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

[jteymoori]

This indicates that you are using manage_externals but fates is using git-fleximod, try removing the
.gitmodules file from the fates directory and see if that solves the problem
or you can go to the CTSM/src/fates directory and manually checkout the fates code indicated by the
top level Externals_CLM.cfg file.

There is no file with gitmodules or Externals_CLM.cfg in the fate directory.
How can I remove them?

 

[oleson]

The file name has a period in the front of it, i.e., ".gitmodules".
Don't remove Externals_CLM.cfg

 

[jedwards]

ls -la will revile the files which start with .
standard linux hidden file mechanism.

 

[jteymoori]

Hi
I applied all the suggestions to solve the error, including removing ".gitmodules" from CTSM/src/fates directory, but I faced the error again.
Do you know how I can solve it?

 

[slevis]

Given the confusion all around (yours and mine and possibly everyone's), I would recommend @jedwards and @oleson's advice of starting over clean, i.e. checking out a new copy of ctsm5.2.005 in a new directory.

 

[slevis]

I expect that from the 10 previous pages of support from mostly @oleson (and a bit from me and @jedwards), plus anything you picked up from CLM's User's Guide and Technote, you can recreate the steps that you need.

 

[jteymoori]

Dear @slevis and @oleson
Thank you so much for your helpful suggestions; I could solve the error related to the ctsm version and manage_externals.
The name of the case that I created it is newland_clm50_ctsm520_0.05x0.05conus_GSWP3V1_2000
I created and submitted this case, but it did not run. I checked the run directory, but there is no error in the lnd.log and atm.log files.
How can I find the errors and solve them for a run?

 

[wwieder]

looking at the cesm.log I see this error

dec2318.hsn.de.hpc.ucar.edu 4: (shr_strdata_advance) ERROR: for stream 1 and calendar GREGORIAN
dec2318.hsn.de.hpc.ucar.edu 4: (shr_strdata_advance) ERROR: dtime, dtmax, dtmin, dtlimit =
dec2318.hsn.de.hpc.ucar.edu 4: 0.125000000000000 5479.12500000000 0.125000000000000

I agree this isn't enough to determine the issue, but digging a bit into the atm.log file it seems like it was trying to read the following file

/glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Solar/clmforc.Daymet4.0.05x0.05.Solar.2005-01.nc
an ncdump -h on this file shows the following time metadata

float time(time) ;
time:_FillValue = NaNf ;
time:standard_name = "time" ;
time:long_name = "time" ;
time:description = "time stamp in UTC, middle of each 3-hour" ;
time:bounds = "time_bnds" ;
time:units = "days since 1950-01-01 00:00:00" ;
time:calendar = "standard" ;

My hunch is that your input data time metadata needs to be either GREGORIAN or NO_LEAP. These are the only two options that CESM supports. I'd modify your input data accordingly and see if this avoids the issue

More broadly, I'd like to ask that you spend a bit more time investigating issues on your own before posting to the bulletin board. I appreciate that running CLM is difficult and that this is likely new to you, but the log files typically provide enough of a thread that can be helpful in diagnosing issues like this.

 

[jteymoori]

I changed the time calendar of my Atmospheric Forcing data to "No Leap" and ran the model for one month (Jan 2005), but I faced the same previous error in the cesm.log file in the run directory.
Why did I face this error?
Does my Atmospheric Forcing data have any problem?
I have attached a screenshot of the error
I ran the model for just one month (Jan 2005); the case name is:Jan_clm50_ctsm520_0.05x0.05conus_GSWP3V1_2000

 

[wwieder]

It looks like you have issues with your time intervals. For example,

ncdump -h /glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Solar/clmforc.Daymet4.0.05x0.05.Solar.2005-01.nc shows there are 248 time steps in your file.

ncdump -h /glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Solar/clmforc.Daymet4.0.05x0.05.Solar.2005-0w.nc ALSO shows there are 248 time steps in your file.

