VTK reading of files is broken in Jammy

[stephankramer]

This severely breaks CI because Jammy runs the most extensive test suite

Bug is due to vtk non-standard binary AppendedData that newer versions of libexpat1 chokes on, see:

https://bugs.launchpad.net/ubuntu/+source/paraview/+bug/2058415

In particular this comment: https://bugs.launchpad.net/ubuntu/+source/paraview/+bug/2058415/comments/6 pins it down to libexpat1>=2.4.7-1ubuntu0.3
Luckily 2.4.7-1ubuntu0.2 is still available at http://launchpadlibrarian.net/635321776/libexpat1_2.4.7-1ubuntu0.2_amd64.deb
but note that pinning to this version reverts some security CVE fixes (and libexpat1 is used by many parts of the OS) so doing this on your desktop is not recommended.

To get the CI running again I'll push the (not recommended) libexpat1 downgrade workaround to the Jammy baseimage.

For a proper fix vtk needs patching. In particular: https://gitlab.kitware.com/vtk/vtk/-/commit/db8f9efca220c9d16a30958e179abae3379d0011 Note that this affects both vtk7 and vtk9, although vtk9 has been fixed upstream. It's unclear to me at the moment whether Noble's vtk9 version includes this fix yet (bug has been open for a year) or whether Ubuntu or Debian will backport the patch to vtk7.

Assuming the fix has landed/will land soon in Noble, the best way forward is addressing #387

[drhodrid]

Hey @stephankramer -- thanks for looking at this. @angus-g has (late 2024) looked at building Fluidity against more recently libraries with some (but not total) success. We've had to put it down for a while, given a few more urgent G-ADOPT priorities, but the plan at some stage soon will be for Dale to take a look at this and potentially finish things off. From memory, there were a few GAMG issues on newer PETSc (as usual), but nothing else of major concern. We'll need a month or so before we can revisit, but perhaps worth us all chatting over zoom at some stage before planning a route forward.

[stephankramer]

That sounds great. Well, in the mean time at least we're green again!

[stephankramer]

Also I've committed my workaround to the actions Jammy Dockerfile (which gets build and pushed by the CI), not the baseimage - because the action Dockerfile, does an apt update (for good reasons) which undoes the downgrade of libexpat1 (unless you pin it).

[Patol75]

Addressed by #390.