1. 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.

2. 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 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 http://plumeri.vims.edu:8080/thredds/dodsC/daveAll/ XU_etal_2011_Paper.ncml Remote access to slices of data through DODs/OpenDAP –aware tools

3. 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_Pap er.ncml |head -30 ocean_time: type NC_DOUBLE, 1 dimension, 4 attributes, chunked? no, compressed? no, packed? no ocean_time size (RAM) = 731*sizeof(NC_DOUBLE) = 731*8 = 5848 bytes ocean_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 initialization ocean_time attribute 1: units, size = 33 NC_CHAR, value = seconds since 1970-01-01 00:00:00 ocean_time attribute 2: calendar, size = 9 NC_CHAR, value = gregorian ocean_time attribute 3: field, size = 20 NC_CHAR, value = time, scalar, series ocean_time[0]=725846400 seconds since 1970-01-01 00:00:00 ocean_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_P aper.ncml netcdf 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.n cml’; >> 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.ncml Ncview 2.1.2 David W. Pierce 24 Oct 2012

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

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

6. Julia’s ncml file

7. OpenDAP Data URL $ cat /export/home2/moriarty/public_html/testdata/01_aggreg.ncml

8. Matlab NCToolbox plumeri:/export/home/drf/2015/PROJECTS/MS698/xuModel.m