How to fix segfaulting error with pyvista version 0.34.1

dolfinx
1

I am a newbie to dolfinx and ran into an error with pyvista.
I pull the dolfinx/lab image and create a container. Note that
ipyvtklink has been installed. In testing pyvista

from pyvista import examples
mesh = examples.download_st_helens()
warped = mesh.warp_by_scalar(‘Elevation’)
surf = warped.extract_surface().triangulate()
surf = surf.decimate_pro(0.75) # reduce the density of the mesh by 75%
surf.plot(cmap=‘gist_earth’)

Getting the following error.

/usr/local/lib/python3.9/dist-packages/pyvista/plotting/plotting.py:115: UserWarning:
This system does not appear to be running an xserver.
PyVista will likely segfault when rendering.

Try starting a virtual frame buffer with xvfb, or using
pyvista.start_xvfb()

warnings.warn(
/usr/local/lib/python3.9/dist-packages/pyvista/jupyter/notebook.py:60: UserWarning: Failed to use notebook backend:

Please install ipyvtklink to use this feature: GitHub - Kitware/ipyvtklink: 🔗 minimalist ipywidget to interface with any Python vtkRenderWindow

Falling back to a static output.
warnings.warn(
ERROR:root:bad X server connection. DISPLAY=
2022-04-24 22:11:04.402 ( 40.906s) [ E6510C00]vtkXOpenGLRenderWindow.:464 ERR| vtkXOpenGLRenderWindow (0x559e810): bad X server connection. DISPLAY=

2

The reason for this segfault is that you can’t run gui applications by default inside a docker container. This is what is meant by

This provides a detailed description of how one might go about enabling gui applications to be run inside a docker container.

If you happen to use Ubuntu (it may also work for some other linux operating systems), following this post allowed me to use PyVista from within a docker container, without using JupyerLab. Note: I use Ubuntu 20.04.

Alternatively, you can use PyVista from within a docker container through JupyterLab, see here . I haven’t actually tried this myself but should work well.

3

If you are running (like me) the container in VS Code or something that is not jupyter lab, try this, that worked for my case:
https://fenicsproject.discourse.group/t/cannot-display-pyvista-plot-in-docker-container/8202/9