc his_bbleh_wide_0102.nc his_bbleh_wide_0154.nchis_bbleh_wide_0051.nc his_bbleh_wide_0103.nc wide.ncml

$more wide.ncml

<netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"> <aggregation dimName="ocean_time" type="joinExisting"> <scan location="." regExp=".*wide.*_[0-9]{4}\.nc$"/> </aggregation></netcdf>

Browsing WMS with Godiva2Browsing WMS with Godiva2

GI-CAT catalog broker service architectureGI-CAT catalog broker service architecture

Searching for DataSearching for Data

USGS COAWST East Coast ForecastUSGS COAWST East Coast Forecast

Automated model comparisonAutomated model comparison

Summary (1 of 2)Summary (1 of 2)

• Common data models for “feature types” (structured and unstructured grids, time series, profiles, swaths) (Unidata CDM)

• Standard web services for delivering these data and metadata (OGC, Unidata)

• Tools to access and process these services in common analysis environments: R, Matlab, Python, ArcGIS, JavaScript

Summary (2 of 2)Summary (2 of 2)

• It’s easy (1 hour) to deploy free, supported systems that allow for standards-based delivery of aggregated data from native model grids that put little effort on the data provider

• What do you get? – Lots of choices for data access (Browser, Matlab, Python, Excel, IDV,

R, IDL)– More usage of model results by more people– Faster feedback to modelers, leading to improved models– Shared code base in the community– Increased community support for standards-based access– Less time wasted messing with data, more time spent on ecosystem

based management• What should you do? Encourage providers to use these

standards, and develop tools that use standardized access

• It’s easy (1 hour) to deploy free, supported systems that allow for standards-based delivery of aggregated data from native model grids that put little effort on the data provider

• What do you get? – Lots of choices for data access (Browser, Matlab, Python, Excel, IDV,

R, IDL)– More usage of model results by more people– Faster feedback to modelers, leading to improved models– Shared code base in the community– Increased community support for standards-based access– Less time wasted messing with data, more time spent on ecosystem

based management• What should you do? Encourage providers to use these

standards, and develop tools that use standardized access

It’s all on GitHub + rsignellIt’s all on GitHub + rsignell

Glossary (1/6)Glossary (1/6)

• CF Conventions: NetCDF Climate and Forecast Metadata Conventionshttp://cf-pcmdi.llnl.gov/(Standards for identifying geospatial coordinates in NetCDF files andgrid relationships)

• DMAC: Data Management And Communications subsystem http://www.ioos.gov/data/dmac/welcome.html (One of three subsystems of IOOS, providing infrastructure for the Observing and the Modeling and Applications subsystems)

• ECOM: Estuarine, Coastal, and Ocean Model. http://www.hydroqual.com/ehst_env_hyd.html(3D ocean circulation model developed principally by Alan Blumberg)

• ERDDAP: Environmental Research Division's Data Access Programhttp://coastwatch.pfeg.noaa.gov/erddap/index.html(A web service that aggregates data from diverse remote sources and offers a simple, consistent way to access the data)

• CF Conventions: NetCDF Climate and Forecast Metadata Conventionshttp://cf-pcmdi.llnl.gov/(Standards for identifying geospatial coordinates in NetCDF files andgrid relationships)

• DMAC: Data Management And Communications subsystem http://www.ioos.gov/data/dmac/welcome.html (One of three subsystems of IOOS, providing infrastructure for the Observing and the Modeling and Applications subsystems)

• ECOM: Estuarine, Coastal, and Ocean Model. http://www.hydroqual.com/ehst_env_hyd.html(3D ocean circulation model developed principally by Alan Blumberg)

• ERDDAP: Environmental Research Division's Data Access Programhttp://coastwatch.pfeg.noaa.gov/erddap/index.html(A web service that aggregates data from diverse remote sources and offers a simple, consistent way to access the data)

Glossary (2/6)Glossary (2/6)

• ESMF: Earth System Modeling Frameworkhttp://www.esmf.ucar.edu/

(Software for building and coupling weather, climate, and related models)• GO-ESSP: Global Organization for Earth System Science Portal

http://go-essp.gfdl.noaa.gov/(Collaboration designed to develop a new generation of software infrastructure that will provide distributed access to observed and simulated data from the climate and weather communities)

• IDV: Integrated Data Viewerhttp://www.unidata.ucar.edu/software/idv/(Java-based software for analyzing and visualizing geoscience data)

• IOOS: Integrated Ocean Observing System http://ioos.noaa.gov/(Multidisciplinary system designed to collect, deliver, and use ocean information)

• IOOC: Interagency Ocean Observing Committeehttp://www.iooc.us/

• ESMF: Earth System Modeling Frameworkhttp://www.esmf.ucar.edu/

(Software for building and coupling weather, climate, and related models)• GO-ESSP: Global Organization for Earth System Science Portal

http://go-essp.gfdl.noaa.gov/(Collaboration designed to develop a new generation of software infrastructure that will provide distributed access to observed and simulated data from the climate and weather communities)

• IDV: Integrated Data Viewerhttp://www.unidata.ucar.edu/software/idv/(Java-based software for analyzing and visualizing geoscience data)

