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Segmentation fault in cdo python bindings

Added by Neil Swart over 10 years ago

Since upgrading to scipy 0.14 (Anaconda v2.1.0) I've been having trouble with cdo.setrtomiss and other operators. The following code snippet results in a python segmentation fault:

import cdo; cdo = cdo.Cdo()  
ifile="gistemp1200_ERSST.nc"
varname='tempanomaly'
var = cdo.setrtomiss(1e34,1.1e34, input=ifile, returnMaArray=varname)
Segmentation fault (core dumped)

The cdo binary does not have any problems with this operation, but python seg faults on the return. I noticed the comment on the github page, and tried following the recomendation there,
but the problem persists:

cdf = cdo.setrtomiss(1e34,1.1e34, input=ifile, returnCdf=True)
var = cdf.variables[varname][:]
print var
Segmentation fault (core dumped)

Is this known and reproducible by others? Is there a solution? The above all works fine with scipy 0.13.

Thanks
Neil


Replies (1)

RE: Segmentation fault in cdo python bindings - Added by Ralf Mueller about 10 years ago

Hi!

It's seems to be a bug, I recomment using the netcdf4 library: https://github.com/Try2Code/cdo-bindings/issues/4
the current version of cdo.py has a work around for this.

cheers
ralf

    (1-1/1)