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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
1975845455 I_kwDOAMm_X851xQJP 8410 Segmentation fault 139 (SIGSEGV) lucadix 39524075 closed 0     4 2023-11-03T10:14:03Z 2023-11-06T20:34:46Z 2023-11-06T20:34:45Z NONE      

What happened?

While opening a set of netCDF files in a for loop, using xr.open_dataset().load(), I get a segmentation error (nr. 139). Please see code example below: ``` for region in region_list: [some code to read data associated to each region...]

region_pred = xr.open_dataset(io.BytesIO(data)).load()

[other code working on region_pred...] The error is shown in Linux/Mac after running my Python code, whereas Windows seems to be masking it. I was able to catch that on Windows by launching my code as: python3 my_code.py && echo ok || echo KO ```

In this way, KO gets printed and the segmentation fault is now noticeable. I managed to fix the issue by using a second variable (called reg_pred) in addition to region_pred: ``` for region in region_list: [some code to read data associated to each region...]

region_pred = xr.open_dataset(io.BytesIO(data)) reg_pred = region_pred.load()

[other code working on reg_pred...] ```

What did you expect to happen?

I don't know if the issue I described is something that the developers made on purpose. Personally, I think it is an issue and that's why I am reporting it. If it is not an issue, I would like to get a clarification in order to understand what am I missing. Thank you in advance.

Minimal Complete Verifiable Example

```Python for region in region_list: with storage_client.open(region, "rb") as f: data = f.read() region_pred = xr.open_dataset(io.BytesIO(data)).load()

# some code working on region_pred to compute weather indices... ```

MVCE confirmation

  • [X] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • [ ] Complete example — the example is self-contained, including all data and the text of any traceback.
  • [ ] 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.
  • [ ] Recent environment — the issue occurs with the latest version of xarray and its dependencies.

Relevant log output

No response

Anything else we need to know?

No response

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.9.13 (tags/v3.9.13:6de2ca5, May 17 2022, 16:36:42) [MSC v.1929 64 bit (AMD64)] python-bits: 64 OS: Windows OS-release: 10 machine: AMD64 processor: Intel64 Family 6 Model 141 Stepping 1, GenuineIntel byteorder: little LC_ALL: None LANG: it_IT.UTF-8 LOCALE: ('Italian_Italy', '1252') libhdf5: 1.14.0 libnetcdf: 4.9.2 xarray: 2023.8.0 pandas: 2.1.0 numpy: 1.26.0 scipy: 1.11.2 netCDF4: 1.6.4 pydap: None h5netcdf: 1.2.0 h5py: 3.9.0 Nio: None zarr: None cftime: 1.6.2 nc_time_axis: None PseudoNetCDF: None iris: None bottleneck: None dask: 2023.10.0 distributed: 2023.10.0 matplotlib: 3.8.0 cartopy: None seaborn: None numbagg: None fsspec: 2023.9.1 cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 68.2.2 pip: 23.2.1 conda: None pytest: None mypy: None IPython: 8.15.0 sphinx: None 
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   not_planned xarray 13221727 issue

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