• IOOS: Integrated Ocean Observing System http://ioos.noaa.gov/(Multidisciplinary system designed to collect, deliver, and use ocean information)

• IOOC: Interagency Ocean Observing Committeehttp://www.iooc.us/

Glossary (3/6)Glossary (3/6)

• NcWMS: Web Map Servicehttp://www.resc.rdg.ac.uk/trac/ncWMS/(ncWMS is a Web Map Service for geospatial data that are stored in CF-compliant NetCDF files. )

• NcML: NetCDF Markup Languagehttp://www.unidata.ucar.edu/software/netcdf/ncml/(Used to standardize and aggregate non-standard NetCDF files)

• NetCDF-Java: NetCDF-Java Libraryhttp://www.unidata.ucar.edu/software/netcdf-java/(Library that takes advantage of CF conventions, NcML to facilitatebuilding standards-based clients)

• NcWMS: Web Map Servicehttp://www.resc.rdg.ac.uk/trac/ncWMS/(ncWMS is a Web Map Service for geospatial data that are stored in CF-compliant NetCDF files. )

• NcML: NetCDF Markup Languagehttp://www.unidata.ucar.edu/software/netcdf/ncml/(Used to standardize and aggregate non-standard NetCDF files)

• NetCDF-Java: NetCDF-Java Libraryhttp://www.unidata.ucar.edu/software/netcdf-java/(Library that takes advantage of CF conventions, NcML to facilitatebuilding standards-based clients)

Glossary (4/6)Glossary (4/6)

• OPeNDAP: Open-source Project for a Network Data Access Protocolhttp://opendap.org(allows efficient hyperslabbing of geospatial data)

• POM: Princeton Ocean Modelhttp://www.aos.princeton.edu/WWWPUBLIC/htdocs.pom/(Sigma coordinate, free surface ocean model with embedded turbulence and wave sub-models, and wet-dry capability)

• RCOOS: Regional Coastal Ocean Observing System• http://www.ioosassociation.org/

(Generic term for one of the 11 regional observing systems in IOOS)

• OPeNDAP: Open-source Project for a Network Data Access Protocolhttp://opendap.org(allows efficient hyperslabbing of geospatial data)

• POM: Princeton Ocean Modelhttp://www.aos.princeton.edu/WWWPUBLIC/htdocs.pom/(Sigma coordinate, free surface ocean model with embedded turbulence and wave sub-models, and wet-dry capability)

• RCOOS: Regional Coastal Ocean Observing System• http://www.ioosassociation.org/

(Generic term for one of the 11 regional observing systems in IOOS)

Glossary (5/6)Glossary (5/6)

• ROMS: Regional Ocean Modeling System

www.myroms.org

(A free-surface, terrain-following, primitive equations ocean model widely used by the scientific community for a diverse range of applications)

• SCCOOS: Southern California Coastal Ocean Observing System

http://www.sccoos.org/

(Brings together coastal observations in the Southern California Bight to provide information necessary to address issues in climate change, ecosystem preservation and management, coastal water quality, maritime operations, coastal hazards and national security. One of the 11 IOOS regions.)

• THREDDS (Thematic Realtime Environmental Distributed Data Services)

http://www.unidata.ucar.edu/projects/THREDDS

(Services for delivering standards-based geospatial data via OpenDAP,

WCS and more, works with NcML)

• ROMS: Regional Ocean Modeling System

www.myroms.org

(A free-surface, terrain-following, primitive equations ocean model widely used by the scientific community for a diverse range of applications)

• SCCOOS: Southern California Coastal Ocean Observing System

http://www.sccoos.org/

(Brings together coastal observations in the Southern California Bight to provide information necessary to address issues in climate change, ecosystem preservation and management, coastal water quality, maritime operations, coastal hazards and national security. One of the 11 IOOS regions.)

• THREDDS (Thematic Realtime Environmental Distributed Data Services)

http://www.unidata.ucar.edu/projects/THREDDS

(Services for delivering standards-based geospatial data via OpenDAP,

WCS and more, works with NcML)

Glossary (6/6)Glossary (6/6)

• WCS: Web Coverage Servicehttp://www.opengeospatial.org/standards/wcs(OGC standard for serving gridded information: time series, profiles,hyperslabs of remote sensing data, bathymetry, model output)

• WW3: WaveWatch III

http://polar.ncep.noaa.gov/waves/wavewatch/wavewatch.html

(Ocean wave model developed by Hendrik Tolman)• WRF: Weather Research and Forecasting Model

http://www.wrf-model.org/index.php

(Next-generation mesocale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs)

• WCS: Web Coverage Servicehttp://www.opengeospatial.org/standards/wcs(OGC standard for serving gridded information: time series, profiles,hyperslabs of remote sensing data, bathymetry, model output)

• WW3: WaveWatch III

http://polar.ncep.noaa.gov/waves/wavewatch/wavewatch.html

(Ocean wave model developed by Hendrik Tolman)• WRF: Weather Research and Forecasting Model

http://www.wrf-model.org/index.php

(Next-generation mesocale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs)