Failure to load OPeNDAP in Colab #1179
Comments
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Additional information: When using |
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I've run into this issue as well: Additionally, it looks as though this issue only happens when in a pure python environment running |
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Update: I think the wheel being supplied via PyPI is broken. After compiling You may want to consider rebuilding your wheels (for For reference: CSHS-CWRA/RavenPy@5bab92e |
What specifically do you think needs to be done differently when building the manylinux wheels? |
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BTW, the screenshots in #1179 (comment) make it hard to read about the real issue. It seems that the problem is with curl and some SSL certificates. I get this when I try it locally: @jswhit what version/build of curl are you using in the wheel? |
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curl i s 7.75.0, openssl is 1.0.2u |
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It may be a version problem or something with the wheel build. I guess the only way to figure this out is to add an OPeNDAP test during the wheel test phase. This is how I reproduced it locally in case you want to check it out: conda create --name TEST python=3 pip
pip install netcdf4
python -c "import netCDF4; ds = netCDF4.Dataset('http://thredds.socib.es/thredds/dodsC/hf_radar/hf_radar_ibiza-scb_codarssproc001/L1/2016/dep0001_hf-radar-ibiza_scb-codarssproc001_L1_2016-02.nc')"
Error:curl error: Problem with the SSL CA cert (path? access rights?)
curl error details:
Warning:oc_open: Could not read url
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "src/netCDF4/_netCDF4.pyx", line 2353, in netCDF4._netCDF4.Dataset.__init__
File "src/netCDF4/_netCDF4.pyx", line 1963, in netCDF4._netCDF4._ensure_nc_success
OSError: [Errno -68] NetCDF: I/O failure: b'http://thredds.socib.es/thredds/dodsC/hf_radar/hf_radar_ibiza-scb_codarssproc001/L1/2016/dep0001_hf-radar-ibiza_scb-codarssproc001_L1_2016-02.nc'Then, if I do a conda install netcdf4, the test pass and I have these packages installed: |
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I believe that the wheel should be rebuilt. One test folks could try is to conda install it on colab and see if that works. |
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I was having the same problem. I installed once with "%pip install netcdf4<1.6" and once with "%pip install netcdf4<1.6". I can confirm it works with one, but not the other. For each, I used Below is a more narrow list of just where versions have changed. |
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The newest release (1.6.1) hasn't fixed the problems for my use case either: |
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@jswhit, I am available to do some digging and try to solve this issue since it is causing a lot of problem for other libraries. Do you have any suggestions to where should I start looking? |
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This is not a solution, just a work around, but you can try: !pip install -q condacolab
import condacolab
condacolab.install()
import condacolab
condacolab.check()
!mamba install netcdf4and then, import netCDF4
ds = netCDF4.Dataset('http://thredds.socib.es/thredds/dodsC/hf_radar/hf_radar_ibiza-scb_codarssproc001/L1/2016/dep0001_hf-radar-ibiza_scb-codarssproc001_L1_2016-02.nc')I'll check the openssl version used and try to add a regression test in the wheel building process to investigate. I can confirm that this doesn't happen in the Windows wheel and @ngam confirmed it doesn't happen in the M1 wheel. It must be the Linux openssl version then. |
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In the Aug 8 traceback above (and pasted below), the URL string gets turned into a byte string by netCDF4. Could that be relevant? I had this problem and fixed it by using an older version of netCDF4 that keeps the string as a string. There was a similar issue with strings converted to byte strings 2 years ago: pydata/xarray#4859 Traceback (most recent call last): |
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Still having this problem with netcdf4==1.6.3. |
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I just used the colab notebook pinned in the first comment and used the new I think this issue was solved. See #1246 (comment) |
Recently, reading OPeNDAP files when running notebooks on Google Colab resutss in an OSError:
[Errno -68] NetCDF: I/O failureRelevant info:
Example code:
Error:
Colab Notebook link: https://colab.research.google.com/drive/17juZulxoz8sahoDJVuU4uOMSnBC_xXDA?usp=sharing
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