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 1329407773,I_kwDOAMm_X85PPScd,6877,RuntimeError: NetCDF: HDF error,80203996,closed,0,,,2,2022-08-05T03:45:56Z,2023-03-12T10:14:37Z,2023-03-12T10:14:37Z,NONE,,,,"### What happened? I am reading the era5 nc data and extracting the values by latitude and longitude. My code worked fine for 8 hours but then suddenly it broke. Here is the error message. I'm guessing its an error related to the threads? ### What did you expect to happen? _No response_ ### Minimal Complete Verifiable Example _No response_ ### MVCE confirmation - [ ] 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](https://mybinder.org/v2/gh/pydata/xarray/main?urlpath=lab/tree/doc/examples/blank_template.ipynb), returning the result. - [ ] New issue — a search of GitHub Issues suggests this is not a duplicate. ### Relevant log output ```Python RemoteTraceback: """""" Traceback (most recent call last): File ""C:\ProgramData\Anaconda3\lib\multiprocessing\pool.py"", line 125, in worker result = (True, func(*args, **kwds)) File ""D:\project\assimilation\fun_tools.py"", line 54, in cell_assimilation result = run_ensemble(observations, longitude, latitude) File ""D:\project\assimilation\enkf.py"", line 142, in run_ensemble enkf.setup_wofost() File ""D:\project\assimilation\enkf.py"", line 48, in setup_wofost self.weather_db = NCWeatherDataProvider(self.longitude, self.latitude) File ""D:\project\assimilation\ncweatherdataprovider.py"", line 56, in __init__ self._read_observations() File ""D:\project\assimilation\ncweatherdataprovider.py"", line 105, in _read_observations value = pnt[varname.replace(""-"",""_"")].values[0] File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\dataarray.py"", line 642, in values return self.variable.values File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\variable.py"", line 512, in values return _as_array_or_item(self._data) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\variable.py"", line 252, in _as_array_or_item data = np.asarray(data) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\indexing.py"", line 552, in __array__ self._ensure_cached() File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\indexing.py"", line 549, in _ensure_cached self.array = NumpyIndexingAdapter(np.asarray(self.array)) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\indexing.py"", line 522, in __array__ return np.asarray(self.array, dtype=dtype) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\indexing.py"", line 423, in __array__ return np.asarray(array[self.key], dtype=None) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\coding\variables.py"", line 70, in __array__ return self.func(self.array) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\coding\variables.py"", line 137, in _apply_mask data = np.asarray(data, dtype=dtype) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\indexing.py"", line 423, in __array__ return np.asarray(array[self.key], dtype=None) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\backends\netCDF4_.py"", line 93, in __getitem__ return indexing.explicit_indexing_adapter( File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\core\indexing.py"", line 712, in explicit_indexing_adapter result = raw_indexing_method(raw_key.tuple) File ""C:\ProgramData\Anaconda3\lib\site-packages\xarray\backends\netCDF4_.py"", line 106, in _getitem array = getitem(original_array, key) File ""src\netCDF4\_netCDF4.pyx"", line 4406, in netCDF4._netCDF4.Variable.__getitem__ File ""src\netCDF4\_netCDF4.pyx"", line 5350, in netCDF4._netCDF4.Variable._get File ""src\netCDF4\_netCDF4.pyx"", line 1927, in netCDF4._netCDF4._ensure_nc_success RuntimeError: NetCDF: HDF error """""" ``` ### Anything else we need to know? My code is not easily simplified so it may not be reproducible, the last time I ran the code it was an error after 5 hours of normal work. first: 53%|█████▎ | 952/1803 [5:32:09<4:56:55, 20.93s/it] second: 78%|███████▊ | 1408/1803 [8:02:31<2:15:22, 20.56s/it] The error is the same ### Environment
commit: None python: 3.8.12 (default, Oct 12 2021, 03:01:40) [MSC v.1916 64 bit (AMD64)] python-bits: 64 OS: Windows OS-release: 10 machine: AMD64 processor: Intel64 Family 6 Model 140 Stepping 1, GenuineIntel byteorder: little LC_ALL: None LANG: zh_CN.UTF8 LOCALE: ('Chinese (Simplified)_China', '936') libhdf5: 1.12.1 libnetcdf: 4.8.1 xarray: 2022.3.0 pandas: 1.3.5 numpy: 1.22.3 scipy: 1.7.3 netCDF4: 1.5.8 pydap: None h5netcdf: 1.0.1 h5py: 3.7.0 Nio: None zarr: None cftime: 1.5.1.1 nc_time_axis: None PseudoNetCDF: None rasterio: 1.2.10 cfgrib: None iris: None bottleneck: 1.3.4 dask: 2022.6.1 distributed: 2022.6.1 matplotlib: 3.5.1 cartopy: 0.20.1 seaborn: 0.11.2 numbagg: None fsspec: 2022.3.0 cupy: None pint: None sparse: None setuptools: 61.2.0 pip: 21.2.2 conda: 4.13.0 pytest: 7.1.2 IPython: 7.31.1 sphinx: 4.4.0
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