Issue with gmshio import

Errors
1

I’m working with dolfinx via Google Colab, and I’m having some problems with dolfinx.io.gmshio.

I have gmsh installed in the notebook, and I’m trying to use the extract_geometry and extract_topology_and_markers methods. However, I get AttributeError: module 'dolfinx.io.gmshio' has no attribute 'extract_geometry'.

When calling gmshio._has_gmsh, the console returns False, and gmshio.__all__ only gives the list ['cell_perm_array', 'ufl_mesh'], where "extract_topology_and_markers", "extract_geometry", "model_to_mesh", "read_from_msh" are missing.

Here are the blocks I’m running on Colab:

%%capture
try:
    import dolfinx
except ImportError:
    !wget "https://fem-on-colab.github.io/releases/fenicsx-install-real.sh" -O "/tmp/fenicsx-install.sh" && bash "/tmp/fenicsx-install.sh"
    import dolfinx

!pip install -q gmsh

import gmsh
from dolfinx.io import gmshio

Any idea on why is this happening?
Thanks in advance.

2

As you can see from the source code: dolfinx/gmshio.py at main · FEniCS/dolfinx · GitHub _has_gmsh only checks if one can import gmsh.
What is the message you get if you call import gmsh?

3

Hi dokken,

When I run import gmsh the cell runs successfully. Moreover, running the lines manually for checking that one can import gmsh:

try:
    import gmsh
    _has_gmsh = True
except ModuleNotFoundError:
    _has_gmsh = False

gives _has_gmsh with _has_gmsh==True

4

I would have to ask @francesco-ballarin for his thoughts. I dont know much about how the installation process for colab is.

5

Okay. I’ll be looking forward to your answer. Thanks!

6

Make sure to install the gmsh provided by fem on colab BEFORE installing FEniCSx

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