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Opening remote file with OpenDAP protocol returns "_FillValue type mismatch" error #5882
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Seemed ok for me. You could try installing with conda: http://xarray.pydata.org/en/stable/getting-started-guide/installing.html#instructions |
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")Traceback (most recent call last): During handling of the above exception, another exception occurred: Traceback (most recent call last): |
@saveriogzz what is the output of |
this one for python 3.6
and this one for 3.8
|
@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 Your Python 3.8 environment does have an old version of libnetcdf. Can you try doing |
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.
Unfortunately the error is still the same. |
Can you post the full traceback you get? |
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 Works in the pangeo docker (https://github.com/pangeo-data/pangeo-docker-images/blob/master/pangeo-notebook/environment.yml) if that helps
|
Thanks both for your help! Pangeo's notebook works as expected, I will start using that instead of my custom docker image. |
What happened:
When trying to open a remote file with OpenDAP protocol, I receive the error
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'
.What you expected to happen:
I expect the file to be opened without having to add the string
'#fillmismatch'
to the file's URL (see example below).I am not specifying any
engine
in the methodopen_dataset()
. However, if I specify'pydap'
, I receive a different type of error:unrecognized engine pydap must be one of: ['netcdf4', 'scipy', 'store']
; although I have pydap 3.2.2 installed and ran!pip install xarray[complete]
Minimal Complete Verifiable Example:
Anything else we need to know?:
Unidata/netcdf4-python#929
Environment:
Output of xr.show_versions()
INSTALLED VERSIONS
commit: None
python: 3.7.4 (default, Aug 13 2019, 20:35:49)
[GCC 7.3.0]
python-bits: 64
OS: Linux
OS-release: 5.4.0-88-generic
machine: x86_64
processor: x86_64
byteorder: little
LC_ALL: en_US.UTF-8
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.12.0
libnetcdf: 4.7.4
xarray: 0.18.2
pandas: 1.2.4
numpy: 1.20.3
scipy: 1.6.3
netCDF4: 1.5.6
pydap: installed
h5netcdf: 0.11.0
h5py: 3.5.0
Nio: None
zarr: 2.10.2
cftime: 1.5.0
nc_time_axis: 1.3.1
PseudoNetCDF: None
rasterio: 1.2.10
cfgrib: None
iris: None
bottleneck: 1.3.2
dask: 2021.05.0
distributed: 2021.05.0
matplotlib: 3.4.2
cartopy: None
seaborn: 0.11.2
numbagg: 0.2.1
pint: None
setuptools: 45.1.0.post20200119
pip: 21.1.2
conda: 4.7.12
pytest: 6.2.4
IPython: 7.11.1
sphinx: None
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