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  • Opening remote file with OpenDAP protocol returns "_FillValue type mismatch" error · 4 ✖

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  • NONE · 4 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
954594196 https://github.com/pydata/xarray/issues/5882#issuecomment-954594196 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X8445fOU saveriogzz 42075938 2021-10-29T09:30:40Z 2021-10-29T09:30:40Z NONE

Thanks both for your help! Pangeo's notebook works as expected, I will start using that instead of my custom docker image.
Thanks again!

 
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   Opening remote file with OpenDAP protocol returns "_FillValue type mismatch" error 1032694511
953986135 https://github.com/pydata/xarray/issues/5882#issuecomment-953986135 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X8443KxX saveriogzz 42075938 2021-10-28T16:02:11Z 2021-10-28T16:02:22Z NONE

Sorry, that is in fact confusing! The original python 3.7 is my jupyter lab running in docker, while 3.6 and 3.8 are brand new conda environments.

Your Python 3.8 environment does have an old version of libnetcdf. Can you try doing conda install -n py38 -c conda-forge "libnetcdf>=4.7.4" and see if that fixes your problem?

Unfortunately the error is still the same.

 
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   Opening remote file with OpenDAP protocol returns "_FillValue type mismatch" error 1032694511
952622521 https://github.com/pydata/xarray/issues/5882#issuecomment-952622521 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X844x925 saveriogzz 42075938 2021-10-27T07:35:09Z 2021-10-27T07:35:09Z NONE

this one for python 3.6 ```

packages in environment at /home/myself/miniconda3/envs/py36:

Name Version Build Channel

libnetcdf 4.7.4 nompi_h56d31a8_107 conda-forge ```

and this one for 3.8 ```

packages in environment at /home/myself/miniconda3/envs/py38:

Name Version Build Channel

libnetcdf 4.6.1 h2053bdc_4
```

 
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   Opening remote file with OpenDAP protocol returns "_FillValue type mismatch" error 1032694511
949892277 https://github.com/pydata/xarray/issues/5882#issuecomment-949892277 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X844njS1 saveriogzz 42075938 2021-10-22T19:03:19Z 2021-10-23T15:04:06Z NONE

Thanks for trying out! I have installed xarray with conda in a newly conda environment (both python 3.6 and 3.8), but I still receive the error:

@raybellwaves which python version are you using?

Output of <tt>xr.open_dataset("http://opendap.tudelft.nl/thredds/dodsC/IDRA/2019/10/01/IDRA_2019-10-01_11-00_raw_data.nc")</tt> Traceback (most recent call last): File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/file_manager.py", line 199, in _acquire_with_cache_info file = self._cache[self._key] File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/lru_cache.py", line 53, in __getitem__ value = self._cache[key] KeyError: [<class 'netCDF4._netCDF4.Dataset'>, ('http://opendap.tudelft.nl/thredds/dodsC/IDRA/2019/10/01/IDRA_2019-10-01_11-00_raw_data.nc',), 'r', (('clobber', True), ('diskless', False), ('format', 'NETCDF4'), ('persist', False))] During handling of the above exception, another exception occurred: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/api.py", line 500, in open_dataset **kwargs, File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/netCDF4_.py", line 558, in open_dataset autoclose=autoclose, File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/netCDF4_.py", line 380, in open return cls(manager, group=group, mode=mode, lock=lock, autoclose=autoclose) File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/netCDF4_.py", line 328, in __init__ self.format = self.ds.data_model File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/netCDF4_.py", line 389, in ds return self._acquire() File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/netCDF4_.py", line 383, in _acquire with self._manager.acquire_context(needs_lock) as root: File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/contextlib.py", line 81, in __enter__ return next(self.gen) File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/file_manager.py", line 187, in acquire_context file, cached = self._acquire_with_cache_info(needs_lock) File "/home/sguzzo/miniconda3/envs/py36/lib/python3.6/site-packages/xarray/backends/file_manager.py", line 205, in _acquire_with_cache_info file = self._opener(*self._args, **kwargs) File "src/netCDF4/_netCDF4.pyx", line 2330, in netCDF4._netCDF4.Dataset.__init__ File "src/netCDF4/_netCDF4.pyx", line 1948, in netCDF4._netCDF4._ensure_nc_success OSError: [Errno -45] NetCDF: Not a valid data type or _FillValue type mismatch: b'http://opendap.tudelft.nl/thredds/dodsC/IDRA/2019/10/01/IDRA_2019-10-01_11-00_raw_data.nc'
 
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   Opening remote file with OpenDAP protocol returns "_FillValue type mismatch" error 1032694511

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