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issue 1

  • HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) · 5 ✖

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  • NONE · 5 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1483473963 https://github.com/pydata/xarray/issues/7549#issuecomment-1483473963 https://api.github.com/repos/pydata/xarray/issues/7549 IC_kwDOAMm_X85YbAQr gewitterblitz 13985417 2023-03-24T21:58:38Z 2023-03-24T21:58:38Z NONE

Thanks, @trexfeathers. I had the same problem of HDF5 DIAG warnings after upgrading to xarray v2023.3.0 yesterday. Your diagnosis in SciTools/iris#5187 helped isolate the issue with libnetcdf v4.9.1. Downgrading libnetcdf to v4.8.1 resulted in no HDF5 warnings.

 
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   HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) 1596115847
1461777692 https://github.com/pydata/xarray/issues/7549#issuecomment-1461777692 https://api.github.com/repos/pydata/xarray/issues/7549 IC_kwDOAMm_X85XIPUc pp-mo 2089069 2023-03-09T10:43:50Z 2023-03-09T10:43:50Z NONE

@trexfeathers Before v1.6.1, I believe

Oops, fixed.

 
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   HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) 1596115847
1461751910 https://github.com/pydata/xarray/issues/7549#issuecomment-1461751910 https://api.github.com/repos/pydata/xarray/issues/7549 IC_kwDOAMm_X85XIJBm pp-mo 2089069 2023-03-09T10:28:24Z 2023-03-09T10:43:22Z NONE

@pp-mo 👀

See our issues here : https://github.com/SciTools/iris/issues/5187 It does look a lot like the "same" problem. It is specifically related to the use of dask and multi-threading. Here in python-netCDF4 land, we were protected from all of that before netCDF4 v1.6.1, since before that all netcdf operations held the Python GIL so could not be re-entered by threads.

 
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   HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) 1596115847
1461755281 https://github.com/pydata/xarray/issues/7549#issuecomment-1461755281 https://api.github.com/repos/pydata/xarray/issues/7549 IC_kwDOAMm_X85XIJ2R trexfeathers 40734014 2023-03-09T10:30:28Z 2023-03-09T10:30:28Z NONE

before netCDF4 v1.6.2

Before v1.6.1, I believe

 
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   HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) 1596115847
1460606256 https://github.com/pydata/xarray/issues/7549#issuecomment-1460606256 https://api.github.com/repos/pydata/xarray/issues/7549 IC_kwDOAMm_X85XDxUw trexfeathers 40734014 2023-03-08T18:00:35Z 2023-03-08T18:00:35Z NONE

@pp-mo 👀

 
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   HDF5-DIAG warnings calling `open_mfdataset` with more than `file_cache_maxsize` datasets (hdf5 1.12.2) 1596115847

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