Thus, one issue is that Jan and Feb don't have the same number of days, so their datm files shouldn't have the same number of time steps

The second issue (that's actually seems to be causing the issue that that your time data starts on Jan 15, 2005.

Both of these issues need to be fixed in your datm files

----

I just opened your dataset in xarray, and saw this:
ds = xr.open_dataset('/glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Solar/clmforc.Daymet4.0.05x0.05.Solar.2005-01.nc',
decode_times=True)
ds.time

xarray.DataArray
'time'

• time: 248

• array([cftime.DatetimeNoLeap(2005, 1, 15, 1, 30, 0, 0, has_year_zero=True),
  cftime.DatetimeNoLeap(2005, 1, 15, 4, 30, 0, 0, has_year_zero=True),
  cftime.DatetimeNoLeap(2005, 1, 15, 7, 30, 0, 0, has_year_zero=True),
  ...,
  cftime.DatetimeNoLeap(2005, 2, 14, 16, 30, 0, 0, has_year_zero=True),
  cftime.DatetimeNoLeap(2005, 2, 14, 19, 30, 0, 0, has_year_zero=True),
  cftime.DatetimeNoLeap(2005, 2, 14, 22, 30, 0, 0, has_year_zero=True)],
  dtype=object)
• 
  
• Coordinates:
  
  • time
    (time)
    object
    2005-01-15 01:30:00 ... 2005-02-...
  
  

 

[jteymoori]

Thank you for your response.
I fixed the issue for Jan 2005; and now the data starts on Jan 1st, 2005, and you can see them below:
/glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Solar_Jan/clmforc.Daymet4.0.05x0.05.Solar.2005-01.nc
/glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Precip_Jan/clmforc.Daymet4.0.05x0.05.Prec.2005-01.nc
/glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/TPHWL_Jan/clmforc.Daymet4.0.05x0.05.TPQWL.2005-01.nc
I Only tried to submit the model for one month (Jan 2005) and the time calendar for these data is "no Leap," but after submitting the model just for Jan 2005, I faced the same error in the "cesm.log" files in the run directory.

How Can I solve this error?
Do you think my data are incorrect?

It looks like you have issues with your time intervals. For example,

ncdump -h /glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Solar/clmforc.Daymet4.0.05x0.05.Solar.2005-01.nc shows there are 248 time steps in your file.

ncdump -h /glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Solar/clmforc.Daymet4.0.05x0.05.Solar.2005-0w.nc ALSO shows there are 248 time steps in your file.

Thus, one issue is that Jan and Feb don't have the same number of days, so their datm files shouldn't have the same number of time steps

The second issue (that's actually seems to be causing the issue that that your time data starts on Jan 15, 2005.

Both of these issues need to be fixed in your datm files

----

I just opened your dataset in xarray, and saw this:
ds = xr.open_dataset('/glade/derecho/scratch/jteymoori/Daymet4/Data/atm/datm7/Solar/clmforc.Daymet4.0.05x0.05.Solar.2005-01.nc',
decode_times=True)
ds.time

xarray.DataArray
'time'

• time: 248
• array([cftime.DatetimeNoLeap(2005, 1, 15, 1, 30, 0, 0, has_year_zero=True),
  cftime.DatetimeNoLeap(2005, 1, 15, 4, 30, 0, 0, has_year_zero=True),
  cftime.DatetimeNoLeap(2005, 1, 15, 7, 30, 0, 0, has_year_zero=True),
  ...,
  cftime.DatetimeNoLeap(2005, 2, 14, 16, 30, 0, 0, has_year_zero=True),
  cftime.DatetimeNoLeap(2005, 2, 14, 19, 30, 0, 0, has_year_zero=True),
  cftime.DatetimeNoLeap(2005, 2, 14, 22, 30, 0, 0, has_year_zero=True)],
  dtype=object)
• 
  
• Coordinates:
  • time
    (time)
    object
    2005-01-15 01:30:00 ... 2005-02-...