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  • segfault with hdf4 file · 5 ✖

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123111762 https://github.com/pydata/xarray/issues/484#issuecomment-123111762 https://api.github.com/repos/pydata/xarray/issues/484 MDEyOklzc3VlQ29tbWVudDEyMzExMTc2Mg== rabernat 1197350 2015-07-21T00:45:23Z 2015-07-21T00:45:23Z MEMBER

I think I found the issue with netcdf.

python from netCDF4 import Dataset nc = Dataset('MERRA300.prod.assim.inst3_3d_asm_Cp.20140101.hdf') v = nc.variables['SLP'] v.chunking()

gives the segfault. I'll take this issue to netcdf-python.

 
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   segfault with hdf4 file 96185559
123110874 https://github.com/pydata/xarray/issues/484#issuecomment-123110874 https://api.github.com/repos/pydata/xarray/issues/484 MDEyOklzc3VlQ29tbWVudDEyMzExMDg3NA== rabernat 1197350 2015-07-21T00:41:07Z 2015-07-21T00:41:15Z MEMBER

decode_cf=False doesn't help. Still segfaults on open_dataset

 
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   segfault with hdf4 file 96185559
123108405 https://github.com/pydata/xarray/issues/484#issuecomment-123108405 https://api.github.com/repos/pydata/xarray/issues/484 MDEyOklzc3VlQ29tbWVudDEyMzEwODQwNQ== shoyer 1217238 2015-07-21T00:30:28Z 2015-07-21T00:30:28Z MEMBER

You could try loading the dataset with decode_cf=False in open_dataset. That might delay the segfault until later.

 
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   segfault with hdf4 file 96185559
123107777 https://github.com/pydata/xarray/issues/484#issuecomment-123107777 https://api.github.com/repos/pydata/xarray/issues/484 MDEyOklzc3VlQ29tbWVudDEyMzEwNzc3Nw== rabernat 1197350 2015-07-21T00:28:51Z 2015-07-21T00:28:51Z MEMBER

A stack trace shows that these were the last few functions called

/lib64/libnetcdf.so.7(NC4_inq_var_all+0x1e8)[0x7f370c4baea8] /lib64/libnetcdf.so.7(nc_inq_var_chunking+0xb6)[0x7f370c465ae6] /usr/local/anaconda/lib/python2.7/site-packages/netCDF4/_netCDF4.so(+0x1d930)[0x7f3730126930] ...

So I guess that narrows it down a bit.

 
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   segfault with hdf4 file 96185559
123092900 https://github.com/pydata/xarray/issues/484#issuecomment-123092900 https://api.github.com/repos/pydata/xarray/issues/484 MDEyOklzc3VlQ29tbWVudDEyMzA5MjkwMA== shoyer 1217238 2015-07-20T23:35:03Z 2015-07-20T23:35:03Z MEMBER

xray is using netCDF4-python here internally, so I'm surprised the behavior differs. I have not tested reading hdf4 files myself yet, but if netCDF4-python can handle them then we should be able to, as well.

One possible difference is that xray reads lots of metadata when it opens a file, whereas netCDF4-python just opens the file. It's possible that the segfault is triggered by one of these actions, e.g., reading the variable attributes.

My guess is that this is a upstream bug or build issue with the netCDF packages. However, tracking it down may be easier said than done.

 
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   segfault with hdf4 file 96185559

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