A Super-Regional Modeling Testbed for Improving Forecasts of Environmental Processes for the U.S. Atlantic and Gulf of Mexico Coasts Cyberinfrastructure Status Update March 29, 2011

Testbed web site SOS Server SOS Parser SLOSH Update F-TDS Update Unstructured Grid IMEDS CHPS Matlab Toolbox Status Update : March 29, 2011

Super-Regional Testbed Collaboration Site Group-specific information Project-wide access to data tools Access control for project security Public Information Reports, Documents for Management Review Create documents, meetings, etc One-stop for all Testbed Information and Functionality Ready for integration/hosting of modeling tools Project management tools

Addition of SOS service capabilities to THREDDS server –Get capabilities –Describe sensor –Get observation Payload Service Offerings Catalog services Data Server THREDDSSOSgetCapabilitiesXMLdescribeSensorXMLgetObservationXMLISOWCSWMS TDS Java SOS Service Single and Multi-station Netcdf datafiles: –EPA Netcdf datafiles –NOAA NDBC Station Netcdf datafiles XML payload designed to be compatible with existing SOS Parsers

Javascript SOS Client Parser IOOS DIF and SWE support Cross browser support via jQuery.js GetCapabilities and GetObservation parsing HTML, CSV and JSON string outputs Aimed to work with TDS Java SOS plug-in for time series point observations.

NDBC 12 hours Wave Height from buoy 44007

SLOSH Output Conversion: Status Update Justin R. Davis University of Florida March 29, 2011

Plan Phase I –Work with Dr. Slinn and get his output converted Phase II –Work with NHC and get native SLOSH output converted Note: With the exception of 1 Tecplot figure, all pictures are screen captures taken of graphics “generated” by the SURA Testbed Sever.

Phase I –Dr. Slinn’s Output Format ASCII Text Initial (x,y,t,value) Current (timestamp relative to NAP then spatial data) Approach –F90 Conversion Program »Researcher familiarity with Fortran –Converts to time series output (IMEDS/NetCDF/Tecplot) –Converts to spatial output (NetCDF/Tecplot) –Reads time series output from command line or file »Currently using list of 238 stations compiled by UND »Only use if within 5 km (variable) of grid cell center

Time series CDL (v3-9) CF 1.3 Compliant

NetCDF-Java Tools UI (webstart)

Time Series Output Comparisons (Tecplot)

Spatial CDL (v3-9) CF 1-3 and CDM Compliant

Spatial Output Plots (Godiva2) OWI Wind OWI Wind + Wave OWI Wind + Wave + MF Wind Wind + Garrat Drag

Phase I –Remaining Issues Vertical datum not specified U, V rotation unclear Timestamp output is hardwired

Phase II –Native SLOSH Output Format Rex File Binary with Gif-like compression Contains necessary data/equation (wind) Lots of existing rex file data Approach –Using C Conversion Program –Based on existing time series extraction tool (rexout) –Converts to time series output (NetCDF) »Same CDL as previously developed –Implementing new NetCDF code into 3 files »Header »Time Series »Sparial –Implement as Style 4 –Current version: rexout-1-3-jrd-v1-2

Phase II –Tests Built test cases based on existing rexout cases –andrw.lft –audry.bpt –camil.bix –frederic.emo At the request of Jesse Feyen, compare NHC Ike result with Dr. Slinn’s –Get 80 xy observation stations (Arthur Taylor) –Run rexout at these stations –…

2008Ike_gl2.rex => 2008Ike_gl2.nc

Phase II –Remaining Issues Need to address spatial output Vertical datum not specified –rexout reads several files in addition to data file but none have datum, need to read another file. Needs additional metadata –Version number –Build/run dates Needs appropriate calling hooks in program Needs “SLOSH-approved” style (e.g. GNU ident) Must be compiled in 32-bit –Status at NHC Calls/ s with Arthur Taylor (developer of rex file) at NHC NHC has new code and is integrating –Develops in Windows (MinGW – Minimalist GNU for Windows) –Must build NetCDF/HDF from scratch (HDF binaries are not public domain - SZIP) (done) –Code setup for time series, needs some re-organization to handle spatial output) UF

