2.5.0: Fails to find HDF5

[yurivict]

Describe the bug
This line causes this failure:

-- Unable to determine HDF5 C flags from HDF5 wrapper.
CMake Error at /usr/local/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
  Could NOT find HDF5 (missing: HDF5_LIBRARIES) (found version "1.12.2")
Call Stack (most recent call first):
  /usr/local/share/cmake/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
  /usr/local/share/cmake/Modules/FindHDF5.cmake:1007 (find_package_handle_standard_args)
  CMake/HighFiveTargetDeps.cmake:13 (find_package)
  CMakeLists.txt:63 (include)

hdf5-1.12.2
clang-14
FreeBSD 13.1

[1uc]

I've tried using HighFive as a dependency in a trivial CMake based project. On my particular system a find_package(HighFive) followed by the target_link_libraries(... PUBLIC HighFive) sets the appropriate compiler/linker flags. Therefore, I'm unable to reproduce the issue.

Could you please create a minimal reproducer? And maybe explain why the line you mention is at fault.

[knoepfel]

Is see a similar error when trying to install highfive via Spack:

$ spack install highfive ~mpi ^hdf5 ~mpi
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/pkgconf-1.8.0-ompiatqqad54y2hcr7orar566yw3xmly
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/berkeley-db-18.1.40-nhunv5nlc43jxfcjhprjt3xr7b6lt3h7
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/libiconv-1.16-t5lovvab3mucvhkhun7atgjashyj2yjb
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/zlib-1.2.12-rdxpbj5k3nqwsvdmndim4n6mhjdabfui
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/ncurses-6.2-lkqooz7odlmxte727dkn2a3277o7jnht
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/diffutils-3.8-tap7w6nkh3feut36dyarazjzcpdt4tve
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/readline-8.1-ad4c7fq6tqxju7kopgw3lhmx5o3qvoju
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/bzip2-1.0.8-tg3gwk5jri2hwzlf4oh7wlfun5nsjv6f
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/gdbm-1.19-ob5getbdflin636d3bzs6kjfq4uv5mms
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/perl-5.34.1-v5gegj42iyc4sch2eoxmz7zphbffxpoy
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/openssl-1.1.1o-r5v7slp4fqtcapkduoysbd2eb7wrtgsh
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/cmake-3.23.1-orjfrfun53jz7p2mz2xwgs7xh7mcbjtz
[+] /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/hdf5-1.12.2-sxwlkklfpxngvn2pe2ducoqkecp4snoi
==> Installing highfive-2.3.1-22llogtzgvnhtx6ydeziwwmcaqy3cn5l
==> No binary for highfive-2.3.1-22llogtzgvnhtx6ydeziwwmcaqy3cn5l found: installing from source
==> Using cached archive: /Users/kyleknoepfel/work/spack/var/spack/cache/_source-cache/archive/41/41728a1204bdfcdcef8cbc3ddffe5d744c5331434ce3dcef35614b831234fcd7.tar.gz
==> No patches needed for highfive
==> highfive: Executing phase: 'cmake'
==> Error: ProcessError: Command exited with status 1:
    'cmake' '-G' 'Unix Makefiles' '-DCMAKE_INSTALL_PREFIX:STRING=/Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/highfive-2.3.1-22llogtzgvnhtx6ydeziwwmcaqy3cn5l' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DBUILD_TESTING:BOOL=OFF' '-DCMAKE_INTERPROCEDURAL_OPTIMIZATION:BOOL=OFF' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_FIND_FRAMEWORK:STRING=LAST' '-DCMAKE_FIND_APPBUNDLE:STRING=LAST' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=ON' '-DCMAKE_INSTALL_RPATH:STRING=/Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/highfive-2.3.1-22llogtzgvnhtx6ydeziwwmcaqy3cn5l/lib;/Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/highfive-2.3.1-22llogtzgvnhtx6ydeziwwmcaqy3cn5l/lib64;/Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/hdf5-1.12.2-sxwlkklfpxngvn2pe2ducoqkecp4snoi/lib;/Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/zlib-1.2.12-rdxpbj5k3nqwsvdmndim4n6mhjdabfui/lib' '-DCMAKE_PREFIX_PATH:STRING=/Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/hdf5-1.12.2-sxwlkklfpxngvn2pe2ducoqkecp4snoi;/Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/cmake-3.23.1-orjfrfun53jz7p2mz2xwgs7xh7mcbjtz;/Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/zlib-1.2.12-rdxpbj5k3nqwsvdmndim4n6mhjdabfui' '-DUSE_BOOST:Bool=False' '-DHIGHFIVE_PARALLEL_HDF5:Bool=False' '-DHIGHFIVE_UNIT_TESTS:Bool=false' '-DHIGHFIVE_EXAMPLES:Bool=false' '/var/folders/0t/b8j2y3cs375g1sj7fc4z10b80000gq/T/kyleknoepfel/spack-stage/spack-stage-highfive-2.3.1-22llogtzgvnhtx6ydeziwwmcaqy3cn5l/spack-src'

