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  • Problems with distributed and opendap netCDF endpoint · 10 ✖

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  • CONTRIBUTOR · 10 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
432796835 https://github.com/pydata/xarray/issues/2503#issuecomment-432796835 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjc5NjgzNQ== ocefpaf 950575 2018-10-24T19:29:11Z 2018-10-24T19:29:11Z CONTRIBUTOR

h10edf3e_1 contains the timeout fix and is build against hdf5 1.10.2. The conda-forge h9cd6fdc_11 build is against hdf5 1.10.3 perhaps that makes a different?

There are many variables at play here. The env that solved it in https://github.com/pydata/xarray/issues/2503#issuecomment-432645477 seems quite different from the env where the problem happened, including an xarray dev version. I'm not sure hdf5 is a good candidate to blame :smile:

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432788686 https://github.com/pydata/xarray/issues/2503#issuecomment-432788686 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjc4ODY4Ng== jjhelmus 1050278 2018-10-24T19:04:44Z 2018-10-24T19:04:44Z CONTRIBUTOR

h10edf3e_1 contains the timeout fix and is build against hdf5 1.10.2. The conda-forge h9cd6fdc_11 build is against hdf5 1.10.3 perhaps that makes a different?

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432784219 https://github.com/pydata/xarray/issues/2503#issuecomment-432784219 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjc4NDIxOQ== ocefpaf 950575 2018-10-24T18:53:22Z 2018-10-24T18:53:22Z CONTRIBUTOR

In defaults libnetcdf4 4.6.1 build 1 and above contain the timeout fix, build 0 has the original timeout.

Thanks @jjhelmus! I guess that info and https://github.com/pydata/xarray/issues/2503#issuecomment-432483817 eliminates the timeout issue from the equation.

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432783232 https://github.com/pydata/xarray/issues/2503#issuecomment-432783232 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjc4MzIzMg== jjhelmus 1050278 2018-10-24T18:50:48Z 2018-10-24T18:50:48Z CONTRIBUTOR

In defaults libnetcdf4 4.6.1 build 1 and above contain the timeout fix, build 0 has the original timeout.

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432747410 https://github.com/pydata/xarray/issues/2503#issuecomment-432747410 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjc0NzQxMA== dopplershift 221526 2018-10-24T17:13:14Z 2018-10-24T17:13:14Z CONTRIBUTOR

Oh, I didn't even catch that the original was on defaults.

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432746421 https://github.com/pydata/xarray/issues/2503#issuecomment-432746421 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjc0NjQyMQ== ocefpaf 950575 2018-10-24T17:10:44Z 2018-10-24T17:10:44Z CONTRIBUTOR

That version has the fix for the issue.

I know that @jjhelmus ported the fix to defaults but I'm not sure which build number has it, and/or if the previous one was remove, b/c defaults builds are not as transparent as conda-forge's :smile:

He can probably say more about that.

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432744441 https://github.com/pydata/xarray/issues/2503#issuecomment-432744441 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjc0NDQ0MQ== dopplershift 221526 2018-10-24T17:06:01Z 2018-10-24T17:06:01Z CONTRIBUTOR

That version has the fix for the issue.

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432739449 https://github.com/pydata/xarray/issues/2503#issuecomment-432739449 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjczOTQ0OQ== dopplershift 221526 2018-10-24T16:54:05Z 2018-10-24T16:54:05Z CONTRIBUTOR

The original version of libnetcdf in @rabernat 's environment definitely had the opendap timeout issue. Not sure if that's the root cause of the problem, or not, but it's suspect.

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432422763 https://github.com/pydata/xarray/issues/2503#issuecomment-432422763 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjQyMjc2Mw== dopplershift 221526 2018-10-23T21:16:05Z 2018-10-23T21:16:16Z CONTRIBUTOR

@lesserwhirls That's an interesting idea. (@rsignell-usgs That's the one.)

@rabernat What version of the conda-forge libnetcdf package is deployed wherever you're running?

 
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   Problems with distributed and opendap netCDF endpoint 373121666
432370887 https://github.com/pydata/xarray/issues/2503#issuecomment-432370887 https://api.github.com/repos/pydata/xarray/issues/2503 MDEyOklzc3VlQ29tbWVudDQzMjM3MDg4Nw== dopplershift 221526 2018-10-23T18:43:23Z 2018-10-23T18:43:23Z CONTRIBUTOR

Just so I'm clear on how the workflow looks: 1. Open dataset with NetCDF/OPeNDAP 2. Serialize NetCDFDataStore (pickle? netcdf file?) 3. Ship to Dask workers 4. Reconstitute NetCDFDataStore

Certainly does seem like there's something stale in what the remote workers are getting. Confused why it works for the others, though.

I can prioritize this a bit and dig in to see what I can figure out--though I'm teaching through tomorrow. May be able to dig into this while at ECMWF.

 
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   Problems with distributed and opendap netCDF endpoint 373121666

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