Runtime segmentation fault using conda-forge netcdf4

[ngoldbaum]

This is very similar to #44.

The following code triggers a seg fault using netcdf4 1.4.1 from conda-forge (build py37h08833f9_0):

In [1]: from netCDF4 import Dataset

In [2]: Dataset('disk_mhdhdf5_chk_0020')
Assertion failed: (var->varid == grp->vars.nelems), function nc4_vararray_add, file /opt/concourse/worker/volumes/live/fc562f18-66b3-463b-5e64-a8624403e593/volume/libnetcdf_1536427225238/work/libsrc4/nc4var.c, line 431.

The file that triggers this is available here: http://use.yt/upload/4e49c548

Note that this is not a valid netcdf4 file. We hit this because yt will try to load random hdf5 files as netcdf4 files as a means to test if a given hdf5 file is a valid netcdf4 file.

Note that if I install netcdf4 from homebrew and the python bindings from pip, I get a RuntimeError and not a hard crash of the interpreter:

In [1]: from netCDF4 import Dataset

In [2]: Dataset('disk_mhdhdf5_chk_0020')
---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-2-a67635ee387f> in <module>()
----> 1 Dataset('disk_mhdhdf5_chk_0020')

netCDF4/_netCDF4.pyx in netCDF4._netCDF4.Dataset.__init__()

netCDF4/_netCDF4.pyx in netCDF4._netCDF4._get_vars()

netCDF4/_netCDF4.pyx in netCDF4._netCDF4._ensure_nc_success()

RuntimeError: NetCDF: Variable not found

[ngoldbaum]

maybe @isuruf knows of another compile-time flag conda-forge should be using to turn off these checks?

[isuruf]

What's the libnetcdf version?

[ngoldbaum]

Ah sorry, didn't realize they were separate packages:

libnetcdf                 4.6.1                h4e6abe9_1

[isuruf]

You need to remove https://github.com/conda-forge/libnetcdf-feedstock/blob/master/recipe/build.sh#L45-L46 and https://github.com/conda-forge/libnetcdf-feedstock/blob/master/recipe/build.sh#L69-L70

[ngoldbaum]

OK, I don't know enough about cmake to feel confident to propose that pull request and work out any issues that happen as a result.

[ngoldbaum]

@conda-forge-admin please rerender

[conda-forge-linter]

Hi! This is the friendly automated conda-forge-webservice.

I just wanted to let you know that I rerendered the recipe in #62.

[ngoldbaum]

This is fixed with the latest build.