Unify Chaste and PyChaste docker images

[kwabenantim]

Summary

Pros:

• One docker image for everything Chaste.
• Using dependencies from the Ubuntu repository that work together instead of trying to resolve conda-forge dependency conflicts for PyChaste (although this will still need to be done for the PyChaste conda package).

Cons:

• Larger image: chaste-docker (~2.2 GB) + pychaste-docker(~700 MB) - overlapping dependencies.
• Need to work out what happens when a container launches. For the PyChaste image, it automatically launches a Jupyter notebook.

[kwabenantim]

TODO

• Create image with pychaste and check if resulting size is reasonable.
• Maintain current terminal interface as default and add extra instructions for launching with a Jupyter notebook e.g. adding an extra environment variable.

[kwabenantim]

Note from discussion

Find out if theres's a suitable workaround for removing PyChaste dependency on Xvfb.

Potential alternatives to Xvfb

EGL (headless rendering on GPU or CPU)

• EGL support defaults to TRUE in VTK build options for Linux; may already be supported in standard Ubuntu VTK build (need to check this).
• Pre-built VTK with EGL support available from conda-forge.
• Building a custom VTK with EGL support (VTK_OPENGL_HAS_EGL=TRUE):
  • Default to headless rendering mode (VTK_DEFAULT_RENDER_WINDOW_HEADLESS=TRUE).
  • Optionally, disable normal X rendering mode (VTK_USE_X=FALSE).

OSMesa (headless rendering on CPU)

• Pre-built VTK with OSMesa support available from conda-forge.
• Building custom VTK with OSMesa support (VTK_OPENGL_HAS_OSMESA=TRUE):
  • Default to headless rendering mode (VTK_DEFAULT_RENDER_WINDOW_HEADLESS=TRUE).
  • Optionally, disable normal X rendering mode (VTK_USE_X=FALSE).

Switching to headless rendering
With EGL/OSMesa support enabled,

• Set an environment variable to use off-screen rendering
  • VTK_DEFAULT_OPENGL_WINDOW=vtkEGLRenderWindow
  • VTK_DEFAULT_OPENGL_WINDOW=vtkOSOpenGLRenderWindow
• Alternatively, perform all PyChaste rendering off-screen only [C++ example] [Python example]

VTK 9.4+
From VTK 9.4,

On Linux, VTK will now automatically fallback to EGL when there is no X display present or it is not capable of OpenGL. In case the system is not configured for EGL, VTK will fallback to OSMesa.

Standard VTK package now has headless rendering support

Starting from VTK 9.4, scheduled for November, 2024, your project can rely on just a single vtk package for onscreen, offscreen and headless rendering.

VTK.js or VTK.wasm

Does rendering directly in the browser using WebGL or wasm .

[bdevans]

Further notes

Presently the chaste/base image without pychaste is 3.4GB. With pychaste (built with the changes in https://github.com/Chaste/chaste-docker/tree/pychaste) this rises to 10GB.

Suggestion: create a new CI workflow to build chaste/base-pychaste as a separate image from chaste/base and from there build chaste/develop and chaste/develop-pychaste etc.