using alt_hdf5_dir causes XDMF build to fail to find HDF5 headers

[BenWibking]

On macOS Sequoia 15.1, I tried to build VisIt 3.4RC from source, but it fails due to being unable to build HDF5 1.8 with the version of XCode supported on this macOS.

I then built HDF5 1.14 with the --with-default-api-version=v18 flag and set --alt_hdf5_dir to point to install directory of my custom HDF5 build.

But when building the XDMF dependency, it fails, saying it's unable to find H5public.h (which I've checked is present in my custom HDF5 install):

/Users/benwibking/visit/src/tools/dev/scripts/Xdmf/libsrc/XdmfHDFSupport.h:30:10: fatal error: 'H5public.h' file not found
   30 | #include "H5public.h"
      |          ^~~~~~~~~~~~
2 warnings and 1 error generated.
make[2]: *** [libsrc/CMakeFiles/Xdmf.dir/XdmfArray.o] Error 1
make[1]: *** [libsrc/CMakeFiles/Xdmf.dir/all] Error 2
make: *** [all] Error 2
Xdmf build failed. Giving up
Unable to build or install Xdmf. Bailing out.

Build visit command:

./build_visit --blosc2 --boxlib --hdf5 --alt-hdf5-dir $HOME/hdf5_visit_install --xdmf --makeflags -j8

Full build_visit_log:
build_visit_log.tar.gz

For reference, this build_visit command (including HDF5 but excluding XDMF) produces a successful build:

env CXXFLAGS="-DH5_USE_18_API" ./build_visit --blosc2 --boxlib --hdf5 --alt-hdf5-dir $HOME/hdf5_visit_install --adios2 --makeflags -j8

[JustinPrivitera]

Perhaps one of our Mac developers will be able to help @cyrush @markcmiller86

[BenWibking]

Ok, it looks like XDMF directly manipulates internal HDF5 data structures, so this won't work. In principle, there are patches for XDMF that should work around the problem:

• https://github.com/spack/spack/blob/cd2d6a6397a34244ee9af3f102be801cd0f14d84/var/spack/repos/builtin/packages/paraview/vtk-xdmf2-hdf51.13.1.patch
• https://github.com/spack/spack/blob/cd2d6a6397a34244ee9af3f102be801cd0f14d84/var/spack/repos/builtin/packages/paraview/vtk-xdmf2-hdf51.13.2.patch

I can then get build_visit to use a newer HDF5 version by instead setting these env vars:

env HDF5_COMPATIBILITY_VERSION="1.13" HDF5_FILE="hdf5-1.13.0.tar.bz2" HDF5_VERSION="1.13.0" HDF5_DIR="hdf5-1.13.0" ./build_visit --blosc2 --boxlib --hdf5 --adios2 --xdmf --makeflags -j16

I've applied the patches (modulo some path changes) successfully, but the XDMF build still fails for some reason I can't diagnose. It looks like this issue is much more complicated than I thought...

[markcmiller86]

@BenWibking when you went back and started to rebuild with HDF5-1.14, did you blow away everything and start afresh? You need to. I did a build of VisIt with HDF5-1.14.4 on Linux but just went and looked and I missed Xdmf. I will try to build there with Xdmf also and see if I run into same issues you have. Can you wait a day or two for me to report back?

[markcmiller86]

Ok, I was able to get Xdmf 2.1.1 to compile with HDF5-1.14.3. The problem is the H5FD_class_t data structure has changed in HDF5 versions. And, in earlier versions, that data structure was not versioned. If looks like that part of Xdmf has been modified on a few occasions to handle various versions of HDF5. Here is a patch that works for HDF5-1.14 but probably will not work for 1.12 and/or 1.10...

XdmfH5Driver.cxx.patch.gz

Copy the above file to top Xdmf dir, unzip it and run the command patch -p0 < XdmfH5Driver.cxx.patch

[BenWibking]

That worked, thanks!