Custom Query – src

Description

The following update corrects a parallel bug in the HF radial observation operator, corrects CPP options typo in distribute.F, and adds the variables needed to compute Desroziers et al. (2005) statistics for a 4D-Var analysis.

The routine obs_write.F is corrected to remove a parallel bug in the processing of HF radial observations. The fractional coordinate tile range argument passed to extract_obs3d was increased by value of 0.5. It is completely incorrect and caused a parallel bug that yielded an observation screening value of obs_scale=2.0 because the datum is accounted in two different tiles:

          CALL extract_obs3d (ng, 1, Lm(ng)+1, 0, Mm(ng)+1,             &
     &                        LBi, UBi, LBj, UBj, 1, N(ng),             &
     &                        ObsState2Type(isRadial),                  &
     &                        Mobs, Mstr, Mend,                         &
     &                        uXmin(ng)+0.5_r8, uXmax(ng)+0.5_r8,       &
     &                        uYmin(ng), uYmax(ng),                     &
     &                        time(ng), dt(ng),                         &
     &                        ObsType,  ObsVetting,                     &
     &                        Tobs, Xobs+0.5_r8, Yobs, Zobs,            &
     &                        OCEAN(ng)%u(:,:,:,NOUT),                  &
     &                        GRID(ng)%z_v,                             &
#   ifdef MASKING
     &                        GRID(ng)%umask,                           &
#   endif
     &                        uradial)

          CALL extract_obs3d (ng, 0, Lm(ng)+1, 1, Mm(ng)+1,             &
     &                        LBi, UBi, LBj, UBj, 1, N(ng),             &
     &                        ObsState2Type(isRadial),                  &
     &                        Mobs, Mstr, Mend,                         &
     &                        vXmin(ng), vXmax(ng),                     &
     &                        vYmin(ng)+0.5_r8, vYmax(ng)+0.5_r8,       &
     &                        time(ng), dt(ng),                         &
     &                        ObsType, ObsVetting,                      &
     &                        Tobs, Xobs, Yobs+0.5_r8, Zobs,            &
     &                        OCEAN(ng)%v(:,:,:,NOUT),                  &
     &                        GRID(ng)%z_v,                             &
#   ifdef MASKING
     &                        GRID(ng)%vmask,                           &
#   endif
     &                        vradial)

The values for uXmin, uXmax, and Xobs where wrong when computing uradial. Similarly, the values of vYmin, vYmax, and Yobs were wrong when computing vradial. There is a confusion of staggered grid location here. We need to have instead:

          CALL extract_obs3d (ng, 1, Lm(ng)+1, 0, Mm(ng)+1,             &
     &                        LBi, UBi, LBj, UBj, 1, N(ng),             &
     &                        ObsState2Type(isRadial),                  &
     &                        Mobs, Mstr, Mend,                         &
     &                        uXmin(ng), uXmax(ng),                     &
     &                        uYmin(ng), uYmax(ng),                     &
     &                        time(ng), dt(ng),                         &
     &                        ObsType,  ObsVetting,                     &
     &                        Tobs, Xobs, Yobs, Zobs,                   &
     &                        OCEAN(ng)%u(:,:,:,NOUT),                  &
     &                        GRID(ng)%z_v,                             &
#   ifdef MASKING
     &                        GRID(ng)%umask,                           &
#   endif
     &                        uradial)

          CALL extract_obs3d (ng, 0, Lm(ng)+1, 1, Mm(ng)+1,             &
     &                        LBi, UBi, LBj, UBj, 1, N(ng),             &
     &                        ObsState2Type(isRadial),                  &
     &                        Mobs, Mstr, Mend,                         &
     &                        vXmin(ng), vXmax(ng),                     &
     &                        vYmin(ng), vYmax(ng),                     &
     &                        time(ng), dt(ng),                         &
     &                        ObsType, ObsVetting,                      &
     &                        Tobs, Xobs, Yobs, Zobs,                   &
     &                        OCEAN(ng)%v(:,:,:,NOUT),                  &
     &                        GRID(ng)%z_v,                             &
#   ifdef MASKING
     &                        GRID(ng)%vmask,                           &
#   endif
     &                        vradial)

The bug caused that such observation lying on the tile edge have the observation error covariance increased by a factor of two, which affected the observation impact and sensitivity computations.

