dealii and hdf5 compile problem

[Praveen C]

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

[Praveen C]

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

[Praveen C]

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 <esterc...@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 deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see https://groups.google.com/d/forum/dealii?hl=en
---
You received this message because you are subscribed to the Google Groups "deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dealii+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/ae92d984-ea52-4a5e-8609-4123deff23b2n%40googlegroups.com.

[Ester Comellas]

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 <pra...@gmx.net> del dia dc., 15 de febr. 2023 a les 3:54:

You received this message because you are subscribed to a topic in the Google Groups "deal.II User Group" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/dealii/nodblNqEjd4/unsubscribe.
To unsubscribe from this group and all its topics, send an email to dealii+un...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dealii/2aef3f8a-83da-46d2-9482-634e691a4502%40Spark.