Thanks for your quick response, Praveen. Unfortunately, your solution
didn't work for me because I don't have a "configure_50_hdf5.cmake" file
(or any similarly named file) in my deal.II folder in spack. It did point
me in the right direction and I have now been able to compile and run all
my deal.II codes successfully, thanks!
I'll summarize below how I solved this problem in case someone else faces
the same error in the future. Hope it helps!
The error I encountered when I compile any deal.II code is:
* 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
I checked my spack installation of hdf5 and everything seemed correct.
However, when I checked deal.II's detailed.log, which I have in the path:
/Users/ecomellas/spack/opt/spack/darwin-ventura-skylake/apple-clang-14.0.0_spack/dealii-9.4.0-eyotztjepnxo24vrevovh6bdejcvs2u5/share/deal.II/detailed.log
I saw the problem was that "HDF5_LIBRARIES" pointed to "hdf5-shared", which
the system couldn't find (as indicated by the compiler error). It should be
replaced with the correct path, which is for me:
/Users/ecomellas/spack/opt/spack/darwin-ventura-skylake/apple-clang-14.0.0_spack/hdf5-1.10.7-6i6oulsc3hyehgkevx56xykhibxlmbmc/lib/
libhdf5.dylib
In deal.II's configure files, which I found in the folder:
/Users/ecomellas/spack/opt/spack/darwin-ventura-skylake/apple-clang-14.0.0_spack/dealii-9.4.0-eyotztjepnxo24vrevovh6bdejcvs2u5/lib/cmake/deal.II/
I replaced every instance of "hdf5-shared" with "
/Users/ecomellas/spack/opt/spack/darwin-ventura-skylake/apple-clang-14.0.0_spack/hdf5-1.10.7-6i6oulsc3hyehgkevx56xykhibxlmbmc/lib/
libhdf5.dylib". The files I ended up changing are:
deal.IIConfig.cmake
deal.IIFeatureConfig.cmake
deal.IITargets.cmake
And that's it. I compiled my deal.II codes again from scratch and now it
works!
Best,
Ester
Missatge de Praveen C <[email protected]> del dia dc., 15 de febr. 2023 a les
3:54:
> 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 ${var})
> ENDIF()
> ENDMACRO()
>
> best
> praveen
> On 14 Feb 2023 at 8:03 PM +0530, Ester Comellas <[email protected]>,
> wrote:
>
> Hi All,
>
> Praveen, I'm getting this exact same error message when I try to compile
> my deal.II code. It's been a while since your post... do your recall how
> you solved it?
>
> I recently reinstalled deal.II via spack after upgrading macOS to Ventura
> 13.2. This is my error message:
>
> *Consolidate compiler generated dependencies of target TuringPatterns*
> [ 50%] *Linking CXX executable TuringPatterns*
> ld: library not found for -lhdf5-shared
> clang: *error:* *linker command failed with exit code 1 (use -v to see
> invocation)*
> make[2]: *** [TuringPatterns] Error 1
> make[1]: *** [CMakeFiles/TuringPatterns.dir/all] Error 2
> make: *** [all] Error 2
>
> And the detailed.log shows:
> # DEAL_II_WITH_HDF5 set up with external dependencies
> # HDF5_VERSION = 1.10.7
> # HDF5_DIR =
> /Users/ecomellas/spack/opt/spack/darwin-ventura-skylake/apple-clang-14.0.0_spack/hdf5-1$
> # 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 <[email protected]> wrote:
>>
>> Hello
>>
>> I am compiling [email protected] 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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