I would like to try to help bug fixing, thus I was wondering where I can
find the commands which are run when building deal.II the first time (which
compile the test programs)?
Thanks!
Am Donnerstag, 5. Oktober 2017 15:53:00 UTC+2 schrieb Maxi Miller:
>
> When removing everything, and starting from a clean build-directory, I get
> LANG=eng cmake .. -DCMAKE_CXX_COMPILER=/share/apps/software/Compiler/intel
> /2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx -DCMAKE_C_COMPILER
> =/share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1
> .132/bin64/mpicc -DCMAKE_Fortran_COMPILER=/share/apps/software/Compiler/
> intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpifc
> -- This is CMake 2.8.12.2
> --
> -- Include ~/Downloads/dealii/cmake/setup_external_macros.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_find_package.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_reset_cmake_required.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_invoke_autopilot.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_decorate_with_stars.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_check_compiler_setup.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_clear_cmake_required.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_find_file.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_item_matches.cmake
> -- Include ~/Downloads/dealii/cmake/macros/
> macro_deal_ii_query_git_information.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_to_string_and_add_prefix.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_remove_duplicates.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_strip_flag.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_evaluate_expression.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_to_string.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_enable_if_links.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_add_test.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_replace_flag.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_enable_if_supported.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_expand_instantiations.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_purge_feature.cmake
> -- Include ~/Downloads/dealii/cmake/macros/
> macro_deal_ii_initialize_cached_variables.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_enable_language_optional.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_find_library.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_add_library.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_register_feature.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_find_path.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_configure_feature.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_add_definitions.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_package_handle.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_verbose_include.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_setup_unity_target.cmake
> -- Include ~/Downloads/dealii/cmake/macros/
> macro_deal_ii_insource_setup_target.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_check_mpi_interface.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_pickup_tests.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_check_cxx_compiler_bug.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_filter_system_libraries.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_add_flags.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_setup_source_list.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_set_if_empty.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_deal_ii_setup_target.
> cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_push_cmake_required.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_find_system_library.cmake
> -- Include ~/Downloads/dealii/cmake/macros/macro_switch_library_preference
> .cmake
> --
> -- Include ~/Downloads/dealii/cmake/setup_cached_variables.cmake
> -- Prepending ${CUDA_NVCC_FLAGS} to ${DEAL_II_CUDA_FLAGS}
> -- The CXX compiler identification is GNU 6.3.0
> -- The C compiler identification is GNU 6.3.0
> -- Check for working CXX compiler: /share/apps/software/Compiler/intel/
> 2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx
> -- Check for working CXX compiler: /share/apps/software/Compiler/intel/
> 2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx -- broken
> CMake Error at /usr/share/cmake/Modules/CMakeTestCXXCompiler.cmake:54 (
> message):
> The C++ compiler
>
> "/share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx"
> is not able to compile a simple test program.
>
> It fails with the following output:
>
> Change Dir: ~/Downloads/dealii/build/CMakeFiles/CMakeTmp
>
>
>
> Run Build Command:/usr/bin/gmake "cmTryCompileExec427003707/fast"
>
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec427003707.dir/build.make
> CMakeFiles/cmTryCompileExec427003707.dir/build
>
> gmake[1]: Entering directory
> `~/Downloads/dealii/build/CMakeFiles/CMakeTmp'
>
> /usr/bin/cmake -E cmake_progress_report
> ~/Downloads/dealii/build/CMakeFiles/CMakeTmp/CMakeFiles 1
>
> Building CXX object
> CMakeFiles/cmTryCompileExec427003707.dir/testCXXCompiler.cxx.o
>
>
>
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx
> -o CMakeFiles/cmTryCompileExec427003707.dir/testCXXCompiler.cxx.o -c
> ~/Downloads/dealii/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
>
>
> Linking CXX executable cmTryCompileExec427003707
>
> /usr/bin/cmake -E cmake_link_script
> CMakeFiles/cmTryCompileExec427003707.dir/link.txt --verbose=1
>
>
>
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx
> CMakeFiles/cmTryCompileExec427003707.dir/testCXXCompiler.cxx.o -o
> cmTryCompileExec427003707 -rdynamic
>
>
>
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/intel64/lib/release_mt/libmpi.so:
> error: undefined reference to 'pthread_sigmask'
>
>
>
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/intel64/lib/release_mt/libmpi.so:
> error: undefined reference to 'pthread_create'
>
> collect2: error: ld returned 1 exit status
>
> gmake[1]: *** [cmTryCompileExec427003707] Error 1
>
> gmake[1]: Leaving directory
> `~/Downloads/dealii/build/CMakeFiles/CMakeTmp'
>
> gmake: *** [cmTryCompileExec427003707/fast] Error 2
>
>
>
>
>
> CMake will not be able to correctly generate this project.
> Call Stack (most recent call first):
> CMakeLists.txt:95 (PROJECT)
>
>
> -- Configuring incomplete, errors occurred!
> See also "~/Downloads/dealii/build/CMakeFiles/CMakeOutput.log".
> See also "~/Downloads/dealii/build/CMakeFiles/CMakeError.log".
