How select a special region to run the CLM from the global model in CLM?

[jteymoori]

Hi
I am running the CLM model, but this model is global, and I want to select a special region ( the U.S.) for my case. How can I do it and select just this region from the global model?

 

[oleson]

I would recommend using subset_data which is available in tools/site_and_regional.

 

[jteymoori]

As I said I am working on CLM, and the tools/site_and_regional are in the CTSM not CLM.
in The CLM code, has a direction that includes " tools":
cd / glade/work/jteymoori/code_cesm/my_cesm_code/cime/tools
tools> : configure cprnc load_balancing_tool MakeRedsky.sh mapping Readme.configure statistical_ensemble_test utils ChangeLog_template config doc LICENSE.TXT scripts tools
It does not include site_and_regional

but in the CTSM it has a direction which is including " tools":
cd / glade/work/jteymoori/code_ctsm/CTSM/tools
tools> : contrib mkmapgrids mksurfdata_map ncl_scripts README.filecopies site_and_regional mkmapdata mkprocdata_map modify_input_files README README.testing

In this situation, must I first run the CTSM, select the specific region by site_and_regional, and finally link it to CLM?
If it is true, how do I do it?

 

[jteymoori]

As I said I am working on CLM, and the tools/site_and_regional are in the CTSM not CLM.
in The CLM code, has a direction that includes " tools":
cd / glade/work/jteymoori/code_cesm/my_cesm_code/cime/tools
tools> : configure cprnc load_balancing_tool MakeRedsky.sh mapping Readme.configure statistical_ensemble_test utils ChangeLog_template config doc LICENSE.TXT scripts tools
It does not include site_and_regional

but in the CTSM it has a direction which is including " tools":
cd / glade/work/jteymoori/code_ctsm/CTSM/tools
tools> : contrib mkmapgrids mksurfdata_map ncl_scripts README.filecopies site_and_regional mkmapdata mkprocdata_map modify_input_files README README.testing

In this situation, must I first run the CTSM, select the specific region by site_and_regional, and finally link it to CLM?
If it is true, how do I do it?

 

[slevis]

I understand the confusion between CTSM and CLM. Yes, first run the tool that @oleson recommended to subset the global surface dataset. Then run the CLM with the new surface dataset.

 

[slevis]

I think you may find it useful to seek help in this discussion about regional simulations:

Setting up (high-res sparse) regional-grid CTSM simulations · ESCOMP CTSM · Discussion #1919

Context This started as issue #1773 from which I linked a google doc (now out of date and obsolete) with step-by-step instructions intended initially for a case that @XiulinGao needed to run. To th...

github.com

 

[jteymoori]

Based on the instructions for using CTSM, I tried to make it using these scripts:

cd /glade/work/jteymoori
mkdir cases

git clone GitHub - ESCOMP/CTSM: Community Terrestrial Systems Model (includes the Community Land Model of CESM)
cd CTSM
./manage_externals/checkout_externals

cd / CTSM/cime/scripts
./create_newcase -case ~/cases --compset I2000Clm50BgcCropGs --res CLM_USRDAT --machine cheyenne --run-unsupported --project UCNN0040

But after running this last line script for create a case I faced this error:


Traceback (most recent call last):
File "./create_newcase", line 15, in <module>
from CIME.scripts.create_newcase import _main_func
File "/glade/work/jteymoori/CTSM/cime/CIME/scripts/create_newcase.py", line 179
f"The default is {srcroot_default}",
^
SyntaxError: invalid syntax

 

[oleson]

Have you loaded python, i.e., module load python?

 

[jteymoori]

I loaded Python, and my problem with that part was solved.
After creating a case with the below script:
./create_newcase --case ~/cases/test1 --mach cheyenne --compset I2000Clm50Fates --res CLM_USRDAT --run-unsupported --project UCNN0040

And select the united states with the below scripts:
./subset_data region --lat1 24.5 --lat2 49.4 --lon1 235 --lon2 294 --reg united_states --create_domain True --create_surface True

when I want to set up my case with : ./case.setup in my case directory, I face this error:

/glade/work/jteymoori/cases/test1> ./case.setup
No such file or directory

If it is normal after creating the case, run this script to set it up. But it doesn't work for me.