Next Steps Get rexout to handle spatial output Iterate with NHC regarding source integration Facilitate comparisons between Dr. Slinn’s results and NHC Results Investigate other SLOSH domains –Sabine Pass –Extra-tropical Domain

The OPeNDAP Story Local access to remote data... Clients which use well-known API’s like netCDF are re-linked with the OPeNDAP client library Data providers install OPeNDAP server software (several are available) and data files Clients can access remote data via the API as if the data files were local 23

Server-side Analysis In general server-side analysis is a computation made by an OPeNDAP server at the request of a client. The specification of the computation is transmitted to the server via the OPeNDAP URL. The data returned are the results (and only the results) of the computation 24

F-TDS The Ferret-THREDDS Data Server (F- TDS) is an implementation of a general purpose server-side analysis engine which plugs into new or existing TDS installations. Where TDS is an OPeNDAP server implemented in Java and available from Unidata. 25

F-TDS Capabilities F-TDS takes advantage of several characteristics of Ferret. New "virtual" data variables can be defined Can build the metadata (netCDF header described by dimensions, coordinate variables and the structure of data variables) without performing any heavy calculations for both data read from files and “virtual” data variables Only performs calculations when the data are requested Only calculates the minimal set needed to fulfil the current request 26

ChesROMS: a practical example We are serving data from Chesapeake Bay ROMS Community model We’d like images of the water velocity model output. Water velocity is produced in the model as separate eastward and northward velocities on the U and V elements of a single Arakawa computational grid. Need to combine the eastward and northward components to produce velocity. But to do this, the values need to be on the same grid. We do this with an F/TDS script. This produces an OpenDAP accessible URL, which can be operated on in standard tools such as Matlab. The eastward and northward values are translated to a common “rho” grid. 27

ChessROMS Eastward and Northward ComputationalGrids 28 Full view and detail of grid: eastward grid in red, northward grid in green. These are the original computation points on which the model outputs data.

The ChessROMS grids including the “RHO” grid 29 Black diamonds are “Rho” grid points. Eastward points in red, northward points in green. Eastward and northward velocity model output have been translated to the RHO grid by the F/TDS script.

Matlab code to plot the velocity # Get the data from the F/TDS URL url=' hesroms/vectors.nc'; nc=mDataset(url); getVars(nc) # grab the rotated u,v and grid points. The grid # is the same for both UBARROT and VBARROT u=nc{'UBARROT'}(1,:,:); v=nc{'VBARROT'}(1,:,:); g=nc{'VBARROT'}(1,:,:).grid # Convert u and v to a complex for graphing U=complex(u,v); # plot the data figure pcolorjw(g.lon,g.lat,double(abs(U))); arrows(g.lon,g.lat,U,.05,'black'); axeq colorbar 30

The ChesROMS Water Velocity 31 ChessROMS Absolute Water Velocity in Meters/second ChessROMS Absolute Water Velocity in Meters/second detail with directional vectors

Plotting ChesROMS Water Temperature ChesROMS temperature grid seems to overlap itself and is very difficult to plot. There is a mask variable in the data set: we use F/TDS to apply the mask to the temperature data and produce a plotable data set. We can not yet plot this in WMS and we don’t know why, but the Ferret itself has a plotting engine and the data looks reasonable plotted. 32

ChesROMS Water Temperature plotted in Ferret 33 ChessROMS variable temp from dodsC/estuarine_hypoxia/cbofs2/agg- masked.nc ChessROMS variable temp_masked from odsC/estuarine_hypoxia/cbofs2/agg- masked.nc

IMEDS Target Diagrams Target Diagrams for error parameters Currently developing target diagram format Ease of integration to current IMEDS version

Unstructured Grid Support

CHPS

MATLAB Interoperability Tools Steps and Status Merging njtbx functionality with nctoolbox’s (Brian Schlining) codebase ( Creating methods for SURA Testbed use case (timeseries extraction, geographic bounding boxes, search api, unstructured grid support, comparisons/assessment…) Merging changes with nctoolbox open source development on Google Code ( Testing current state of the toolbox and distributing to others for feedback (hopefully friendly!) Whats Next? Refactor/other changes based on feedback Fill out discrete sampling geometry methods Fill out unstructured grid methods More testing with lots of datasets Leverage with java desktop client front end???