[CMake] Use hdf target as opposed to HDF5_CXX_LIBRARIES

[KrisThielemans]

Using targets is recommended, as it will add compiler flags etc as needed. It might also resolve
conda-forge/stir-feedstock#149, as with this update, STIRTargets.cmake contains hdf5::hdf5_cpp as opposed to explicit filenames.

This fix was recommended by @traversaro at #general > dependency on $BUILD_PREFIX/...libpthread.so problem @ 💬

[KrisThielemans]

hmmm. The "demos" that link against STIR have

[435/606] Linking CXX executable src/examples/C++/using_STIR_LOCAL/demo1
FAILED: [code=1] src/examples/C++/using_STIR_LOCAL/demo1 
 && /usr/bin/g++ -O3 -DNDEBUG -ffast-math -Wl,--dependency-file=src/examples/C++/using_STIR_LOCAL/CMakeFiles/demo4_obj_fun.dir/link.d src/CMakeFiles/stir_registries.dir/IO/IO_registries.cxx.o src/CMakeFiles/stir_registries.dir/buildblock/buildblock_registries.cxx.o src/CMakeFiles/stir_registries.dir/recon_buildblock/recon_buildblock_registries.cxx.o src/CMakeFiles/stir_registries.dir/data_buildblock/data_buildblock_registries.cxx.o src/CMakeFiles/stir_registries.dir/Shape_buildblock/Shape_buildblock_registries.cxx.o src/CMakeFiles/stir_registries.dir/modelling_buildblock/modelling_registries.cxx.o src/CMakeFiles/stir_registries.dir/spatial_transformation_buildblock/spatial_transformation_registries.cxx.o src/CMakeFiles/stir_registries.dir/scatter_buildblock/scatter_registries.cxx.o src/examples/C++/using_STIR_LOCAL/CMakeFiles/demo4_obj_fun.dir/demo4_obj_fun.cxx.o -o src/examples/C++/using_STIR_LOCAL/demo4_obj_fun  -Wl,-rpath,/usr/lib/x86_64-linux-gnu/hdf5/serial:/home/runner/work/STIR/STIR/install/lib:  src/analytic/FBP3DRP/libanalytic_FBP3DRP.a  src/analytic/FBP2D/libanalytic_FBP2D.a  src/analytic/SRT2D/libanalytic_SRT2D.a  src/analytic/SRT2DSPECT/libanalytic_SRT2DSPECT.a  src/analytic/GRD2D/libanalytic_GRD2D.a  src/analytic/DDSR2D/libanalytic_DDSR2D.a  src/iterative/OSMAPOSL/libiterative_OSMAPOSL.a  src/iterative/KOSMAPOSL/libiterative_KOSMAPOSL.a  src/iterative/OSSPS/libiterative_OSSPS.a  src/scatter_buildblock/libscatter_buildblock.a  src/Shape_buildblock/libShape_buildblock.a  src/eval_buildblock/libeval_buildblock.a  src/buildblock/libstir_buildblock.a  /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so  /home/runner/work/STIR/STIR/install/lib/libparallelproj_c.so.1.7.3 && :
/usr/bin/ld: src/buildblock/libstir_buildblock.a(GEHDF5Wrapper.cxx.o): undefined reference to symbol 'H5check_version@@HDF5_SERIAL_1.8.7'
/usr/bin/ld: /lib/x86_64-linux-gnu/libhdf5_serial.so.103: error adding symbols: DSO missing from command line

I also see this on my machine, including for lm_to_projdata

[KrisThielemans]

Multiple possible causes:

• When compiling GEHDF5Wrapper.cxx, an hdf5.h incompatible with the rest is found
• The target is incomplete. In particular, adding libhdf5.so to the linker line makes this problem go away.

