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Dave, This is indeed a very strange problem., and appears not to be a FMRC issue per se, but a netCDF-Java problem reading NetCDF4. If you download one of the unaggregated NetCDF4 files that you are trying to aggregate: http://tds.marine.rutgers.edu:8080/thredds/fileServer/espresso/2013_da/files/his/espresso_his_20130913_0000_0007.nc and try to open it in NetCDF-Java ToolsUI, you can see that the variable "h" is missing. But if you do "ncdump -h" you can see that the variable "h" is in fact there. And if you convert the NetCDF4 file to NetCDF3 nccopy -k 1 espresso_his_20130913_0000_0007.nc espresso_nc3.nc and then open "espresso_nc3.nc" with NetCDF-Java, the variable "h" reappears. Very strange. I tried NetCDF-java from 4.3.18 back to 4.3.12 and they all had the same behavior. -Rich On Mon, Sep 16, 2013 at 2:26 PM, David Robertson <robertson@xxxxxxxxxxxxxxxxxx> wrote: > Hi, > > I have discovered what I believe is a very curious bug in the FMRC. We have > a ROMS ocean model including 4D variational data assimilation (4D-Var) that > we are serving both averages and history output for. There are no issues > with the averages files but history files trigger a strange bug in which the > "bathymetry at RHO-points" variable (named h) is removed by the FMRC. > > As part of the 4D-Var system, additional variables are written to the > history files and 4 of them seem to be triggering this bug: > > float DU_avg1(ocean_time, eta_u, xi_u) ; > DU_avg1:long_name = "time averaged u-flux for 2D equations" > ; > DU_avg1:units = "meter3 second-1" ; > DU_avg1:time = "ocean_time" ; > DU_avg1:coordinates = "lon_u lat_u ocean_time" ; > DU_avg1:field = "DU_avg1, scalar, series" ; > DU_avg1:_FillValue = 1.e+37f ; > float DU_avg2(ocean_time, eta_u, xi_u) ; > DU_avg2:long_name = "time averaged u-flux for 3D equations > coupling" ; > DU_avg2:units = "meter3 second-1" ; > DU_avg2:time = "ocean_time" ; > DU_avg2:coordinates = "lon_u lat_u ocean_time" ; > DU_avg2:field = "DU_avg2, scalar, series" ; > DU_avg2:_FillValue = 1.e+37f ; > float DV_avg1(ocean_time, eta_v, xi_v) ; > DV_avg1:long_name = "time averaged v-flux for 2D equations" > ; > DV_avg1:units = "meter3 second-1" ; > DV_avg1:time = "ocean_time" ; > DV_avg1:coordinates = "lon_v lat_v ocean_time" ; > DV_avg1:field = "DV_avg1, scalar, series" ; > DV_avg1:_FillValue = 1.e+37f ; > float DV_avg2(ocean_time, eta_v, xi_v) ; > DV_avg2:long_name = "time averaged v-flux for 3D equations > coupling" ; > DV_avg2:units = "meter3 second-1" ; > DV_avg2:time = "ocean_time" ; > DV_avg2:coordinates = "lon_v lat_v ocean_time" ; > DV_avg2:field = "DV_avg2, scalar, series" ; > DV_avg2:_FillValue = 1.e+37f ; > > > I don't know if it's significant but the long_name attribute does contain > "time averaged". If I remove these variables with ncks, "h" magically > reappears in the FMRC. I tried removing with ncml but while it did remove > the variables it did not bring back "h". I believe this is because the ncml > is applied after at least part of the FMRC processing so "h" has already > been discarded. > > Cheers, > David Robertson > > _______________________________________________ > thredds mailing list > thredds@xxxxxxxxxxxxxxxx > For list information or to unsubscribe, visit: > http://www.unidata.ucar.edu/mailing_lists/ -- Dr. Richard P. Signell (508) 457-2229 USGS, 384 Woods Hole Rd. Woods Hole, MA 02543-1598
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