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Errors of cdo=Cdo(), in Ubuntu 16.04, Anaconda2-5.0.1-Linux-x86_64

Added by Guobao Song over 6 years ago

Hi all:

I refreshed my system with new Utuntu 16.04, and installed the Anaconda2.

Through the termimal, I put in the cdo and python-cdo, by using the followed commands, referring to https://code.mpimet.mpg.de/projects/cdo/wiki/Anaconda

conda config --add channels conda-forge
conda install cdo
conda install python-cdo

cdo and python-cdo are available

But when I opened Spyder by Anaconda-navigator, and typed:

from cdo import *
cdo=Cdo()

errors appeared as follows:

Traceback (most recent call last):

File "<ipython-input-3-85114636e53e>", line 1, in <module>
    cdo=Cdo()
File "/home/gbsong/anaconda2/lib/python2.7/site-packages/cdo.py", line 97, in init
    self.operators              = self.getOperators()
File "/home/gbsong/anaconda2/lib/python2.7/site-packages/cdo.py", line 302, in getOperators
    if (parse_version(getCdoVersion(self.CDO)) > parse_version('1.7.0')):
File "/home/gbsong/anaconda2/lib/python2.7/site-packages/cdo.py", line 50, in getCdoVersion
    return match.group(1)

AttributeError: 'NoneType' object has no attribute 'group'

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cdo and python-cdo are available.png (125 KB) cdo and python-cdo are available.png cdo and python-cdo are available
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Replies (7)

RE: Errors of cdo=Cdo(), in Ubuntu 16.04, Anaconda2-5.0.1-Linux-x86_64 - Added by Guobao Song over 6 years ago

Thank you very much

kind regards,

Guobao Song

RE: Errors of cdo=Cdo(), in Ubuntu 16.04, Anaconda2-5.0.1-Linux-x86_64 - Added by Ralf Mueller over 6 years ago

I will try to reproduce this on a debian system

cheers
ralf

RE: Errors of cdo=Cdo(), in Ubuntu 16.04, Anaconda2-5.0.1-Linux-x86_64 - Added by Ralf Mueller over 6 years ago

I get the same error. On my system the cdo installed by conda does not work. it lacks a library:

m300064@breeze3:~$ cdo -V
cdo: error while loading shared libraries: libiconv.so.2: cannot open shared object file: No such file or directory

on my system tweo libs ar missing

  • libiconv: can be installed with conda install libiconv
  • libcom_err: which seem to be related to e2fsprogs, but that has to be installed on the system already - conda does not have any package like this. I guess it is on the building system for conda, but not on my machine. Since a special shared object is needed (libcom_err.so.3) it should be added to conda or used static linking.

hth
ralf

RE: Errors of cdo=Cdo(), in Ubuntu 16.04, Anaconda2-5.0.1-Linux-x86_64 - Added by Ralf Mueller over 6 years ago

I could solve the problem using miniconda3 by calling 

cdo install hdf5
after the two other packages (cdo,python-cdo). But with Anaconda2 it is not solvable for me - maybe with root-access

RE: Errors of cdo=Cdo(), in Ubuntu 16.04, Anaconda2-5.0.1-Linux-x86_64 - Added by Ralf Mueller over 6 years ago

Found the fix for Anaconda: 

conda install krb5

at least solved the issue for me ;-)

RE: Errors of cdo=Cdo(), in Ubuntu 16.04, Anaconda2-5.0.1-Linux-x86_64 - Added by Guobao Song over 6 years ago

Dear ralf:

Thank you very much for your time-intensive effort to help me address this issue.

In terminal, the issue was resolved by updating all package version by using the follows:

conda update -all

Thanks again :) (/)

Guobao

RE: Errors of cdo=Cdo(), in Ubuntu 16.04, Anaconda2-5.0.1-Linux-x86_64 - Added by Ralf Mueller over 6 years ago

Thx for the hint - I put this into the Anaconda docu.

cheers
ralf

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