On my system, when using a conda-forge hdf5, adding

    cmake_print_properties(
      TARGETS hdf5::hdf5_cpp hdf5::hdf5 HDF5::HDF5
      PROPERTIES LOCATION INTERFACE_INCLUDE_DIRECTORIES IMPORTED_LINK_INTERFACE_LIBRARIES IMPORTED_LINK_DEPENDENT_LIBRARIES LINK_INTERFACE_LIBRARIES
      )

and using -DHDF5_FIND_DEBUG=ON, I see

- HDF5 CXX compiler wrapper is unable to compile a minimal HDF5 program.
-- HDF5_DIR: HDF5_DIR-NOTFOUND
-- HDF5_DEFINITIONS: 
-- HDF5_INCLUDE_DIRS: /home/sirfuser/mambaforge/envs/stirdev/include
-- HDF5_LIBRARIES: /home/sirfuser/mambaforge/envs/stirdev/lib/libhdf5_cpp.so;/home/sirfuser/mambaforge/envs/stirdev/lib/libhdf5.so
-- HDF5_HL_LIBRARIES: 
-- HDF5_CXX_DEFINITIONS: 
-- HDF5_CXX_INCLUDE_DIR: /home/sirfuser/mambaforge/envs/stirdev/include
-- HDF5_CXX_INCLUDE_DIRS: /home/sirfuser/mambaforge/envs/stirdev/include
-- HDF5_CXX_LIBRARY: 
-- HDF5_CXX_LIBRARIES: /home/sirfuser/mambaforge/envs/stirdev/lib/libhdf5_cpp.so;/home/sirfuser/mambaforge/envs/stirdev/lib/libhdf5.so
-- HDF5_CXX_HL_LIBRARY: 
-- HDF5_CXX_HL_LIBRARIES: 
-- Defined targets (if any):
-- ... hdf5::hdf5_cpp
-- 
 Properties for TARGET hdf5::hdf5_cpp:
   hdf5::hdf5_cpp.LOCATION = "/home/sirfuser/mambaforge/envs/stirdev/lib/libhdf5_cpp.so"
   hdf5::hdf5_cpp.INTERFACE_INCLUDE_DIRECTORIES = "/home/sirfuser/mambaforge/envs/stirdev/include"
   hdf5::hdf5_cpp.IMPORTED_LINK_INTERFACE_LIBRARIES = <NOTFOUND>
   hdf5::hdf5_cpp.IMPORTED_LINK_DEPENDENT_LIBRARIES = <NOTFOUND>
   hdf5::hdf5_cpp.LINK_INTERFACE_LIBRARIES = <NOTFOUND>

 No such TARGET "hdf5::hdf5" !

 Properties for TARGET HDF5::HDF5:
   HDF5::HDF5.LOCATION = <NOTFOUND>
   HDF5::HDF5.INTERFACE_INCLUDE_DIRECTORIES = "/home/sirfuser/mambaforge/envs/stirdev/include"
   HDF5::HDF5.IMPORTED_LINK_INTERFACE_LIBRARIES = <NOTFOUND>
   HDF5::HDF5.IMPORTED_LINK_DEPENDENT_LIBRARIES = <NOTFOUND>
   HDF5::HDF5.LINK_INTERFACE_LIBRARIES = <NOTFOUND>

This is the usual case where if there is no HDF5Config.cmake (and there isn't one in conda (WIP: conda-forge/hdf5-feedstock#255) nor APT), and there is no h5c++ (there isn't one in conda-forge unless you also use cxx-compiler), FindHDF5.cmake fails miserably. Usually, it fails because it doesn't know about depending libraries such as libz. Here it seems a bug in FindHDF5.cmake, as HDF5_CXX_LIBRARIES does have libhdf5.so, but the target doesn't.

sigh

[KrisThielemans]

Apologies, I was printing the old LINK_INTERFACE_LIBRARIES as opposed to INTERFACE_LINK_LIBRARIES

Properties for TARGET hdf5::hdf5_cpp:
   hdf5::hdf5_cpp.LOCATION = "/home/sirfuser/mambaforge/envs/stirdev/lib/libhdf5_cpp.so"
   hdf5::hdf5_cpp.INTERFACE_INCLUDE_DIRECTORIES = "/home/sirfuser/mambaforge/envs/stirdev/include"
   hdf5::hdf5_cpp.IMPORTED_LINK_INTERFACE_LIBRARIES = <NOTFOUND>
   hdf5::hdf5_cpp.IMPORTED_LINK_DEPENDENT_LIBRARIES = <NOTFOUND>
   hdf5::hdf5_cpp.INTERFACE_LINK_LIBRARIES = <NOTFOUND>

 No such TARGET "hdf5::hdf5" !