Similar corrections are done to adjoint observation operator routines ad_htobs.F and ad_misfit.F.

Many thanks to Julia Levin for reporting issues about the assimilation of HF radials and Andy Moore for his help in tracking the problem.

The module distribute.F was corrected because CPP option BOUNDARY_ALLGAHTER was miss-spelled. We need to use BOUNDARY_ALLGATHER instead. The spelling did not affect the solution because the alternated methodology was used for the collective MPI communications of input lateral boundary conditions.

Many thanks to Frank Colberg for reporting this bug.

The output ROMS 4D-Var NetCDF file (MODname) was enhanced to include the variables necessary to compute the Desroziers et al. (2005) statistics. It now includes innovation (observation minus background), increment (analysis minus background), and residual (observation minus analysis), which are used to evaluate the error covariance hypothesis of the 4D-Var analysis. The NetCDF file has the following new variables:

       double innovation(datum) ;
               innovation:long_name = "4D-Var innovation: observation minus background, d_b = y - H(x_b)" ;
               innovation:units = "state variable units" ;
               innovation:_FillValue = 1.e+37 ;
       double increment(datum) ;
               increment:long_name = "4D-Var increment: analysis minus background, dx_a = H(x_a) - H(x_b)" ;
               increment:units = "state variable units" ;
               increment:_FillValue = 1.e+37 ;
       double residual(datum) ;
               residual:long_name = "4D-Var residual: observation minus analysis, d_a = y - H(x_b + dx_a)" ;
               residual:units = "state variable units" ;
               residual:_FillValue = 1.e+37 ;

The module mod_fourdvar.F and mod_ncparam.F were modified to include the new variables.

Many thanks to John Wilkin for suggesting the new variables. We can use third-party analysis software like NOAA's ERDDAP to browse and plot these critical variables and statistics.

Desroziers, G, L. Berre, B. Chapnik, and P. Poli, 2005: Diagnosis of observation, background and analysis-error statistics in observation space, Q. J. R. Meteorol. Soc., 131, 3385-3395, doi: 10.1256/qj.05.108.

Also, the output variable BgError_value is processed and written into MODname even if BGQC is not activated:

       double BgError_value(datum) ;
               BgError_value:long_name = "Background error standard deviation at observation locations" ;
               BgError_value:units = "state variable units" ;
               BgError_value:_FillValue = 1.e+37 ;

Warning: the metadata for some of the MODname output NetCDF variables were updated for clarity in ROMS's varinfo.dat.

Description

This update corrects a CPP logic in obs_write.F and typos in the *_inp.h for the biologial and sediment models.

obs_write.F: in src:ticket:833 several changes were made to include the fields necessary to compute the Desroziers et al. (2005) statistics for the 4D-Var analysis. This logic is still available when the nonlinear model VERIFICATION is activated. Therefore, we need to avoid such computations because of only made sense in a 4D-Var application. Many thanks to Ann Kristin Sperrevik for bringing this problem to my attention.

Corrected the assignment of nl_tnu4 in sediment_inp.h. Many thanks to Catherine Drinkorn reporting this typo.

Similarly, tl_tnu4 was unassigned in all the biological models *_inp.h

Description

If you run the standard upwelling case with NTIMES = 18, NAVG = 9, NDEFAVG = 9, it blows up:

Image              PC                Routine            Line        Source             
oceanG             00000000021D3096  Unknown               Unknown  Unknown
oceanG             000000000092C915  output_                   283  output.f90
oceanG             0000000000813DF1  main3d_                   231  main3d.f90

the line in question is:

283             AVG(ng)%Nrec(Fcount)=0

The test above:

278             IF (iic(ng).eq.ntstart(ng)) THEN

is never true, so AVG(ng)%load starts at 1, goes to 2, then 3. When Fcount is 3, it goes out of bounds with AVG(ng)%Nrec is dimensioned size 2.

