Subsetting Surface Datasets

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ah828

Anthony Holmes
New Member
Per my previous discussion post:
Regional Ensemble Spin-up Error: "Attempt to use feature that was not turned on when netCDF was built"

I am now attempting to use the ncks command to subset the surface and domain data to my region of interest. Using the following command:

ncks -d LONGXY,21.,52. -d LATIXY,-12.,24. /glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc /glade/scratch/anthholmes/regional/surfdata_0.9x1.25_78pfts_CMIP6_simyr2000_E.Africa_ncks.nc

I receive the error:

Code: 
ncks: ERROR dimension LONGXY is not in input file

Running ncdump -h and looking at the variable keys in Python, it is clear this variable exists, but has two dimensions: lsmlat, and lsmlon. The ./subset_surfdata python tool deals with this by converting the variables to a 1D array as follows:

Code: 
# create 1d variables
    lon0=np.asarray(f1['LONGXY'][0,:])
    lon=xr.DataArray(lon0,name='lon',dims='lsmlon',coords={'lsmlon':lon0})
    lat0=np.asarray(f1['LATIXY'][:,0])
    lat=xr.DataArray(lat0,name='lat',dims='lsmlat',coords={'lsmlat':lat0})

How would one accomplish this using NCO? What other tools are people using to subset surface datasets?
 
slevis

slevis

Moderator
Staff member
I wonder whether the "ERROR dimension LONGXY is not in input file" refers to the fact that you typed "ncks -d" where I suspect "d" means dimension, while LONGXY is a variable with dimensions lsmlat, lsmlon.
 
A

ah828

Anthony Holmes
New Member
slevis said:
I wonder whether the "ERROR dimension LONGXY is not in input file" refers to the fact that you typed "ncks -d" where I suspect "d" means dimension, while LONGXY is a variable with dimensions lsmlat, lsmlon.
Click to expand...
That's a good point, I tried running using the lsmlat and lsmlon dims previously, but receive the following error

Code: 
(xESMF) anthholmes@cheyenne1:~/CTSM/tools/mkmapgrids> ncks -d lsmlon,21.,52. -d lsmlat,-12.,24. /glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc /glade/scratch/anthholmes/regional/surfdata_0.9x1.25_78pfts_CMIP6_simyr2000_E.Africa_ncks.nc
ncks: ERROR nco_lmt_evl_dmn_crd() unable to read user-specified coordinate lsmlat. Ensure this coordinate variable is in file and is a 1-D array.
nco_err_exit(): ERROR Short NCO-generated message (usually name of function that triggered error): nc_get_vara_double()
nco_err_exit(): ERROR Error code is -50. Translation into English with nc_strerror(-50) is "NetCDF: Action prohibited on NC_GLOBAL varid"
nco_err_exit(): ERROR NCO will now exit with system call exit(EXIT_FAILURE)

Even though lsmlon and lsmlat show up as dimensions when I run ncdump -h:

Code: 
(xESMF) anthholmes@cheyenne1:~/CTSM/tools/mkmapgrids> ncdump -h /glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc
netcdf surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214 {
dimensions:
        lsmlon = 288 ;
        lsmlat = 192 ;
        nglcec = 10 ;
        nglcecp1 = 11 ;
        ...
 
slevis

slevis

Moderator
Staff member
...what about trying your ncks command but with "ncks -v" where "v" stands for variable. Does that do anything?
 
A

ah828

Anthony Holmes
New Member
slevis said:
...what about trying your ncks command but with "ncks -v" where "v" stands for variable. Does that do anything?
Click to expand...

It created a NetCDF file with the variable "LATIXY":

Code: 
(xESMF) anthholmes@cheyenne1:~/CTSM/tools/mkmapgrids> ncdump -h /glade/scratch/anthholmes/regional/surfdata_0.9x1.25_78pfts_CMIP6_simyr2000_E.Africa_ncks.nc
netcdf surfdata_0.9x1.25_78pfts_CMIP6_simyr2000_E.Africa_ncks {
dimensions:
        lsmlat = 192 ;
        lsmlon = 288 ;
variables:
        double LATIXY(lsmlat, lsmlon) ;
                LATIXY:long_name = "latitude" ;
                LATIXY:units = "degrees north" ;
 
A

ah828

Anthony Holmes
New Member
slevis said:
Definitely not what you wanted...
I assume that you have already consulted the nco user's guide, but in case you haven't:

NCO Homepage

nco.sourceforge.net nco.sourceforge.net
Click to expand...
Always good to check. I posted this question to NCO Help forum Source Forge as well. My guess is that there is no simple command-line option, but I'll update this thread if something comes up.
 
A

ah828

Anthony Holmes
New Member
ncks does work! The issue was that I was incorrectly specifying the lat and lon. Whereas the Python tool uses decimal degrees, ncks needs you to specify the degrees in latitude values ranging from 0 at the S. Pole to 180 at the N. Pole and for longitude values range from 0 at the Greenwich Meridian to 360.

I used the following code to get the results I wanted:

Code: 
ncks -d lsmlon,21,52 -d lsmlat,78,114 /glade/p/cesmdata/cseg/inputdata/lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc /glade/scratch/anthholmes/regional/surfdata_0.9x1.25_78pfts_CMIP6_simyr2000_E.Africa_ncks_v2.nc
 
E

evasinha

Eva Sinha
New Member
@aherring and @slevis I experienced the same error mentioned above by Anthony when extracting a surface dataset. I learned from Charlie Zender: "when the lsmlat and lsmlon dimensions do not have corresponding coordinate arrays, then the arguments to -d lsmlat and -d lsmlon need to be indices not actual lats and lons".

The indices can be found using the following command
ncks -C --trd -v LATIXY,LONGXY in.nc | more
Click to expand...
 
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