 Properties for TARGET HDF5::HDF5:
   HDF5::HDF5.LOCATION = <NOTFOUND>
   HDF5::HDF5.INTERFACE_INCLUDE_DIRECTORIES = "/home/sirfuser/mambaforge/envs/stirdev/include"
   HDF5::HDF5.IMPORTED_LINK_INTERFACE_LIBRARIES = <NOTFOUND>
   HDF5::HDF5.IMPORTED_LINK_DEPENDENT_LIBRARIES = <NOTFOUND>
   HDF5::HDF5.INTERFACE_LINK_LIBRARIES = "/home/sirfuser/mambaforge/envs/stirdev/lib/libhdf5_cpp.so;/home/sirfuser/mambaforge/envs/stirdev/lib/libhdf5.so"

When using the system (APT) version, and h5c++ installed

-- HDF5: Using hdf5 compiler wrapper to determine CXX configuration
-- HDF5_DIR: HDF5_DIR-NOTFOUND
-- HDF5_DEFINITIONS: -D_FORTIFY_SOURCE=2
-- HDF5_INCLUDE_DIRS: /usr/include/hdf5/serial
-- HDF5_LIBRARIES: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/home/sirfuser/devel/install/lib/libz.a;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_HL_LIBRARIES: 
-- HDF5_CXX_DEFINITIONS: -D_FORTIFY_SOURCE=2
-- HDF5_CXX_INCLUDE_DIR: 
-- HDF5_CXX_INCLUDE_DIRS: /usr/include/hdf5/serial
-- HDF5_CXX_LIBRARY: 
-- HDF5_CXX_LIBRARIES: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/home/sirfuser/devel/install/lib/libz.a;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
-- HDF5_CXX_HL_LIBRARY: 
-- HDF5_CXX_HL_LIBRARIES: 
-- Defined targets (if any):
-- ... hdf5::hdf5_cpp
-- 
 Properties for TARGET hdf5::hdf5_cpp:
   hdf5::hdf5_cpp.LOCATION = "/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so"
   hdf5::hdf5_cpp.INTERFACE_INCLUDE_DIRECTORIES = "/usr/include/hdf5/serial"
   hdf5::hdf5_cpp.IMPORTED_LINK_INTERFACE_LIBRARIES = <NOTFOUND>
   hdf5::hdf5_cpp.IMPORTED_LINK_DEPENDENT_LIBRARIES = <NOTFOUND>
   hdf5::hdf5_cpp.INTERFACE_LINK_LIBRARIES = <NOTFOUND>

 No such TARGET "hdf5::hdf5" !

 Properties for TARGET HDF5::HDF5:
   HDF5::HDF5.LOCATION = <NOTFOUND>
   HDF5::HDF5.INTERFACE_INCLUDE_DIRECTORIES = "/usr/include/hdf5/serial"
   HDF5::HDF5.IMPORTED_LINK_INTERFACE_LIBRARIES = <NOTFOUND>
   HDF5::HDF5.IMPORTED_LINK_DEPENDENT_LIBRARIES = <NOTFOUND>
   HDF5::HDF5.INTERFACE_LINK_LIBRARIES = "/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5_cpp.so;/usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/home/sirfuser/devel/install/lib/libz.a;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so"

So, it seems we would have more chance with using HDF5::HDF5.

[KrisThielemans]

I've created https://gitlab.kitware.com/cmake/cmake/-/issues/27379