Lab Activity 5:Analyze Data from Gulf of Mexico Model Run• Data from Xu et al. (2011) model (or a very similar model

run) is stored on plumeri:/data/users-tmp/ckharris/MCH2mod/RESULTS/XU_etal_2011_Paper

• Use the tools that Dave and Julia suggest to do the following:– Plot the model grid and model bathymetry.– Plot a time series of wave heights for a site along the 30-m isobath

on the open shelf.– Make an animation for a one-week period that includes the biggest

storm of the year. Animation should include:• One panel that shows depth-averaged current velocities as arrows, and

salinity as color.• A second panel that shows near-bed suspended sediment concentration

as color, and near-bed current velocity as arrows.• Try to make your animation look nice.

Using THREDDS to access the data

• Aggregation with NCML• Interoperability with DODs-enabled ncview, ncdump, nco,

Matlab ncread, Matlab nctoolbox• Catalog http://plumeri.vims.edu:8080/thredds/

catalog.html – Ask Dave to configure a public_html/testdata entry for you

• DODS data URL: http://plumeri.vims.edu:8080/thredds/dodsC/daveAll/XU_etal_2011_Paper.ncml

• Remote access to slices of data through DODs/OpenDAP –aware tools

DODs-aware tools (ncdump, ncview, nco, matlab)

• From Indian:

• From plain Matlab:

1005 [drf@indian ~]$ /export/home/drf/bin/ncks -v ocean_time http://plumeri.vims.edu:8080/thredds/dodsC/daveAll/XU_etal_2011_Paper.ncml |head -30ocean_time: type NC_DOUBLE, 1 dimension, 4 attributes, chunked? no, compressed? no, packed? noocean_time size (RAM) = 731*sizeof(NC_DOUBLE) = 731*8 = 5848 bytesocean_time dimension 0: ocean_time, size = 731 NC_DOUBLE (Coordinate is ocean_time)ocean_time attribute 0: long_name, size = 25 NC_CHAR, value = time since initializationocean_time attribute 1: units, size = 33 NC_CHAR, value = seconds since 1970-01-01 00:00:00ocean_time attribute 2: calendar, size = 9 NC_CHAR, value = gregorianocean_time attribute 3: field, size = 20 NC_CHAR, value = time, scalar, series

ocean_time[0]=725846400 seconds since 1970-01-01 00:00:00ocean_time[1]=725889600 seconds since 1970-01-01 00:00:00…

1006 [drf@indian ~]$ /export/home/drf/bin/ncdump -h http://plumeri.vims.edu:8080/thredds/dodsC/daveAll/XU_etal_2011_Paper.ncmlnetcdf XU_etal_2011_Paper {dimensions:

Nbed = 4 ;Nuser = 25 ;eta_psi = 63 ;

…

>>> uri='http://plumeri.vims.edu:8080/thredds/dodsC/daveAll/XU_etal_2011_Paper.ncml’;>> tvec = ncread(uri,'ocean_time');>> length(tvec)

ans =

731

999 [drf@indian ~]$ /export/home/drf/bin/ncview http://plumeri.vims.edu:8080/thredds/dodsC/daveAll/XU_etal_2011_Paper.ncmlNcview 2.1.2 David W. Pierce 24 Oct 2012

THREDDS on Plumeri:http://plumeri.vims.edu:8080/thredds

THREDDS on Plumeri for Juliahttp://plumeri.vims.edu:8080/thredds/catalog/Julia/catalog.html

Julia’s ncml file

OpenDAP Data URL$ cat /export/home2/moriarty/public_html/testdata/01_aggreg.ncml <netcdf xmlns="http://www.unidata.ucar.edu/namespaces/netcdf/ncml-2.2"> <aggregation dimName="ocean_time" type="joinExisting"> <netcdf location="/data/users-tmp/ckharris/MCH2mod/RESULTS/XU_etal_2011_Paper/mch_his_0001.nc" /> <netcdf location="/data/users-tmp/ckharris/MCH2mod/RESULTS/XU_etal_2011_Paper/mch_his_0002.nc" /> <netcdf location="/data/users-tmp/ckharris/MCH2mod/RESULTS/XU_etal_2011_Paper/mch_his_0003.nc" /> <netcdf location="/data/users-tmp/ckharris/MCH2mod/RESULTS/XU_etal_2011_Paper/mch_his_0004.nc" /> <netcdf location="/data/users-tmp/ckharris/MCH2mod/RESULTS/XU_etal_2011_Paper/mch_his_0005.nc" /> </aggregation></netcdf>

Matlab NCToolboxplumeri:/export/home/drf/2015/PROJECTS/MS698/xuModel.m