 

[oleson]

Part of the problem might be that you are specifying your case here: ~/cases/test1
but then you are running ./case.setup from here /glade/work/jteymoori/cases/test1

 

[jteymoori]

I want to select a region and make a model for that region. by running the below cod I faced an error:

git clone GitHub - ESCOMP/CTSM: Community Terrestrial Systems Model (includes the Community Land Model of CESM)
cd CTSM
./manage_externals/checkout_externals
cd /CTSM/cime/scripts
module load python
./create_newcase --case ~/cases --mach cheyenne style='font-size:9.0pt;mso-fareast-font-family:"Times New Roman";mso-bidi-font-family:
"Courier New";color:#404040'>--res f09_g16 --compset I2000Clm50BgcCrop
--run-unsupported --project UCNN0040
Cd CTSM/tools/site_and_regional
pip install numpy
pip install xarray
./subset_data region --lat1 24.5 --lat2 49.4 --lon1 235 --lon2 294 --reg united_states --create_domain True --create_surface True

subset_data: error: unrecognized arguments: --create_domain True --create_surface True

How can I define and change the --create-surface , --create-landuse,--create-datm, --create-landuse?

 

[slevis]

I think it may be as simple as replacing the "_" with "-"
i.e. the underbars with dashes.

 

[jteymoori]

in the below code by replacing the "_" with "-", I faced an error again:

./subset_data region --lat1 24.5 --lat2 49.4 --lon1 235 --lon2 294 --reg united_states --create-domain True --create-surface True

subset_data: error: unrecognized arguments: True True

 

[slevis]

I think it may work if you remove the "True" and the "True"

For help using this tool, type:
./subset_data --help

 

[jteymoori]

I made a model and submitted my case based on the below code:
mkdir cases
git clone GitHub - ESCOMP/CTSM: Community Terrestrial Systems Model (includes the Community Land Model of CESM)
cd CTSM
./manage_externals/checkout_externals
cd /CTSM/cime/scripts
module load python
./create_newcase --case ~/case --mach cheyenne --res f09_g16 --compset I200Clm50BgcCrop --run-unsupported --project UCNN0040
cd CTSM/tools/site_and_regional
pip install numpy
pip install xarray
./subset_data region --lat1 24.5 --lat2 49.4 --lon1 235 --lon2 294 --reg united_states –-create-domain –-create-surface
cd cases
./case.setup
qcmd -- ./case.build
./case.submit

Now How Can I see the output of this model that I made as the map or .nc file or any other version?

 

[oleson]

You will need to use the surface dataset you created by specifying it in your user_nl_clm in your case directory. I see you created a domain file but in recent versions of the model you need a mesh file, not a domain file. There is a --create-mesh option in subset_data but it doesn't appear to work. In that case then, I would follow the steps @slevis noted in the post above to create a regional mesh file and point the model to it.
@slevis , do you have anything to add here?

Your case seems to be named "cases", which is a bit odd, is that intentional? Regardless, your land history output would be here:

/glade/scratch/jteymoori/archive/cases/lnd/hist

Even though your (global) case ran successfully, you won't have any output there because you only ran 5 days. You need to run at least a month to get output by default.

 

[jteymoori]

Thank you for your response
Based on this tutorial by Sam Levis created (Setting up (high-res sparse) regional-grid CTSM simulations · ESCOMP/CTSM · Discussion #1919), I followed step-by-step Instructions for running regional CTSM-FATES at regular 1-degree resolution.
in step B I used these scripts for my work:
./subset_data region --lat1 24.5 --lat2 49.4 --lon1 235 --lon2 294 --reg united_states --create-surface
for next step (C) I used :
cd ctsm/tools/site_and_regional/subset_data_regional
1- module load nco
2- ncks --rgr infer --rgr scrip=scrip.nc <fsurdat_generated_in_B> foo.nc
but I faced an error because it needs to " <fsurdat_generated_in_B>"
what I should replaced with "<fsurdat_generated_in_B>"

 

[oleson]

The surface dataset you generated in B:
/glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231004.nc

 

[jteymoori]

In the above instruction, I reached this step: Add this line to user_nl_clm:
fsurdat = ‘surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231004.nc’
How can I add this line to user_nl_clm? By which scripts?

 

[oleson]

Just use an editor (e.g., vim, emacs, etc)