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  • import xarray causes fatal python crash on windows when h5netcdf and netcdf4 are installed · 3 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1269993497 https://github.com/pydata/xarray/issues/7136#issuecomment-1269993497 https://api.github.com/repos/pydata/xarray/issues/7136 IC_kwDOAMm_X85LspAZ daanscheltens 21100296 2022-10-06T12:55:32Z 2022-10-06T13:11:14Z NONE

Thanks for the quick reply.

I indeed get the same error when trying import netcdf4 import h5netcdf

Since the h5py libary is used by h5netcdf, I also tried the next imports, which again give the same error. import netcdf4 import h5py

Conclusion is that indead the hdf5 library inside netcdf4 is older, and the check in h5py gives the fatal error.

Both netCDF4 and h5netcdf are optional requirements for xarray. Why is netCDF4 then imported when I don't use it for a certain calculation?

Note that conda is not an option for me, as this is incompatible with nessecary third party software.

 
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   import xarray causes fatal python crash on windows when h5netcdf and netcdf4 are installed 1399324758
1269997530 https://github.com/pydata/xarray/issues/7136#issuecomment-1269997530 https://api.github.com/repos/pydata/xarray/issues/7136 IC_kwDOAMm_X85Lsp_a headtr1ck 43316012 2022-10-06T12:58:00Z 2022-10-06T12:58:00Z COLLABORATOR

See https://github.com/pydata/xarray/issues/6726#issuecomment-1257279640.

We are thinking in doing the backend imports only when needed.

 
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   import xarray causes fatal python crash on windows when h5netcdf and netcdf4 are installed 1399324758
1269865784 https://github.com/pydata/xarray/issues/7136#issuecomment-1269865784 https://api.github.com/repos/pydata/xarray/issues/7136 IC_kwDOAMm_X85LsJ04 keewis 14808389 2022-10-06T11:34:27Z 2022-10-06T11:34:51Z MEMBER

I suspect that's because you're installing via pip, where both the h5netcdf and the netcdf4 wheel bundle the HDF5 library (but different versions, apparently). If that's correct, you should get the same error if you're importing netcdf4 then h5netcdf: python import netCDF4 import h5netcdf

Note that because there is a separate libhdf5 package for conda you don't have that issue (and you might want to use micromamba in CI)

 
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   import xarray causes fatal python crash on windows when h5netcdf and netcdf4 are installed 1399324758

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