Deep time SOM run.

[Riley]

I get numerous questions about the new SOM in the data ocean model of CESM. So, I thought it appropriate to add a sort of FAQ here.

1. Why does the SOM mode no longer run out of the box?

Earlier versions were set up with a test SOM forcing file (pop_frc.1x1d.090130.nc) This forcing file was not intended for science purposes and should not be used except in testing. Hence we made the decision to remove a default SOM forcing file from CESM1.1 and onward.

2. How do I set the SOM forcing file?

As long as the forcing file you wish to use is in the standard input directory, i.e. $DIN_LOC_ROOT/ocn/docn7/SOM, then as of CESM 1.1., one simply modifies DOCN_SOM_FILENAME in env_run.xml. The default value of this variable is UNSET. In older versions of the code, this had to be modified in the docn.buildnml.csh script or the docn.stream.txt file.

3. What if my SOM forcing file is in a different directory?

Here you will need to modify the docn.streams.txt file to manually point to the directory you wish. As of CESM 1.1, you can copy $CASEROOT/CaseDocs/docn.streams.txt to $CASEROOT/user_docn.streams.txt and edit it.

*Note this has changed slightly for CESM2*

Here you will need to modify the docn.streams.txt.som file to manually point to the directory you wish. As of CESM 1.1, you can copy $CASEROOT/CaseDocs/docn.streams.txt.som to $CASEROOT/user_docn.streams.txt.som and edit it.

4. Do you have some scientifically valid SOM forcing files available?

Yes! These are in the input data repository at:

https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/ocn/docn7/SOM/

For the most part, they are documented as to the run they came from by doing an 'ncdump -h' on the file.

5. Can I create my own SOM forcing file?

Yes! The tools for this are available from the release code repository at:

https://svn-ccsm-release.cgd.ucar.edu/model_versions/cesm1_1_1/models/ocn/docn/tools/pop_som_frc/

We are striving to keep these up to date, but there may still be issues with them. There is a simple README file here with a description of the tools.

6. Can I run the old CAM3 SOM method with gensom?

The short answer is no. This mode is no longer supported in CESM. If you wish to use this technique to generate SOM forcing, we cannot help you.

7. Why can't I run the old CAM3 SOM?

We believe that it is scientifically better to use the new SOM method. We recommend reading the following paper that discusses the old SOM versus the new SOM at:

Bitz et al. 2012, J. Climate, Climate Sensitivity of the Community Climate System Model, Version 4 | Journal of Climate | American Meteorological Society

Also, there is a white paper on the subject under the CESM DOCN user's guide at:

http://www.cesm.ucar.edu/models/cesm1.1/data8/doc/x362.html

8. What compsets is the DOCN-SOM used in?

The E compset with fully active atmosphere, land, and sea ice components uses the DOCN-SOM component as does the active ice only compset (D).

9. Why do I have to run fully active ice with the SOM?

This is more of a scientific question, but we have found that when computing the sea surface temperature (SST) prognostically as is done in the DOCN-SOM, it is better to use fully active ice with it. One could potentially turn on thermodynamic-only ice by turning off the sea ice dynamics (kdyn = 0), but we do not routinely run that way. Much work has been done over the years stressing the importance of the sea ice dynamics. We do not support prescribed ice mode with the DOCN-SOM. When specifying the sea ice fraction, one must also use specified SST (in an F compset).

10. These did not answer my question:

If you have issues with parts of this, or further questions, you can post something to this forum and we will attempt to address it as soon as possible.

Hi Dave, I would like to run E1850CN (f09_g16) with deep-time topography. I created my own SOM forcing file by using pop_frc_mlt.ncl. But there is always one same wrong. (The forcing file I used is "pop_frc.gx1v6.ctl.nc")

The error in cesm.log is :

Reading setup_nml
Reading grid_nml
Reading ice_nml
Reading tracer_nml
CalcWorkPerBlock: Total blocks: 480 Ice blocks: 154 IceFree blocks: 276 Land blocks: 50
...
COLDSST: encountered in cldfrc: 344 15 0.700032921436772
1.21151233024990
urban net longwave radiation error: no convergence
clm model is stopping
ENDRUN: called without a message string

And in other logs, the components initialized.