1 error found in build log:
     10    -- Detecting CXX compiler ABI info
     11    -- Detecting CXX compiler ABI info - done
     12    -- Check for working CXX compiler: /Users/kyleknoepfel/work/spack/lib/spack/env/clang/clang++ - skipped
     13    -- Detecting CXX compile features
     14    -- Detecting CXX compile features - done
     15    -- Unable to determine HDF5 C flags from HDF5 wrapper.
  >> 16    CMake Error at /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/cmake-3.23.1-orjfrfun53jz7p2mz2xwgs7xh7mcbjtz/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:230 (message):
     17      Could NOT find HDF5 (missing: HDF5_LIBRARIES) (found version "1.12.2")
     18    Call Stack (most recent call first):
     19      /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/cmake-3.23.1-orjfrfun53jz7p2mz2xwgs7xh7mcbjtz/share/cmake-3.23/Modules/FindPackageHandleStandardArgs.cmake:594 (_FPHSA_FAILURE_MESSAGE)
     20      /Users/kyleknoepfel/work/spack/opt/spack/darwin-monterey-skylake/apple-clang-14.0.0/cmake-3.23.1-orjfrfun53jz7p2mz2xwgs7xh7mcbjtz/share/cmake-3.23/Modules/FindHDF5.cmake:1007 (find_package_handle_standard_args)
     21      CMake/HighFiveTargetDeps.cmake:13 (find_package)
     22      CMakeLists.txt:63 (include)

See build log for details:
  /var/folders/0t/b8j2y3cs375g1sj7fc4z10b80000gq/T/kyleknoepfel/spack-stage/spack-stage-highfive-2.3.1-22llogtzgvnhtx6ydeziwwmcaqy3cn5l/spack-build-out.txt

Notice the version here is with highfive 2.3.1.

[1uc]

Thank you, this is reproducible. Also makes it clear why the mentioned line would be the issue:

$ ls $(spack location --install-dir hdf5)/cmake
hdf5-config.cmake  hdf5-config-version.cmake  hdf5-targets.cmake  hdf5-targets-relwithdebinfo.cmake

[matz-e]

I think we're triggering this oddity of CMake: https://gitlab.kitware.com/cmake/cmake/-/issues/23667

But I think it should be safe by now to remove the offending line.

[1uc]

I don't think so, because we get the error also when requesting cmake@3.22.0:

1 error found in build log:
     10    -- Detecting CXX compiler ABI info
     11    -- Detecting CXX compiler ABI info - done
     12    -- Check for working CXX compiler: /home/.../upstream-spack/lib/spack/env/gcc/g++ - skipped
     13    -- Detecting CXX compile features
     14    -- Detecting CXX compile features - done
     15    -- Unable to determine HDF5 C flags from HDF5 wrapper.
  >> 16    CMake Error at /home/.../upstream-spack/opt/spack/linux-archrolling-zen3/gcc-12.2.0/cmake-3.22.0-yqenr66upo42txp4txvf26ktomkmdw2t/share/cmake-3.22
           /Modules/FindPackageHandleStandardArgs.cmake:230 (message):
     17      Could NOT find HDF5 (missing: HDF5_LIBRARIES) (found version "1.12.2")

[matz-e]

Fair enough. In that case the linked issue still points at unreliable behavior :)

[1uc]

The ~mpi seem relevant.

[matz-e]

OK, was just able to reproduce this earlier with @heerener.

Basically, HDF5 1.12.1 works, but 1.12.2 fails with a variety of CMake versions. We were able to get HighFive to build by patching

find_package(HDF5 REQUIRED)

to

find_package(HDF5 REQUIRED CONFIG)

skipping the CMake Find* modules and directly using the CMake config provided by HDF5. Offending line is here. I'm not sure if first importing HDF5 with that setting and HighFive afterwards would be a good work-around.

[alkino]

Should be fixed with v2.6.2

[yurivict]

It is fixed indeed.
Thank you.