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how to select variables (surface and some vertical levels with index)?

Added by Jagdish Prajapati about 2 years ago

Hello,
I am new to CDO. I have a WRF model ncfile. I want to extract some surface variables and some variables on vertical levels (using index value:29,17,13,9 and 6). I used the following two commands

cdo -selvar,"U10,V10,PSFC,T2,Q2" infile.nc outfile1.nc

cdo -sellevidx,29,17,13,9,6 -selvar,"U,V,W,T,P,PB,PH,PHB,QVAPOR" infile.nc outfile2.nc

and then used

cdo merge outfile1.nc outfile2.nc outfile

If I am applying the same set of procedures to 5 files, It worked well for the first 3 files but not for the last 2.

What is wrong I am doing, is there a way to do the same in one line command? Any help will be greatly appreciated.


Replies (8)

RE: how to select variables (surface and some vertical levels with index)? - Added by Ralf Mueller about 2 years ago

hi!

Please upload some input. would be perfect to have 1 file, that causes the error and another one, that works fine

cheers
ralf

RE: how to select variables (surface and some vertical levels with index)? - Added by Jagdish Prajapati about 2 years ago

Hi Ralf,
Thanks for your quick response. The data file is too large to upload(around 5 gb). Actually, the commands are working well when I am running it manually for the file one by one. I think the problem is in automation. Please check the script if you can. Also, consider replying to how to judge the data at different indexes.

##
import glob
import subprocess
list_of_files = sorted(glob.glob("/home/imdhwrf/OLD_PYTHON_PACK_JAGDISH/PYTHON-PLOT/TRY/KE/WRF/itr1/202203*00/wrfout_d01_2022-03-*_*:00:00.nc"))
for fl in list_of_files:
#print (file)
dt = fl[72:74]
utc = fl[99:101]
if int(dt) >= 3 and int(dt) <= 3 and int(utc) >= 0 and int(utc) <= 4:
subprocess.call('cdo -selvar,U10,V10,PSFC,T2,Q2 %s out1.nc' % fl, shell=True)
subprocess.call('cdo -sellevidx,29,17,13,9,6 -selvar,U,V,W,T,P,PB,PH,PHB,QVAPOR %s out2.nc' % fl, shell=True)
subprocess.call('cdo merge out1.nc out2.nc new_'+fl[77:110], shell=True)
#subprocess.call(['rm' '-f' 'out1.nc'])
#subprocess.call(['rm' '-f' 'out2.nc'])
subprocess.call(['rm','-r','out1.nc'])
subprocess.call(['rm','-r','out2.nc'])

Thanks and Regards
Jagdish

RE: how to select variables (surface and some vertical levels with index)? - Added by Ralf Mueller about 2 years ago

hi!

In case of error, it would be helpful to provide the error messages. so far the calls look ok to me.

cheers
ralf

RE: how to select variables (surface and some vertical levels with index)? - Added by Jagdish Prajapati about 2 years ago

Please check it.

Warning (cdfInqContents): Coordinates variable XTIME can't be assigned!
cdf_get_vara_float: ncid = 65536 varid = 9

Error (cdf_get_vara_float): NetCDF: HDF error
Warning (cdfCheckVarname): Changed double entry of variable name 'XLONG' to 'XLONG_2'!
Warning (cdfCheckVarname): Changed double entry of variable name 'XLAT' to 'XLAT_2'!
cdo merge: Processed 11 variables over 2 timesteps [0.82s 224MB].

RE: how to select variables (surface and some vertical levels with index)? - Added by Ralf Mueller about 2 years ago

this is clearly related to the input, which makes it hard to comment on this. WRF output can be tricky to handle.

I would print the filename before executing cdo in the loop. This identifies the file(s) which causes the issues. you might upload the output of ncdump -h on that file here. This represents the internal structure of the netcdf files.

RE: how to select variables (surface and some vertical levels with index)? - Added by Ralf Mueller about 2 years ago

These wrf files .... here are my recommendations to make them work with CDO

  1. rename the variable 'XTIME' to 'Time'
  2. remove the string 'XTIME' from all 'coordinates' attributes (if the coordinates are NOT time constant, which is the case, I think)
  3. remove the coordinates attribute from the variables 'XLONG' and 'XLAT'

If your XLONG/XLAT fields really do change with Time, then CDO won't be able to do proper analysis on these files. CDO does not handle time-dependant coordinates

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