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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
309949357 MDU6SXNzdWUzMDk5NDkzNTc= 2029 Can't re-save netCDF after opening it and modifying it? fasiha 37649 closed 0     4 2018-03-30T01:16:11Z 2019-01-06T10:46:40Z 2018-03-31T22:30:50Z NONE      

Code Sample, copy-pastable

```python import xarray as xr import numpy as np import pandas as pd

filename = 'foo.nc'

print('creating fresh file') temp = 15 + 8 * np.random.randn(2, 2, 3) precip = 10 * np.random.rand(2, 2, 3) lon = [[-99.83, -99.32], [-99.79, -99.23]] lat = [[42.25, 42.21], [42.63, 42.59]] ds = xr.Dataset( { 'temperature': (['x', 'y', 'time'], temp), 'precipitation': (['x', 'y', 'time'], precip) }, coords={ 'lon': (['x', 'y'], lon), 'lat': (['x', 'y'], lat), 'time': pd.date_range('2014-09-06', periods=3), 'reference_time': pd.Timestamp('2014-09-05') }) ds.to_netcdf(filename)

del ds

ds = xr.open_dataset(filename, autoclose=True) print('opened file') print(ds['temperature']) ds['temperature'][0, 0, 0] += 1000

ds.to_netcdf(filename) ### Crashes

import os

ds.to_netcdf(filename + '2')

os.rename(filename + '2', filename)

```

Problem description

<snipped very long stacktrace, can produce if desired> OSError: [Errno -51] NetCDF: Unknown file format: b'/path/to/foo.nc' I encountered this problem when opening a netCDF file, modifying it, and trying to save it back. This is with netCDF4==1.3.1 and scipy==1.0.1. (Potentially related: #2019?)

Expected Output

If instead of to_netcdf overwriting the just-opened file, I write to a new file and then os.rename (see the three commented lines above) the new file to the original location, all is well. ncdump reports that my change took.

Output of xr.show_versions()

INSTALLED VERSIONS commit: None python: 3.6.4.final.0 python-bits: 64 OS: Darwin OS-release: 17.4.0 machine: x86_64 processor: i386 byteorder: little LC_ALL: None LANG: en_US.UTF-8 LOCALE: en_US.UTF-8 xarray: 0.10.2 pandas: 0.22.0 numpy: 1.14.2 scipy: 1.0.1 netCDF4: 1.3.1 h5netcdf: None h5py: None Nio: None zarr: None bottleneck: None cyordereddict: None dask: None distributed: None matplotlib: None cartopy: None seaborn: None setuptools: 39.0.1 pip: 9.0.3 conda: None pytest: None IPython: 6.2.1 sphinx: None 
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   completed xarray 13221727 issue

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