Re: [thredds] Disappearing bathymetry

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
>
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-- 
Dr. Richard P. Signell   (508) 457-2229
USGS, 384 Woods Hole Rd.
Woods Hole, MA 02543-1598



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