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  • xarray · 1 ✖
id node_id number title user state locked assignee milestone comments created_at updated_at ▲ closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
1285001323 I_kwDOAMm_X85Ml5Br 6728 open_dataset segfaults when opening hdf5 with array of strings Xarthisius 352673 closed 0     8 2022-06-26T18:48:04Z 2022-06-27T16:10:21Z 2022-06-27T16:10:20Z NONE      

What happened?

An attempt to open non netCDF4 hdf5 file with xarray.open_dataset results in a segmentation fault.

What did you expect to happen?

Code execute and not die a horrible death.

Minimal Complete Verifiable Example

```Python import h5py import numpy as np from xarray import open_dataset

filename = "foobar.h5"

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

with open_dataset(filename, engine="netcdf4") as ds: print("yay") ```

MVCE confirmation

  • [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • [X] Complete example — the example is self-contained, including all data and the text of any traceback.
  • [X] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • [X] New issue — a search of GitHub Issues suggests this is not a duplicate.

Relevant log output

```Python $ python3 -Wd -X faulthandler bug.py Fatal Python error: Segmentation fault

Current thread 0x00007f2283947740 (most recent call first): File "/home/xarth/codes/xarthisius/xarray/xarray/backends/netCDF4_.py", line 106 in getitem File "/home/xarth/codes/xarthisius/xarray/xarray/core/indexing.py", line 816 in explicit_indexing_adapter File "/home/xarth/codes/xarthisius/xarray/xarray/backends/netCDF4.py", line 93 in getitem File "/home/xarth/codes/xarthisius/xarray/xarray/core/indexing.py", line 527 in array File "/home/xarth/codes/xarthisius/xarray/xarray/core/variable.py", line 250 in as_array_or_item File "/home/xarth/codes/xarthisius/xarray/xarray/core/variable.py", line 510 in values File "/home/xarth/codes/xarthisius/xarray/xarray/core/variable.py", line 337 in data File "/home/xarth/codes/xarthisius/xarray/xarray/core/common.py", line 1866 in contains_cftime_datetimes File "/home/xarth/codes/xarthisius/xarray/xarray/core/common.py", line 1875 in _contains_datetime_like_objects File "/home/xarth/codes/xarthisius/xarray/xarray/conventions.py", line 345 in decode_cf_variable File "/home/xarth/codes/xarthisius/xarray/xarray/conventions.py", line 521 in decode_cf_variables File "/home/xarth/codes/xarthisius/xarray/xarray/backends/store.py", line 27 in open_dataset File "/home/xarth/codes/xarthisius/xarray/xarray/backends/netCDF4.py", line 567 in open_dataset File "/home/xarth/codes/xarthisius/xarray/xarray/backends/api.py", line 495 in open_dataset File "/home/xarth/codes/xarthisius/yt/bug.py", line 10 in <module> Segmentation fault (core dumped) ```

Anything else we need to know?

This regression was introduced in #6489

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.9.5 (default, Nov 23 2021, 15:27:38) [GCC 9.3.0] python-bits: 64 OS: Linux OS-release: 5.4.0-121-generic machine: x86_64 processor: x86_64 byteorder: little LC_ALL: en_US.utf8 LANG: en_US.utf8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.12.2 libnetcdf: 4.9.0 xarray: 2022.3.1.dev60+g5f01c115 pandas: 1.4.3 numpy: 1.23.0 scipy: 1.9.0rc1 netCDF4: 1.6.0 pydap: None h5netcdf: None h5py: 3.7.0 Nio: None zarr: None cftime: 1.6.0 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: 2022.6.1 distributed: None matplotlib: 3.5.2 cartopy: None seaborn: None numbagg: None fsspec: 2022.5.0 cupy: None pint: None sparse: None setuptools: 44.0.0 pip: 20.0.2 conda: None pytest: 7.1.2 IPython: 8.4.0 sphinx: None 
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   completed xarray 13221727 issue

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