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  • Hangs while saving netcdf file opened using xr.open_mfdataset with lock=None · 3 ✖

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  • CONTRIBUTOR · 3 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
731254101 https://github.com/pydata/xarray/issues/3961#issuecomment-731254101 https://api.github.com/repos/pydata/xarray/issues/3961 MDEyOklzc3VlQ29tbWVudDczMTI1NDEwMQ== jklymak 1562854 2020-11-20T16:01:03Z 2020-11-20T16:01:03Z CONTRIBUTOR

Lock false sometimes throws hd5 error. No clear solution.

I haven't seen that yet, but I'd still far prefer an occasional error to a hung process. 

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   Hangs while saving netcdf file opened using xr.open_mfdataset with lock=None 597657663
730007824 https://github.com/pydata/xarray/issues/3961#issuecomment-730007824 https://api.github.com/repos/pydata/xarray/issues/3961 MDEyOklzc3VlQ29tbWVudDczMDAwNzgyNA== jklymak 1562854 2020-11-18T22:51:47Z 2020-11-18T22:51:47Z CONTRIBUTOR

I have the same behaviour with MacOS (10.15). xarray=0.16.1, dask=2.30.0, netcdf4=1.5.4. Sometimes saves, sometimes doesn't. lock=False seems to work.

 
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   Hangs while saving netcdf file opened using xr.open_mfdataset with lock=None 597657663
623402330 https://github.com/pydata/xarray/issues/3961#issuecomment-623402330 https://api.github.com/repos/pydata/xarray/issues/3961 MDEyOklzc3VlQ29tbWVudDYyMzQwMjMzMA== markelg 6883049 2020-05-04T11:12:25Z 2020-05-06T08:47:46Z CONTRIBUTOR

Thanks @jessicaaustin. We have run into the same issue. Setting lock=False works, but as hdf5 is not thread safe, we are not sure if this could have unexpected consequences.

Edit: Actually, I have checked, and the hdf5 version we are using (from conda-forge) is build in thread safe mode. This means that concurrent reads are possible, and that the lock=False in open_mfdataset would be safe. In fact it is more efficient as it does not make sense to handle locks if hdf5 is already thread safe. Am I right?

 
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   Hangs while saving netcdf file opened using xr.open_mfdataset with lock=None 597657663

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