I had hdf+mpi installed by spack, so I commented out the check in deal.II in
the file
cmake/configure/configure_50_hdf5.cmake
MACRO(FEATURE_HDF5_FIND_EXTERNAL var)
FIND_PACKAGE(HDF5)
IF(HDF5_FOUND)
SET(${var} TRUE)
# IF(NOT HDF5_IS_PARALLEL)
# MESSAGE(STATUS "Insufficient hdf5 installation found: "
# "hdf5 has to be configured with MPI support."
# )
# SET(HDF5_ADDITIONAL_ERROR_STRING
# "Insufficient hdf5 installation found!\n"
# "hdf5 has to be configured with MPI support.\n"
# )
# SET(${var} FALSE)
# ENDIF()
CHECK_MPI_INTERFACE(HDF5 ${var})
ENDIF()
ENDMACRO()
best
praveen
On 14 Feb 2023 at 8:03 PM +0530, Ester Comellas <estercomel...@gmail.com>,
wrote:
> Hi All,
>
> Praveen, I'm getting this exact same error message when I try to compile my
> deal.II code. It's been a while since your post... do your recall how you
> solved it?
>
> I recently reinstalled deal.II via spack after upgrading macOS to Ventura
> 13.2. This is my error message:
> Consolidate compiler generated dependencies of target TuringPatterns
> [ 50%] Linking CXX executable TuringPatterns
> ld: library not found for -lhdf5-shared
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make[2]: *** [TuringPatterns] Error 1
> make[1]: *** [CMakeFiles/TuringPatterns.dir/all] Error 2
> make: *** [all] Error 2
>
> And the detailed.log shows:
> # DEAL_II_WITH_HDF5 set up with external dependencies
> # HDF5_VERSION = 1.10.7
> # HDF5_DIR =
> /Users/ecomellas/spack/opt/spack/darwin-ventura-skylake/apple-clang-14.0.0_spack/hdf5-1$
> # HDF5_INCLUDE_DIRS =
> /Users/ecomellas/spack/opt/spack/darwin-ventura-skylake/apple-clang-14.0.0_spa$
> # HDF5_USER_INCLUDE_DIRS =
> /Users/ecomellas/spack/opt/spack/darwin-ventura-skylake/apple-clang-14.0.$
> # HDF5_LIBRARIES = hdf5-shared
>
> The file "macro_find_package.cmake" Praveen mentioned in his original post
> doesn't exist in my installation. I don't know why spack didn't install the
> preferred version of hdf5 (1.12.2). I'm wondering whether I should install
> the preferred version or the most recent version (1.13.2) of hdf5 and try
> reinstalling deal.II? Could this solve the problem? Any suggestions would be
> really welcome. Thanks!
>
> Best,
> Ester
>
> > El dia dimecres, 17 d’agost de 2022 a les 10:19:40 UTC+2, Praveen C va
> > escriure:
> > > The detailed.log shows this
> > >
> > > # DEAL_II_WITH_HDF5 set up with external dependencies
> > > # HDF5_VERSION = 1.12.2
> > > # HDF5_DIR =
> > > /Users/praveen/Applications/spack/opt/spack/darwin-monterey-m1/apple-clang-13.1.6/hdf5-1.12.2-gxrwbuzg3xom562obmqaqtu5forevio5/cmake
> > > # HDF5_INCLUDE_DIRS =
> > > /Users/praveen/Applications/spack/opt/spack/darwin-monterey-m1/apple-
> > > clang-13.1.6/hdf5-1.12.2-gxrwbuzg3xom562obmqaqtu5forevio5/include
> > > # HDF5_USER_INCLUDE_DIRS =
> > > /Users/praveen/Applications/spack/opt/spack/darwin-monterey-m1/
> > > apple-clang-13.1.6/hdf5-1.12.2-gxrwbuzg3xom562obmqaqtu5forevio5/include
> > > # HDF5_LIBRARIES = hdf5-shared
> > >
> > > and last line above seems wrong.
> > >
> > > Thanks
> > > praveen
> > >
> > > > On 17-Aug-2022, at 11:49 AM, Praveen C <pra...@gmx.net> wrote:
> > > >
> > > > Hello
> > > >
> > > > I am compiling dea...@9.4.0 myself using dependent packages installed
> > > > via spack.
> > > >
> > > > I am facing the issue reported here
> > > >
> > > > https://github.com/spack/spack/issues/32023
> > > >
> > > > and is fixed here
> > > >
> > > > https://github.com/spack/spack/pull/32079
> > > >
> > > > This fix seems to remove the file
> > > >
> > > > cmake/macros/macro_find_package.cmake
> > > > I removed it and was able to compile dealii. But when I compile an
> > > > example, I get this error
> > > >
> > > > Consolidate compiler generated dependencies of target step-1
> > > > [ 50%] Linking CXX executable step-1
> > > > ld: library not found for -lhdf5-shared
> > > > clang: error: linker command failed with exit code 1 (use -v to see
> > > > invocation)
> > > > make[2]: *** [step-1] Error 1
> > > > make[1]: *** [CMakeFiles/step-1.dir/all] Error 2
> > > > make: *** [all] Error 2
> > > >
> > > > Thanks for any help.
> > > > Best
> > > > praveen
> > >
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