Re: [thredds] Disappearing bathymetry

• To: thredds@xxxxxxxxxxxxxxxx
• Subject: Re: [thredds] Disappearing bathymetry
• From: John Caron <caron@xxxxxxxxxxxxxxxx>
• Date: Wed, 02 Oct 2013 07:00:57 -0600

Hi David:

thanks for reporting

John

On 9/16/2013 12:26 PM, David Robertson 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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• References:
  • [thredds] Disappearing bathymetry
    • From: David Robertson