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  • open_dataset segfaults when opening hdf5 with array of strings · 5 ✖

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id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1167548711 https://github.com/pydata/xarray/issues/6728#issuecomment-1167548711 https://api.github.com/repos/pydata/xarray/issues/6728 IC_kwDOAMm_X85Fl2En dcherian 2448579 2022-06-27T16:10:20Z 2022-06-27T16:10:20Z MEMBER

Thanks @kmuehlbauer 

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   open_dataset segfaults when opening hdf5 with array of strings 1285001323
1167398217 https://github.com/pydata/xarray/issues/6728#issuecomment-1167398217 https://api.github.com/repos/pydata/xarray/issues/6728 IC_kwDOAMm_X85FlRVJ kmuehlbauer 5821660 2022-06-27T14:06:27Z 2022-06-27T14:06:27Z MEMBER 
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   open_dataset segfaults when opening hdf5 with array of strings 1285001323
1167339640 https://github.com/pydata/xarray/issues/6728#issuecomment-1167339640 https://api.github.com/repos/pydata/xarray/issues/6728 IC_kwDOAMm_X85FlDB4 keewis 14808389 2022-06-27T13:15:25Z 2022-06-27T13:15:25Z MEMBER

the segfault should definitely be reported upstream (Unidata/netcdf4-python, I think), but we can also try to avoid hitting this or the UnicodeDecodeError: I can successfully read the dataset with xarray=2022.03.0 and netcdf4=1.5.8.

 
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   open_dataset segfaults when opening hdf5 with array of strings 1285001323
1167320520 https://github.com/pydata/xarray/issues/6728#issuecomment-1167320520 https://api.github.com/repos/pydata/xarray/issues/6728 IC_kwDOAMm_X85Fk-XI mathause 10194086 2022-06-27T12:57:52Z 2022-06-27T12:57:52Z MEMBER

Can you reproduce this without xarray? It should probably be reported upstream? (In the netCDF4 repo?)

 
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   open_dataset segfaults when opening hdf5 with array of strings 1285001323
1166635630 https://github.com/pydata/xarray/issues/6728#issuecomment-1166635630 https://api.github.com/repos/pydata/xarray/issues/6728 IC_kwDOAMm_X85FiXJu keewis 14808389 2022-06-26T20:22:01Z 2022-06-26T20:49:46Z MEMBER

Can you check if that's due to the new version of netcdf4? I can't seem to install that from conda-forge, and if I execute your MCVE using engine="netcdf4" and netCDF4==1.5.8 I get a UnicodeDecodeError (which is not perfect but definitely better than a segfault).

Edit: I can successfully reproduce if I use netcdf4 and h5py from PyPI, which I guess means that the combination of the new versions and the change you mentioned triggers the segfault Edit2: this is curious, all my new environments get the segfault but my old development environment raises a UnicodeDecodeError

 
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   open_dataset segfaults when opening hdf5 with array of strings 1285001323

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