Ubuntu 24.04 support

[mirams]

Official release on Thursday.

• Update debs
• update instructions on https://chaste.github.io/docs/installguides/ubuntu-package/
• a docker set up to run Chaste on 24.04
• list any failures on here
• Fix them all!
• Update https://chaste.github.io/docs/installguides/dependency-versions/
  • https://github.com/Chaste/Chaste.github.io/pull/88
• Make this new one the main testing environment and update portability builds
  • Add portability dependencies for Ubuntu 24.04 dependency-modules#68.

Dependency versions:

• Boost 1.83
• HDF5 1.10.10
• Parmetis 4.0.3 (supported)
• PETSc 3.19
• Sundials 6.4.1
• VTK 9.1.0 (supported)
• Xerces-C 3.2.4 (supported)
• XSD 4.0.0 (supported)

Feel free to update list above @fcooper8472 @kwabenantim @ptheywood @jmpf

[bdevans]

When building the chaste/develop image from noble branch again with the latest ubuntu:noble image as a base, I get the following warnings which are set to error (so it fails):

[  1%] Generating Build Config and Version Info
-- Found Git: /usr/bin/git
-- Current Chaste Git Revision = f2ff7ee. Chaste Modified = false
-- updating buildtime...
CMake Warning (dev) at /home/chaste/src/cmake/Modules/ChasteGenerateVersionAndBuildInfo.cmake:89 (find_package):
Policy CMP0148 is not set: The FindPythonInterp and FindPythonLibs modules
are removed.  Run "cmake --help-policy CMP0148" for policy details.  Use
the cmake_policy command to set the policy and suppress this warning.

This warning is for project developers.  Use -Wno-dev to suppress it.

[  1%] Building CXX object global/CMakeFiles/chaste_global.dir/src/Citations.cpp.o
[  1%] Building CXX object global/CMakeFiles/chaste_global.dir/src/Debug.cpp.o
[  1%] Building CXX object global/CMakeFiles/chaste_global.dir/src/CommandLineArguments.cpp.o
[  1%] Building CXX object global/CMakeFiles/chaste_global.dir/src/Exception.cpp.o
[  1%] Building CXX object global/CMakeFiles/chaste_global.dir/src/ExecutableSupport.cpp.o
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/FileFinder.cpp.o
[  2%] Linking CXX static library libtestglobal.a
[  2%] Built target testglobal
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/GetCurrentWorkingDirectory.cpp.o
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/LogFile.cpp.o
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/MathsCustomFunctions.cpp.o
/home/chaste/src/global/src/ExecutableSupport.cpp:115:13: error: PETSC_NULL is deprecated, use PETSC_NULLPTR instead (since version 3.19) [-Werror]
115 |     PETSCEXCEPT(PetscInitialize(pArgc, pArgv, PETSC_NULL, PETSC_NULL));
|             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/chaste/src/global/src/ExecutableSupport.cpp:115:13: error: PETSC_NULL is deprecated, use PETSC_NULLPTR instead (since version 3.19) [-Werror]
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/OutputDirectoryFifoQueue.cpp.o
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/OutputFileHandler.cpp.o
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/PosixPathFixer.cpp.o
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/ProgressReporter.cpp.o
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/RandomNumberGenerator.cpp.o
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/TimeStepper.cpp.o
[  2%] Linking CXX static library libtestode.a
[  2%] Built target testode
[  2%] Building CXX object global/CMakeFiles/chaste_global.dir/src/Warnings.cpp.o
cc1plus: all warnings being treated as errors
make[2]: *** [global/CMakeFiles/chaste_global.dir/build.make:139: global/CMakeFiles/chaste_global.dir/src/ExecutableSupport.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
[  2%] Linking CXX static library libtestpde.a
[  2%] Built target testpde
make[1]: *** [CMakeFiles/Makefile2:3650: global/CMakeFiles/chaste_global.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[  2%] Linking CXX shared library dynamic/libDynamicallyLoadableLr91.so
[  2%] Built target DynamicallyLoadableLr91
[  2%] Linking CXX static library libtestcell_based.a
[  2%] Built target testcell_based
make: *** [Makefile:166: all] Error 2

I have also tried building Chaste 2024.1 with noble and the tests get stuck at TestVisualizingWithParaviewTutorial (see #238). A few other tests also currently fail.

[bdevans]

After turning off Chaste_ERROR_ON_WARNING and building the latest code from develop on the noble base image, then running the Continuous tests with 1 core, I get the following:

Total Test time (real) = 614.76 sec

The following tests FAILED:
          3 - TestCitations (Failed)
         78 - TestQuadraticMesh (Failed)
         93 - TestVtkMeshReader (Subprocess aborted)
        113 - TestXmlMeshWriters (Failed)
        175 - TestHdf5Converters (Subprocess aborted)
        190 - TestCompressibleNonlinearElasticitySolver (Failed)
        198 - TestStokesFlowSolver (Failed)
        262 - TestNodeBasedCellPopulation (Failed)
        290 - TestOnLatticeSimulationWithPottsBasedCellPopulation (Failed)
        367 - TestMajorAirwaysCentreLinesCleaner (Subprocess aborted)
        382 - TestBidomainProblem (Failed)
        420 - TestMonodomainProblem (Failed)
        432 - TestPostProcessingWriter (Subprocess aborted)

[kwabenantim]

Canonical releases Ubuntu 24.04 LTS Noble Numbat

[fcooper8472]

• Ubuntu 22.04 PETSC 3.19.6 compiler warnings #263
• Ubuntu 24.04 PETSC citation update #264

It looks as though it MAY just be these two. As far as I can tell, the other tests that are failing are all to do with the VTK error (#249)

[fcooper8472]

There are still compiler warnings being emitted that relate to:

• Create GitHub runner docker images for newer Ubuntus #197 Test Chaste compatibility with newer Ubuntus #198 Ignore some specific -Wmaybe-uninitialized c_vector warnings #231

One specific issue relates to a weird interaction between std::vector and ublas::c_vector when the c_vector has dimension 1:

• Broken interaction between std::vector and ublas::c_vector #280