It was working before: src:ticket:825, trunk@982

Ticket	Owner	Reporter	Resolution	Summary
#833		arango	Fixed	VERY IMPORTANT: Corrected HF radials 4D-Var Operator
Description	The following update corrects a parallel bug in the HF radial observation operator, corrects CPP options typo in distribute.F, and adds the variables needed to compute Desroziers et al. (2005) statistics for a 4D-Var analysis. The routine obs_write.F is corrected to remove a parallel bug in the processing of HF radial observations. The fractional coordinate tile range argument passed to extract_obs3d was increased by value of 0.5. It is completely incorrect and caused a parallel bug that yielded an observation screening value of obs_scale=2.0 because the datum is accounted in two different tiles: CALL extract_obs3d (ng, 1, Lm(ng)+1, 0, Mm(ng)+1, & & LBi, UBi, LBj, UBj, 1, N(ng), & & ObsState2Type(isRadial), & & Mobs, Mstr, Mend, & & uXmin(ng)+0.5_r8, uXmax(ng)+0.5_r8, & & uYmin(ng), uYmax(ng), & & time(ng), dt(ng), & & ObsType, ObsVetting, & & Tobs, Xobs+0.5_r8, Yobs, Zobs, & & OCEAN(ng)%u(:,:,:,NOUT), & & GRID(ng)%z_v, & # ifdef MASKING & GRID(ng)%umask, & # endif & uradial) CALL extract_obs3d (ng, 0, Lm(ng)+1, 1, Mm(ng)+1, & & LBi, UBi, LBj, UBj, 1, N(ng), & & ObsState2Type(isRadial), & & Mobs, Mstr, Mend, & & vXmin(ng), vXmax(ng), & & vYmin(ng)+0.5_r8, vYmax(ng)+0.5_r8, & & time(ng), dt(ng), & & ObsType, ObsVetting, & & Tobs, Xobs, Yobs+0.5_r8, Zobs, & & OCEAN(ng)%v(:,:,:,NOUT), & & GRID(ng)%z_v, & # ifdef MASKING & GRID(ng)%vmask, & # endif & vradial) The values for uXmin, uXmax, and Xobs where wrong when computing uradial. Similarly, the values of vYmin, vYmax, and Yobs were wrong when computing vradial. There is a confusion of staggered grid location here. We need to have instead: CALL extract_obs3d (ng, 1, Lm(ng)+1, 0, Mm(ng)+1, & & LBi, UBi, LBj, UBj, 1, N(ng), & & ObsState2Type(isRadial), & & Mobs, Mstr, Mend, & & uXmin(ng), uXmax(ng), & & uYmin(ng), uYmax(ng), & & time(ng), dt(ng), & & ObsType, ObsVetting, & & Tobs, Xobs, Yobs, Zobs, & & OCEAN(ng)%u(:,:,:,NOUT), & & GRID(ng)%z_v, & # ifdef MASKING & GRID(ng)%umask, & # endif & uradial) CALL extract_obs3d (ng, 0, Lm(ng)+1, 1, Mm(ng)+1, & & LBi, UBi, LBj, UBj, 1, N(ng), & & ObsState2Type(isRadial), & & Mobs, Mstr, Mend, & & vXmin(ng), vXmax(ng), & & vYmin(ng), vYmax(ng), & & time(ng), dt(ng), & & ObsType, ObsVetting, & & Tobs, Xobs, Yobs, Zobs, & & OCEAN(ng)%v(:,:,:,NOUT), & & GRID(ng)%z_v, & # ifdef MASKING & GRID(ng)%vmask, & # endif & vradial) The bug caused that such observation lying on the tile edge have the observation error covariance increased by a factor of two, which affected the observation impact and sensitivity computations. Similar corrections are done to adjoint observation operator routines ad_htobs.F and ad_misfit.F. Many thanks to Julia Levin for reporting issues about the assimilation of HF radials and Andy Moore for his help in tracking the problem. The module distribute.F was corrected because CPP option BOUNDARY_ALLGAHTER was miss-spelled. We need to use BOUNDARY_ALLGATHER instead. The spelling did not affect the solution because the alternated methodology was used for the collective MPI communications of input lateral boundary conditions. Many thanks to Frank Colberg for reporting this bug. The output ROMS 4D-Var NetCDF file (MODname) was