update HDF5 Git URL

For those autobuilding the HDF5 library itself, the HDF Group thankfully moved to community-friendly development by moving to GitHub. This broke the HDF5 download however, so we updated the URL.

We also corrected CMake script to disallow in-source builds, which are deprecated by CMake and just make a big mess of your directories.

autobuild hdf5: also autobuild if HDF5 configure test fails

CI: all use autobuild, break tasks into flows (parallel runs)

vendor CMake 3.18.3 FindHDF5.cmake

To greatly increase robustness of FindHDF5, vendor CMake 3.18.3. This is because HDF Group is changing HDF5 library names, and sometimes new bugs are introduced by Kitware when others are fixed.

workaround HDFGroup HDF5 autobuild bugs

beta: workaround for HDFGroup HDF5 CMake bugs to allow HDF5 autobuild.
Tested with

• Intel Fortran (Windows)
• GCC (Windows, Linux)

improve HDF5 build script

deduced that HDF5's CMakeLists has problems including

• cannot always build in parallel
• rebuild avoidance is completely broken

as a result, workaround these issues by using one-time install scripts. Other projects have forked HDF5 to workaround these issues internally but we would like to avoid yet another HDF5 fork.

HDF5 library manual build scripts

If necessary, we provide two ways to build HDF5.

• CMake: the CMAKE_INSTALL_PREFIX variable defaults to ~/libs/hdf5-*
• Python

The autobuild option was too shaky as HDF5 itself has shaky CMake script that is not reliable enough to use the technique we use for libraries like Lapack, Scalapack and Mumps.

add h5fortran_BUILD_TESTING variable

this allows easier control from externalProject as option() (here implicit) overrides the CMAKE_ARGS

autobuild hdf5: limit parallel build

CMake is more correct about using physical CPU core count than GNU Make, so limit with CMake's count when possible. Otherwise the PC can nearly freeze while building HDF5.

HDF5 autobuild option

Using the HDF Group HDF5 Git repo, allow autobuilding a recent release of HDF5 if the system HDF5 library is not available or not working

add BUILD_TESTING option, tighten up HDF5::HDF5 target

v3.1.1

doc