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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
626042217 MDU6SXNzdWU2MjYwNDIyMTc= 4100 open_dataset is not thread-safe paulkernfeld 433803 open 0     6 2020-05-27T21:25:09Z 2022-04-19T15:30:10Z   NONE      

👋 Hi, great library! I've been trying to use xarray from a flask server and have encountered frequent segfaults when trying to load a file.

MCVE Code Sample

Putting together this MCVE example took a bit of time, but it was a good exercise for me. I enjoyed learning more about the MVCE philosophy! 😊 The only caveat is that reproducibility is difficult for this kind of threading issue, so I can't guarantee that the bug will reproduce. If you have any suggestions for improved reproducibility, please let me know what I can do!

```python import threading import xarray as xr

SAVED_FILE_NAME = "saved.nc"

Modifying these items may change the likelihood of hitting a segfault

N_ELEMENTS = 100 N_THREADS = 2

if name == 'main': xr.Dataset({'foo': ('x', range(N_ELEMENTS))}).to_netcdf(SAVED_FILE_NAME)

threads = [
    threading.Thread(target=lambda: xr.load_dataset(SAVED_FILE_NAME, engine="netcdf4"))
    for _ in range(N_THREADS)
]
for thread in threads:
    thread.start()

for thread in threads:
    thread.join()

print("No segfault!") ```

Expected Output

Program prints No segfault! and exits successfully

Problem Description

The program sometimes segfaults. When running with the Python fault handler, I often get an output that looks like this:

``` Fatal Python error: Segmentation fault

Thread 0x0000700002c2f000 (most recent call first): File "/Users/paul/projects/reflectivity-map-segfault/venv/lib/python3.7/site-packages/xarray/backends/file_manager.py", line 204 in acquire_with_cache_info File "/Users/paul/projects/reflectivity-map-segfault/venv/lib/python3.7/site-packages/xarray/backends/file_manager.py", line 186 in acquire_context File "/usr/local/Cellar/python/3.7.4_1/Frameworks/Python.framework/Versions/3.7/lib/python3.7/contextlib.py", line 112 in __enter__ File "/Users/paul/projects/reflectivity-map-segfault/venv/lib/python3.7/site-packages/xarray/backends/netCDF4.py", line 362 in _acquire File "/Users/paul/projects/reflectivity-map-segfault/venv/lib/python3.7/site-packages/xarray/backends/file_manager.py", line 211 in _acquire_with_cache_info File "/Users/paul/projects/reflectivity-map-segfault/venv/lib/python3.7/site-packages/xarray/backends/file_manager.py", line 192 in acquire_context

Current thread 0x0000700004a41000 (most recent call first): File "/Users/paul/projects/reflectivity-map-segfault/venv/lib/python3.7/site-packages/xarray/backends/file_manager.py", line 204 in _acquire_with_cache_info File "/Users/paul/projects/reflectivity-map-segfault/venv/lib/python3.7/site-packages/xarray/backends/file_manager.py", line 186 in acquire_context File "/usrzsh: segmentation fault ./xarray-segfault ```

Versions

Output of <tt>xr.show_versions()</tt> INSTALLED VERSIONS ------------------ commit: None python: 3.7.4 (default, Sep 7 2019, 18:27:02) [Clang 10.0.1 (clang-1001.0.46.4)] python-bits: 64 OS: Darwin OS-release: 19.0.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: en_US.UTF-8 LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 libhdf5: 1.10.2 libnetcdf: 4.6.3 xarray: 0.15.1 pandas: 1.0.3 numpy: 1.18.4 scipy: None netCDF4: 1.5.3 pydap: None h5netcdf: None h5py: None Nio: None zarr: None cftime: 1.1.3 nc_time_axis: None PseudoNetCDF: None rasterio: None cfgrib: None iris: None bottleneck: None dask: None distributed: None matplotlib: None cartopy: None seaborn: None numbagg: None setuptools: 46.4.0 pip: 20.1.1 conda: None pytest: None IPython: None sphinx: None 
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     xarray 13221727 issue

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