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  • Opening remote file with OpenDAP protocol returns "_FillValue type mismatch" error · 9 ✖
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
954053236 https://github.com/pydata/xarray/issues/5882#issuecomment-954053236 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X8443bJ0 raybellwaves 17162724 2021-10-28T17:29:51Z 2021-10-28T17:29:51Z CONTRIBUTOR

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 xr.open_dataset("http://opendap.tudelft.nl/thredds/dodsC/IDRA/2019/10/01/IDRA_2019-10-01_11-00_raw_data.nc")

I'm on 3.9 sorry I can do a full list of my env as I pull from an internal source but the core ones around netcdf I see

netcdf-fortran 4.5.3
netcdf4 1.5.7 libnetcdf 4.8.1

Works in the pangeo docker (https://github.com/pangeo-data/pangeo-docker-images/blob/master/pangeo-notebook/environment.yml) if that helps

docker run -it pangeo/pangeo-notebook /bin/bash python import xarray as xr xr.open_dataset("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
954028015 https://github.com/pydata/xarray/issues/5882#issuecomment-954028015 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X8443U_v dopplershift 221526 2021-10-28T16:55:26Z 2021-10-28T16:55:26Z CONTRIBUTOR

Can you post the full traceback you get?

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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
953921596 https://github.com/pydata/xarray/issues/5882#issuecomment-953921596 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X84427A8 dopplershift 221526 2021-10-28T14:49:26Z 2021-10-28T14:49:26Z CONTRIBUTOR

@saveriogzz I'm confused why you posted results for 3.6 and 3.8, given that the original issue looks like it was posted for 3.7. 🤨 At any rate, looks like your original issue, the output from show_versions() lists libnetcdf=4.7.4. That version should be fixed with regards to the _FillValue type mismatch error.

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?

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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
952246143 https://github.com/pydata/xarray/issues/5882#issuecomment-952246143 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X844wh9_ dopplershift 221526 2021-10-26T19:29:52Z 2021-10-26T19:29:52Z CONTRIBUTOR

@saveriogzz what is the output of conda list libnetcdf?

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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
949880645 https://github.com/pydata/xarray/issues/5882#issuecomment-949880645 https://api.github.com/repos/pydata/xarray/issues/5882 IC_kwDOAMm_X844ngdF raybellwaves 17162724 2021-10-22T18:45:02Z 2021-10-22T18:45:02Z CONTRIBUTOR

Seemed ok for me. You could try installing with conda: http://xarray.pydata.org/en/stable/getting-started-guide/installing.html#instructions

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  Opening remote file with OpenDAP protocol returns "_FillValue type mismatch" error 1032694511

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