Then, I tried to create forcing file in 1x1d, does it work?
But, I also tested the f09_g1v6 simulation in the modern world with "pop_frc.1x1d.090130.nc" as your first guide shown, I got the same error as above. Then I tested simulation with default file "pop_frc.gx1v6.100513.nc", it worked. But I didn't know make my case success.
Appreciate your help, Riley.

 

[dbailey]

I'm going to move this over to the paleo forum. I think you likely have some land/ocean mask issues going on. All of the default SOM files we have are for present day.

 

[Riley]

Hi Dave. Thanks for your reply. I checked it again, and I could run with default SOM files. But my created SOM files didn't work. It may be my interpolation problems, the interpolation could contribute to the bad and cold SST in ocean (the similar error at url: COLDSST: encountered in cldfrc).
After extracting pop data, I firstly used the code ( pop_frc_mlt.ncl.) in your guidence. Then I interpolated som files to 1x1d by using map_g1v6_to_1x1d_xxxx. The error may be from my process. If I use the code at the last step( pop_frc_mlt.ncl.), the error disapeared. Appreciate your help.

And I have an unprofessional problem, what is the function of "u v currrent" in SOM files, and does it change as the simulation runs?


cheers,
Riley

 

[LisaCickyham]

Hi Dave, I would like to run E1850CN (f09_g16) with deep-time topography. I created my own SOM forcing file by using pop_frc_mlt.ncl. But there is always one same wrong. (The forcing file I used is "pop_frc.gx1v6.ctl.nc")

The error in cesm.log is :

Reading setup_nml
Reading grid_nml
Reading ice_nml
Reading tracer_nml
CalcWorkPerBlock: Total blocks: 480 Ice blocks: 154 IceFree blocks: 276 Land blocks: 50
...
COLDSST: encountered in cldfrc: 344 15 0.700032921436772
1.21151233024990
urban net longwave radiation error: no convergence
clm model is stopping
ENDRUN: called without a message string

And in other logs, the components initialized.

Then, I tried to create forcing file in 1x1d, does it work?
But, I also tested the f09_g1v6 simulation in the modern world with "pop_frc.1x1d.090130.nc" as your first guide shown, I got the same error as above. Then I tested simulation with default file "pop_frc.gx1v6.100513.nc", it worked. But I didn't know make my case success.
Appreciate your help, Riley.

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If you're still facing difficulties, it may be helpful to consult the documentation specific to the model version and configuration you're using. Additionally, reaching out to the support channels or forums dedicated to the model or the specific scientific community working with deep-time topography simulations can provide valuable insights and guidance. I hope these suggestions help you resolve the issue and successfully run your simulation. Good luck, and if you have any further questions, feel free to ask!

 

[macarew]

Hi Dave. Thanks for your reply. I checked it again, and I could run with default SOM files. But my created SOM files didn't work. It may be my interpolation problems, the interpolation could contribute to the bad and cold SST in ocean (the similar error at url: COLDSST: encountered in cldfrc).
After extracting pop data, I firstly used the code ( pop_frc_mlt.ncl.) in your guidence. Then I interpolated som files to 1x1d by using map_g1v6_to_1x1d_xxxx. The error may be from my process. If I use the code at the last step( pop_frc_mlt.ncl.), the error disapeared. Appreciate your help.

And I have an unprofessional problem, what is the function of "u v currrent" in SOM files, and does it change as the simulation runs?


cheers,
Riley

Hello Riley,

Are you still having trouble with your SOM files?

If so, when you ran the script pop_frc_mlt.ncl, how did you modify the files f1 and f3 for your deep-time case?
In my experience, I have modified f1 to a POP monthly climatology from a deep-time simulation with active POP (case using same domain.ocn netCDF file that I plan to use in new SOM simulation). f3 should also be modified to point to that deep-time domain.ocn netCDF file. If one of these files corresponds to a modern case, that may be why you are experiencing errors for your deep-time case.

Sophia