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  • open_dataset segfaults when opening hdf5 with array of strings · 8 ✖
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
1167405546 https://github.com/pydata/xarray/issues/6728#issuecomment-1167405546 https://api.github.com/repos/pydata/xarray/issues/6728 IC_kwDOAMm_X85FlTHq Xarthisius 352673 2022-06-27T14:11:46Z 2022-06-27T14:11:46Z NONE

Possibly related issue: #5706

Oops, looks like my issue is a dupe. Sorry! I looked but I somehow missed that one.

 
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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
1167344851 https://github.com/pydata/xarray/issues/6728#issuecomment-1167344851 https://api.github.com/repos/pydata/xarray/issues/6728 IC_kwDOAMm_X85FlETT Xarthisius 352673 2022-06-27T13:20:14Z 2022-06-27T13:20:14Z NONE

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

Yeah, it can be triggered with:

```python

from netCDF4 import Dataset import h5py import numpy as np import operator

filename = "foobar.h5" with h5py.File(filename, "w") as fp: fp["test"] = np.array(["foo", "bar", "baz"], dtype="|S3")

rootgrp = Dataset("foobar.h5", "r", format="NETCDF4")

This works

print(rootgrp["/test"][slice(None)])

This segfaults

operator.getitem(rootgrp["/test"], slice(None)) ```

 
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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
1166664112 https://github.com/pydata/xarray/issues/6728#issuecomment-1166664112 https://api.github.com/repos/pydata/xarray/issues/6728 IC_kwDOAMm_X85FieGw Xarthisius 352673 2022-06-26T22:29:11Z 2022-06-26T23:33:03Z NONE

I can confirm that if I downgrade netCDF4 from 1.6.0 to 1.5.8 I get UnicodeDecodeError

Edit1: I checked that if I install netCDF4-1.6.0 from git, it works (i.e. I get the UnicodeDecodeError). Only with pip install netCDF4==1.6.0 I'm able to trigger the segmentation fault.

 
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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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