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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