issue_comments: 520693149

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https://github.com/pydata/xarray/issues/3185#issuecomment-520693149 https://api.github.com/repos/pydata/xarray/issues/3185 520693149 MDEyOklzc3VlQ29tbWVudDUyMDY5MzE0OQ== 23487320 2019-08-13T05:24:06Z 2019-08-13T05:26:03Z CONTRIBUTOR

xr.show_versions() gets its libnetcdf version from netCDF4 (specially netCDF4.__netcdf4libversion__). So I'm guessing that somehow netCDF4 is picking up libnetcdf from somewhere else -- maybe you pip installed it? It might be worth trying another fresh conda environment...

I'm not sure where it's picking up the libnetcdf 4.6.3 version from, but I found your comment at https://github.com/pydata/xarray/issues/2535#issuecomment-445944261 and think it might indeed be an incompatibility issue with rasterio and netCDF4 binary wheels (do rasterio wheels include netcdf binaries?). Probably somewhat related to https://github.com/mapbox/rasterio/issues/1574 too.

Managed to get things to work by combining the workaround in this Pull Request and StackOverflow post, basically having pip compile the netcdf python package from source instead of using the wheel:

bash HDF5_DIR=$CONDA_PREFIX pip install --no-binary netCDF4 netCDF4==1.4.2 where $CONDA_PREFIX is the path to the conda environment e.g. /home/jovyan/.conda/envs/name-of-env. I've tested my MCVE code sample above and it works up to the latest netCDF4==1.5.1.2 version!

 
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