Re: [python-users] netCDF4/h5Py in the same Python 3 script

  • To: Aaron Funk <afunk@xxxxxxxx>
  • Subject: Re: [python-users] netCDF4/h5Py in the same Python 3 script
  • From: Ryan May <rmay@xxxxxxxx>
  • Date: Fri, 24 Jan 2020 13:36:44 -0700

I'm not aware of any reason those two modules should interfere--provided
they're using the same libhdf5. Can you provide the full traceback and text
of the error? Otherwise we're just shooting in the dark here.

I can say that the following code works without error for me on macOS 10.15
and Python 3.8, all from conda-forge:

from netCDF4 import Dataset
import h5py
import numpy as np

nc = Dataset('', 'w')
nc.createDimension('x', 10)
nc.createDimension('y', 20)
var = nc.createVariable('test', np.float64, ('x', 'y'))
var[:] = np.arange(200.).reshape(10, 20)

Does this code fail for you?


On Wed, Jan 22, 2020 at 10:45 AM Aaron Funk <afunk@xxxxxxxx> wrote:

> Hi all,
> I'm new to Python and reaching out here for information on an issue I ran
> into. My issue is that I'm unable to close a netCDF4 object and write a
> file to disk without error if I import h5py and netcdf4 in the same script.
> If I remove the "import h5py" line, the script works fine.
> Is this a known/common issue? Is there a way in which I can use both h5py
> and netcdf4 modules in the same Python script without generating these
> types of errors? What's the best workaround for this?
> I'm not providing an example script here, but some environment details are
> below. I can provide other info as needed.
> Environment:
> CentOS 7
> Python 3.6
> pip virtual environment with h5py and netcdf4 and dependencies installed.
> HDF5 and netCDF-4 C compiled from scratch.
> Thanks,
> Aaron Funk
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Ryan May, Ph.D.
Software Engineer
Boulder, CO
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