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

[oleson]

Why are you changing MASK_MESH twice? Do it once and set it to lnd_mesh.nc.
And as previously instructed, change "cd" to "cp" in this command:
cd /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231213.nc landmask.nc
cd (changing the directory) doesn't make any sense. You simply want to copy your surfdata_.... file to landmask.nc
And as previously instructed, change NTASKS_PER_INST=144, not 44.

 

[oleson]

I should mention that it's not necessary to change NTASKS_PER_INST at all. That will be calculated automatically when you run ./case.setup. The NTASKS for all components except ESP should be changed to -4.
Let us know if you are successful in your run.

 

[jteymoori]

Based on what you told me and corrected the code, I ran the script below exactly but got an error after executing each line. Is it possible to ask you to look carefully at this script and see exactly where the problem is?

.......
......
.....
ctsm/tools/site_and_regional/subset_data_regional:

module load nco

cd /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231214.nc landmask.nc

ncks -v PFTDATA_MASK /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231214.nc landmask.nc
ncks -v PFTDATA_MASK /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231214.nc landmask.nc

ncrename -v PFTDATA_MASK,mod_lnd_props landmask.nc

ncks --rgr infer --rgr scrip=scrip.nc landmask.nc foo.nc

/glade/u/apps/ch/opt/esmf-netcdf/8.0.0/intel/19.0.5/bin/bing/Linux.intel.64.mpiuni.default/ESMF_Scrip2Unstruct scrip.nc lnd_mesh.nc 0

.......
.........
.......

 

[oleson]

This command:
cd /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231214.nc landmask.nc

should be:
cp /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231214.nc landmask.nc

 

[oleson]

You are also missing this step:

ncrename -v PFTDATA_MASK,landmask landmask.nc

which should be done after the cp command.

You also have this line twice:

ncks -v PFTDATA_MASK /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231214.nc landmask.nc

That should only be done once.

See my post from yesterday regarding the correct sequence of steps. Here it is again:

cp /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231205.nc landmask.nc

ncrename -v PFTDATA_MASK,landmask landmask.nc

ncks -A -v PFTDATA_MASK /glade/work/jteymoori/CTSM/tools/site_and_regional/subset_data_regional/surfdata_united_states_hist_16pfts_Irrig_CMIP6_simyr2000_c231205.nc landmask.nc

ncrename -v PFTDATA_MASK,mod_lnd_props landmask.nc

ncks --rgr infer --rgr scrip=scrip.nc landmask.nc foo.nc

/glade/u/apps/ch/opt/esmf-netcdf/8.0.0/intel/19.0.5/bin/bing/Linux.intel.64.mpiuni.default/ESMF_Scrip2Unstruct scrip.nc lnd_mesh.nc 0

 

[jteymoori]

Hi
Happy new year
for transfer my data from scratch in cheyenne to derecho I used the below scripts:

/glade/work/jteymoori> qsub -A UCNN0040 -N scratch_duplication_jteymoori /glade/u/home/csgteam/scripts/scratch_migration/dsync_scratch.sh

after running this scripts i received this massage: 2713099.desched1
Now I could not go to the scratch directory by entering : cd /glade/scratch/jteymoori

How can I find the scratch directory?

 

[oleson]

/glade/derecho/scratch/jteymoori

 

[jteymoori]

I ran the model with default resolution, but I want to run model with finer resolution (4 km).
How can I do it?

 

[slevis]

Please read this document:

1. CLM5.0 User’s Guide — ctsm release-clm5.0 documentation

There is a section on running new resolutions.

 

[jteymoori]

To change the resolution based on the 1. CLM5.0 User’s Guide — ctsm release-clm5.0 documentation . There are two parts to adding files to the build-name list database. The first part is adding new resolution names, which is done in:
cd glade/work/jteymoori
cd CTSM
cd /bld/namelist_files/namelist_definition_ctsm.xml

But it is not a directory.
I am confused; how can I change this resolution? By which scripts?
Should I create a new case first, or can I change the resolution for the previous case?

 

[oleson]

You would need to create the surface datasets first as described in this chapter of the User's Guide:

1.3. Using CLM tools — ctsm CTSM master documentation

The steps you are referring to are how you can "easily have these files available for continued use in your development". Those are not required steps but are more for ease of use.

However, since you are working on derecho, we should note that unfortunately, we are unable to create surface datasets at the moment. mksurfdata_map, which you would need to use to create the surface datasets, doesn't work on casper or on derecho and there are no plans to port it to either of those machines. However, there is active work ongoing to port the new tool, mksurfdata_esmf, to derecho and/or casper. Not sure how soon it will be available but I think you can track progress from this issue: Derecho transition: Get CTSM5.2 mksurfdata_esmf tool working on Derecho, Casper, Izumi · Issue #2201 · ESCOMP/CTSM

 

[jteymoori]

I ran the CTSM with default atmospheric forcing data, but now I want to change the atmospheric forcing data to run the model.
At this stage, I want to know How I can do it and prepare my new atmospheric forcing data in CTSM format.
How can I change the atmospheric forcing data for my model?

 

[oleson]

In general, you would create netcdf files in the same structure and format as that of a supported forcing dataset, e.g., GSWP3, and then modify your datm streams files to point to them.

 

[jteymoori]

Where can I find the GSWP3 format for the NetCDF? And How can I find an instruction for doing this work?

 

[oleson]

You can look at one of the cases you already setup, e.g., Dec 19. Your datm.streams.xml file points to GSWP3 forcing data, e.g., one of the solar files:

/glade/p/cgd/tss/CTSM_datm_forcing_data/atm_forcing.datm7.GSWP3.0.5d.v1.c170516/Solar/clmforc.GSWP3.c2011.0.5x0.5.Solr.1991-01.nc

You'll need to convert your forcing data into files that look like that.
We don't have any detailed instructions, just follow the GSWP3 example.

 

[jteymoori]

I tried to go to this direction: /glade/p/cgd/tss/CTSM_datm_forcing_data/atm_forcing.datm7.GSWP3.0.5d.v1.c170516/Solar/clmforc.GSWP3.c2011.0.5x0.5.Solr.1991-01.nc
to download the forcing data, I can just go to: /glade/p , and for going to cgd//tss/CTSM_datm_forcing_data, I faced an error:

-bash: cd: cgd: Permission denied

 

[oleson]

Right, /glade/p is going away. The data is now available at:

/glade/campaign/cesm/cesmdata/cseg/inputdata/atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516

 

[jteymoori]

whether CLM can run on 4km resolution or does the resolution have to be in degrees (e.g., 0.04 degree)?

 

[oleson]

The grid doesn't necessarily have to be in degrees.

 

[jteymoori]

I ran the model with default Atmospheric forcing data,Now I want to regridd the Atmospheric forcing data from 0.5* 0.5 degree(default resolution) to 50 km and run the model the new regridded Atmospheric forcing data. I want to do it just for one month and compare the results before and after regridding.
should I change all the inputs including Solar, Precip, TPHWL which are in the below directory?
/glade/campaign/cesm/cesmdata/cseg/inputdata/atm/datm7/atm_forcing.datm7.GSWP3.0.5d.v1.c170516