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import cdo does not work although it shows in conda list

Added by Clara Burgard over 3 years ago

Hello,
I want to use cdo through conda and python because the cdo installed on the common machine I am using is missing some properties I need.

I have installed it in my conda environment using conda install cdo and it appears when I do conda list.

However, when I want to import cdo in python, it tells me ModuleNotFoundError: No module named 'cdo'. What am I missing here? Can someone help?

Thank you!


Replies (9)

RE: import cdo does not work although it shows in conda list - Added by Clara Burgard over 3 years ago

Hello again,
I have now understood that I had to install the python wrapper as well! Sorry for the inconvenience!

RE: import cdo does not work although it shows in conda list - Added by Ralf Mueller over 3 years ago

hi clara!

in case you have issues with python-cdo you can also message here

cheers
ralf

RE: import cdo does not work although it shows in conda list - Added by Clara Burgard over 3 years ago

Thank you Ralf!

Actually, I am now stuck when applying the cdo commands in python.

I think I pointed the Cdo() to the right bin-path.

But now I always get the error "FileNotFoundError: [Errno 2] No such file or directory: 'cdo'" (see attached screenshot)

Do you see if I am doing an obviously wrong thing?

Thank you!

RE: import cdo does not work although it shows in conda list - Added by Ralf Mueller over 3 years ago

you have to create the cdo object with a special cdo path like this

cdo = Cdo(cdo=newCdo)

in case you have the cdo package installed in your activated environment, given the explicit path should not be necessary. by default, python-cdo takes the what ever is available in your $PATH variable

hth
ralf

RE: import cdo does not work although it shows in conda list - Added by Clara Burgard over 3 years ago

Thank you again. Unfortunately this does not help :(

'in case you have the cdo package installed in your activated environment, given the explicit path should not be necessary. by default, python-cdo takes the what ever is available in your $PATH variable' => unfortunately, this gives me the error directly, so it seems like he does not find the path directly

if I do:
cdo = Cdo(cdo=newCdo) with newCdo = '/home/burgardc/miniconda3/envs/py38/bin/cdo'

I get exactly the same error as in the screenshot posted above...

RE: import cdo does not work although it shows in conda list - Added by Ralf Mueller over 3 years ago

ok, let me try to set up a similar conda env and test this myself

RE: import cdo does not work although it shows in conda list - Added by Ralf Mueller over 3 years ago

here is what I did

conda update --all
conda create -n cdo
conda activate cdo
conda install cdo python-cdo xarray

checked cdo with
cdo -V                                                                                                                                                                                                                                                                                                                    ─╯
Climate Data Operators version 1.9.9 (https://mpimet.mpg.de/cdo)
System: x86_64-conda-linux-gnu
CXX Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1604652667339/_build_env/bin/x86_64-conda-linux-gnu-c++ -fPIC -DPIC -g -O2 -std=c++11 -fopenmp -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ram/.miniconda3/envs/cdo/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1604652667339/work=/usr/local/src/conda/cdo-1.9.9 -fdebug-prefix-map=/home/ram/.miniconda3/envs/cdo=/usr/local/src/conda-prefix -fopenmp -pthread
CXX version : unknown
C Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1604652667339/_build_env/bin/x86_64-conda-linux-gnu-cc -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H=1  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ram/.miniconda3/envs/cdo/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1604652667339/work=/usr/local/src/conda/cdo-1.9.9 -fdebug-prefix-map=/home/ram/.miniconda3/envs/cdo=/usr/local/src/conda-prefix -fopenmp -pthread -pthread
C version : unknown
F77 Compiler: /home/conda/feedstock_root/build_artifacts/cdo_1604652667339/_build_env/bin/x86_64-conda-linux-gnu-gfortran -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ram/.miniconda3/envs/cdo/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/cdo_1604652667339/work=/usr/local/src/conda/cdo-1.9.9 -fdebug-prefix-map=/home/ram/.miniconda3/envs/cdo=/usr/local/src/conda-prefix
F77 version : GNU Fortran (crosstool-NG 1.24.0.133_b0863d8_dirty) 9.3.0
Features: 15GB 8threads C++11 OpenMP45 Fortran PTHREADS HDF5 NC4/HDF5/threadsafe OPeNDAP UDUNITS2 PROJ XML2 CURL FFTW3 SSE3
Libraries: HDF5/1.10.6 proj/7.2.0 xml2/2.9.10 curl/7.71.1
Filetypes: srv ext ieg grb1 grb2 nc1 nc2 nc4 nc4c nc5 
     CDI library version : 1.9.9
 cgribex library version : 1.9.5
 ecCodes library version : 2.20.0
  NetCDF library version : 4.7.4 of Dec 14 2020 16:14:56 $
    hdf5 library version : 1.10.6 threadsafe
    exse library version : 1.4.1
    FILE library version : 1.9.1

and then I started python:
python                                                                                                                                                                                                                                                                                                                    ─╯
Python 3.9.1 | packaged by conda-forge | (default, Jan 26 2021, 01:34:10) 
[GCC 9.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
Could not open PYTHONSTARTUP
FileNotFoundError: [Errno 2] No such file or directory: '/home/ram/.pythonrc'
>>> from cdo import Cdo
>>> cdo = Cdo()
-->> Could not load netCDF4! <<--
>>> cdo.version()
'1.9.9'
>>> cdo.fldmean(input='-topo')
-->> Could not load netCDF4! <<--
-->> Could not load netCDF4! <<--
'/tmp/cdoPy3be_aalf'

did you work in a loaded conda environment?

RE: import cdo does not work although it shows in conda list - Added by Ralf Mueller over 3 years ago

>>> from cdo import Cdo
>>> cdo = Cdo(cdo='/home/ram/.miniconda3/envs/cdo/bin/cdo')
>>> cdo.version()
'1.9.9'
>>> cdo.fldmean(input='-topo')
'/tmp/cdoPynl7mg2q2'
>>> cdo.fldmean(input='-topo',debug=True)
'/tmp/cdoPyodopu434'

obviously it also works WITHOUT activating a conda environment, when the path to cdo is given

RE: import cdo does not work although it shows in conda list - Added by Clara Burgard over 3 years ago

Very interesting. Thanks for taking the time to try it with me!

Sooo, when I try it in the terminal, it works perfectly well, just as you showed. I just get the error when I import cdo in my jupyter notebook. So it is probably some path problem related to my jupyterlab setup!

Good, then I'll see if I can find out what's the problem there. Seems like it's not a cdo problem then!

Thanks again!

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