HDF error when atempting to read netCDF file using netCDF4 module in python

Question

When I try to open a netcdf4 file containing tropomi data of the ESA copernicus mission, I run into the following error.

[Errno -101] NetCDF: HDF error: b'5P_NRTI_L2__CO_____20190505T104819_20190505T105319_08073_01_010301_20190505T124936.nc'

the code that I use is simply

import netCDF4
rootgrp = netCDF4.Dataset(5P_NRTI_L2__CO_____20190505T104819_20190505T105319_08073_01_010301_20190505T124936.nc, "r",format="NETCDF4")

If i re-install netCDF4 or shutdown my computer a few times it succeeds in reading the file again (though this trick does not always work). But it's just a matter of time before it starts failing again. Does anyone have any idea what causes this problem? I work under Ubuntu 18.

Yes, the error also persists after restarting my computer. So it is probably not that. — Daan
– Daan, Commented May 8, 2019 at 8:12

mrzo · Accepted Answer · 2019-05-06 15:34:56Z

1

python-netCDF4 might be buggy, here is an example with another library which normally works for me (https://github.com/shoyer/h5netcdf):

import h5netcdf.legacyapi as netCDF4

with netCDF4.Dataset('mydata.nc', 'w') as ds:
   ...

answered May 6, 2019 at 15:34

mrzo

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1 Comment

Daan Over a year ago

This works. If it breaks down over time in the same way as the netCDF4 package I will report back.

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