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EC-Earth / ece2cmor3

Post-processing and cmorization of ec-earth output
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The toce_pot fields in the file_def files lead to run errors when tested with EC-Earth #226

Closed treerink closed 5 years ago

treerink commented 5 years ago

The toce_pot fields in the file_def files which are generated by drq2file_def-nemo.py lead to run errors when tested with EC-Earth.

treerink commented 5 years ago

The error for toce_pot (cmor name theteo) is: Numeric conversion not representable

On writing field data: thetao
 In the context : nemo_server
 Error when calling function ncPutVaraType(ncid, varId, start, count, data)
 NetCDF: Numeric conversion not representable
 Unable to write data given the location id: 917504 and the variable whose id: 9 and name: thetao
treerink commented 5 years ago

Remarkable is that if we add this line for thetao which is present in the new generated file_def_nemo-opa.xml in the default file_def_nemo-opa.xml in the ctrl directory, it works.

treerink commented 5 years ago

For a fast test case this piece for daily output can be added in one of the file_def_nemo-opa.xml file:


    <file id="file40" name_suffix="_opa_grid_T_3D" output_freq="1d">

     <field enabled="False" field_ref="e3t" grid_ref="grid_T_3D" id="id_1d_thkcello" name="thkcello">                                                                        </field>
     <field enabled="True" field_ref="toce_pot" grid_ref="grid_T_3D" id="id_1d_thetao" name="thetao">                                                      </field>
     <field enabled="True" field_ref="toce" grid_ref="grid_T_3D" id="id_1d_bigthetao" name="bigthetao">     toce_e3t / e3t                                                     </field>

    </file>
treerink commented 5 years ago

Testing at the SMHI machine showed that if we move a zero initialization line one line down below a line which overwrites it, we are able to output toce_pot. The result will be that the bottom level of toce_pot is filled with zeros (might be not intended?).

It concerns the Shaconemo MY_SRC file (see line 224): sources/nemo-3.6/CONFIG/ORCA1L75_LIM3/MY_SRC/diaar5.F90 If

      IF( nn_eos == -1 ) THEN        ! ! potential temperature (TEOS-10 case)
         ztpot(:,:,jpk) = 0._wp
         ztpot(:,:,:)   = eos_pt_from_ct( tsn(:,:,:,jp_tem), tsn(:,:,:,jp_sal) )
         !
         CALL iom_put( "toce_pot", ztpot(:,:,:) )  ! potential temperature (TEOS-10 case)

is replace by

      IF( nn_eos == -1 ) THEN        ! ! potential temperature (TEOS-10 case)
         ztpot(:,:,:)   = eos_pt_from_ct( tsn(:,:,:,jp_tem), tsn(:,:,:,jp_sal) )
         ztpot(:,:,jpk) = 0._wp
         !
         CALL iom_put( "toce_pot", ztpot(:,:,:) )  ! potential temperature (TEOS-10 case)

So it is just about the line:

         ztpot(:,:,jpk) = 0._wp

I will test it next week also at our HPC at KNMI, also for the other toce_pot related variables which give problems in other data requests.

I will post an Shaconemo issue to get feedback on how this bottom layer should look like (indeed zeros) and if this is a BUG to be fixed.

treerink commented 5 years ago

With the proposed change in diaar5.F90 (see previous post) also at the KNMI HPC the problem with toce_pot is solved, i.e. the run continues and the the fields have values for all layers except the bottom layer gives of course zeros now.

Moreover, a 2 year run with all opa and lim variables switched on (except the transect related ones, see issue 518-31 on the EC-Earth portal) finished successfully. This means the similar problems for toce_pot_mean* are also gone.

treerink commented 5 years ago

I created a Shaconemo ticket concerning this issue (ticket 81).

treerink commented 5 years ago

@klauswyser citing your mail in the "check NaN" mail conversation:

Do I get correctly that the bottom NEMO layer doesn't matter? In that case we can close this issue.

klauswyser commented 5 years ago

My interpretation is that the lowest layer is never used by NEMO and no meaningful values are assigned to it. However, it would be good if somebody from the OceanWG could confirm this.

treerink commented 5 years ago

I asked Andreas here, and in the NEMO_book_3.6_STABLE.pdf (version January 2016) in Fig 4.3 it looks like the lowest level is part of the bottom and not of the ocean.

treerink commented 5 years ago

Correction Fig. 4.3 at page 53: NEMO Ocean engine Gurvan Madec, and the NEMO team ISSN No 1288-1619

Here NEMO_book_3.6_STABLE.pdf at page 55.

goord commented 5 years ago

@treerink I suggest we move this issue to the EC-Earth portal.

treerink commented 5 years ago

At the ec-earth portal issue 518-33 and 518-35 this issue is shortly addressed. But it misses some of the points here, so it needs to add a new specific issue then.

treerink commented 5 years ago

As this is not longer on ece2cmor3 issue I posted it at the ec-earth portal as issue 635.

Closing the issue here.