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  • Xarthisius · 3 ✖

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  • open_dataset segfaults when opening hdf5 with array of strings · 3 ✖

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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
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
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
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

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