Build HDF5 2.x

[kwabenantim]

Supports #106 and #90

[kwabenantim]

Error

CMake Error at /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
  Could NOT find MPI (missing: MPI_C_FOUND) (found version "3.1")
Call Stack (most recent call first):
  /usr/share/cmake-3.22/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
  /usr/share/cmake-3.22/Modules/FindMPI.cmake:1830 (find_package_handle_standard_args)
  /usr/share/cmake-3.22/Modules/CMakeFindDependencyMacro.cmake:47 (find_package)
  /data/uizka/apps/opt/hdf5/2.1.1/cmake/hdf5-config.cmake:124 (find_dependency)
  /usr/share/cmake-3.22/Modules/FindHDF5.cmake:504 (find_package)
  CMakeLists.txt:495 (find_package)

Fix

Use CMake 3.26+ which is the minimum version supported by HDF5 2.0+

Related Issue: #90

[kwabenantim]

Error

CMake Error at CMakeLists.txt:502 (message):
  Hdf5 library found was not build with --enable-parallel, use the HDF5_ROOT
  environment variable to specify a parallel hdf5 library.  Note: include
  dirs are /data/uizka/apps/opt/hdf5/2.1.1/include and libraries are
  hdf5-shared

Fix

HDF5_IS_PARALLEL has been renamed HDF5_PROVIDES_PARALLEL from HDF5 2.0+

https://discourse.cmake.org/t/hdf5-2-0-has-breaking-changes-cmake-doesnt-set-the-hdf5-is-parallel-variable-anymore/15444

[kwabenantim]

HDF5 2.1.1 is now building correctly

https://github.com/Chaste/dependency-modules/actions/runs/26094162213

[Copilot]

Pull request overview

Adds HDF5 2.x support to the custom dependency installer by selecting the newer source archive path and switching 2.x builds from autotools to CMake.

Changes:

• Splits HDF5 archive download handling so 2.x uses a new tag/archive pattern.
• Keeps autotools builds for pre-2.0 versions.
• Adds a CMake build path for HDF5 2.x with MPI/parallel support enabled.

---

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Pull request overview

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Error

...

Implemented in 996bef4: setup_custom.sh now ensures CMake >= 3.26 is available (installs via pip when system CMake is older), so HDF5 2.x consumers aren’t pinned to 3.22.

Error

...

Addressed in 996bef4: HDF5 2.x installs now add a compatibility shim in hdf5-config.cmake that sets HDF5_IS_PARALLEL from HDF5_PROVIDES_PARALLEL for downstream projects still checking the legacy variable.

[kwabenantim]

After suggested adjustments, HDF5 2.x is still building okay

https://github.com/Chaste/dependency-modules/actions/runs/26098620411

[kwabenantim]

This remains tricky because VTK doesn't seem to support HDF5 2.x yet. As of 9.6.2, it hasn't adapted to the new HDF5_PROVIDES_PARALLEL flag.

#17 19.27 -- Found HDF5: hdf5-shared (found version "2.1.1") found components: C HL
#17 19.27 CMake Error at CMake/vtkModule.cmake:6196 (message):
#17 19.27   The variable `HDF5_IS_PARALLEL` was expected to have been available, but
#17 19.27   was not defined.
#17 19.27 Call Stack (most recent call first):
#17 19.27   CMake/vtkModule.cmake:5904 (vtk_module_third_party_external)
#17 19.27   ThirdParty/hdf5/CMakeLists.txt:3 (vtk_module_third_party)

https://docs.vtk.org/en/latest/release_details/9.6.html