enhanced to include the variables necessary to compute the Desroziers et al. (2005) statistics. It now includes innovation (observation minus background), increment (analysis minus background), and residual (observation minus analysis), which are used to evaluate the error covariance hypothesis of the 4D-Var analysis. The NetCDF file has the following new variables: double innovation(datum) ; innovation:long_name = "4D-Var innovation: observation minus background, d_b = y - H(x_b)" ; innovation:units = "state variable units" ; innovation:_FillValue = 1.e+37 ; double increment(datum) ; increment:long_name = "4D-Var increment: analysis minus background, dx_a = H(x_a) - H(x_b)" ; increment:units = "state variable units" ; increment:_FillValue = 1.e+37 ; double residual(datum) ; residual:long_name = "4D-Var residual: observation minus analysis, d_a = y - H(x_b + dx_a)" ; residual:units = "state variable units" ; residual:_FillValue = 1.e+37 ; The module mod_fourdvar.F and mod_ncparam.F were modified to include the new variables. Many thanks to John Wilkin for suggesting the new variables. We can use third-party analysis software like NOAA's ERDDAP to browse and plot these critical variables and statistics. Desroziers, G, L. Berre, B. Chapnik, and P. Poli, 2005: Diagnosis of observation, background and analysis-error statistics in observation space, Q. J. R. Meteorol. Soc., 131, 3385-3395, doi: 10.1256/qj.05.108. Also, the output variable BgError_value is processed and written into MODname even if BGQC is not activated: double BgError_value(datum) ; BgError_value:long_name = "Background error standard deviation at observation locations" ; BgError_value:units = "state variable units" ; BgError_value:_FillValue = 1.e+37 ; Warning: the metadata for some of the MODname output NetCDF variables were updated for clarity in ROMS's varinfo.dat.
#834		arango	Fixed	IMPORTANT: Corrected obs_write.F and other files.
Description	This update corrects a CPP logic in obs_write.F and typos in the _inp.h for the biologial and sediment models. obs_write.F: in src:ticket:833 several changes were made to include the fields necessary to compute the Desroziers et al. (2005) statistics for the 4D-Var analysis. This logic is still available when the nonlinear model VERIFICATION* is activated. Therefore, we need to avoid such computations because of only made sense in a 4D-Var application. Many thanks to Ann Kristin Sperrevik for bringing this problem to my attention. Corrected the assignment of nl_tnu4 in sediment_inp.h. Many thanks to Catherine Drinkorn reporting this typo. Similarly, tl_tnu4 was unassigned in all the biological models *_inp.h
#835		kate	Fixed	Trouble in time-averaged output NetCDF files
Description	If you run the standard upwelling case with NTIMES = 18, NAVG = 9, NDEFAVG = 9, it blows up: Image PC Routine Line Source oceanG 00000000021D3096 Unknown Unknown Unknown oceanG 000000000092C915 output_ 283 output.f90 oceanG 0000000000813DF1 main3d_ 231 main3d.f90 the line in question is: 283 AVG(ng)%Nrec(Fcount)=0 The test above: 278 IF (iic(ng).eq.ntstart(ng)) THEN is never true, so AVG(ng)%load starts at 1, goes to 2, then 3. When Fcount is 3, it goes out of bounds with AVG(ng)%Nrec is dimensioned size 2. It was working before: src:ticket:825, trunk@982

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