>
> CMakeOutput.log is
> The system is: Linux - 3.10.0-693.2.2.el7.x86_64 - x86_64
> Compiling the CXX compiler identification source file
> "CMakeCXXCompilerId.cpp" succeeded.
> Compiler: /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/
> impi/2017.1.132/bin64/mpicxx
> Build flags:
> Id flags: -c
>
> The output was:
> 0
>
>
> Compilation of the CXX compiler identification source
> "CMakeCXXCompilerId.cpp" produced "CMakeCXXCompilerId.o"
>
> The CXX compiler identification is GNU, found in
> "~/Downloads/dealii/build/CMakeFiles/
> 2.8.12.2/CompilerIdCXX/CMakeCXXCompilerId.o"
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> succeeded.
> Compiler: /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/
> impi/2017.1.132/bin64/mpicc
> Build flags:
> Id flags: -c
>
> The output was:
> 0
>
>
> Compilation of the C compiler identification source "CMakeCCompilerId.c"
> produced "CMakeCCompilerId.o"
>
> The C compiler identification is GNU, found in
> "~/Downloads/dealii/build/CMakeFiles/
> 2.8.12.2/CompilerIdC/CMakeCCompilerId.o"
>
> CMakeError.log is
> Compiling the CXX compiler identification source file
> "CMakeCXXCompilerId.cpp" failed.
> Compiler: /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/
> impi/2017.1.132/bin64/mpicxx
> Build flags:
> Id flags:
>
> The output was:
> 1
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.
> 132/intel64/lib/release_mt/libmpi.so: error: undefined reference to
> 'pthread_sigmask'
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.
> 132/intel64/lib/release_mt/libmpi.so: error: undefined reference to
> 'pthread_create'
> collect2: error: ld returned 1 exit status
>
>
> Compiling the C compiler identification source file "CMakeCCompilerId.c"
> failed.
> Compiler: /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/
> impi/2017.1.132/bin64/mpicc
> Build flags:
> Id flags:
>
> The output was:
> 1
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.
> 132/intel64/lib/release_mt/libmpi.so: error: undefined reference to
> 'pthread_create'
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.
> 132/intel64/lib/release_mt/libmpi.so: error: undefined reference to
> 'pthread_sigmask'
> collect2: error: ld returned 1 exit status
>
>
> Determining if the CXX compiler works failed with the following output:
> Change Dir: ~/Downloads/dealii/build/CMakeFiles/CMakeTmp
>
> Run Build Command:/usr/bin/gmake "cmTryCompileExec427003707/fast"
> /usr/bin/gmake -f CMakeFiles/cmTryCompileExec427003707.dir/build.make
> CMakeFiles/cmTryCompileExec427003707.dir/build
> gmake[1]: Entering directory
> `~/Downloads/dealii/build/CMakeFiles/CMakeTmp'
> /usr/bin/cmake -E cmake_progress_report
> ~/Downloads/dealii/build/CMakeFiles/CMakeTmp/CMakeFiles 1
> Building CXX object
> CMakeFiles/cmTryCompileExec427003707.dir/testCXXCompiler.cxx.o
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx
>
> -o CMakeFiles/cmTryCompileExec427003707.dir/testCXXCompiler.cxx.o -c
> ~/Downloads/dealii/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
> Linking CXX executable cmTryCompileExec427003707
> /usr/bin/cmake -E cmake_link_script
> CMakeFiles/cmTryCompileExec427003707.dir/link.txt --verbose=1
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx
>
> CMakeFiles/cmTryCompileExec427003707.dir/testCXXCompiler.cxx.o -o
> cmTryCompileExec427003707 -rdynamic
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/intel64/lib/release_mt/libmpi.so:
>
> error: undefined reference to 'pthread_sigmask'
> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/intel64/lib/release_mt/libmpi.so:
>
> error: undefined reference to 'pthread_create'
> collect2: error: ld returned 1 exit status
> gmake[1]: *** [cmTryCompileExec427003707] Error 1
> gmake[1]: Leaving directory `~/Downloads/dealii/build/CMakeFiles/CMakeTmp'
> gmake: *** [cmTryCompileExec427003707/fast] Error 2
>
>
> Thanks!
>
>
> Am Donnerstag, 5. Oktober 2017 15:30:38 UTC+2 schrieb Daniel Arndt:
>>
>> Maxi,
>>
>> does the problem persist if you start from a clean build directory?
>> This looks as if some flags were wrongly set from a previous
>> configuration.
>>
>> Otherwise, I would be helpful if could provide us with the whole output
>> you get when configuring.
>>
>> Best,
>> Daniel
>>
>> Am Donnerstag, 5. Oktober 2017 10:56:16 UTC+2 schrieb Maxi Miller:
>>>
>>> I tried to set up dealII with the Intel MPI compilers (using gcc 6.3.0
>>> in the background), but already in the initial setup before I can choose
>>> any values I get the error
>>>
>>> Building CXX object CMakeFiles/cmTC_8341d.dir/testCXXCompiler.cxx.o
>>>
>>>
>>>
>>> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx
>>> -o CMakeFiles/cmTC_8341d.dir/testCXXCompiler.cxx.o -c
>>> ~/Downloads/dealii/build/CMakeFiles/CMakeTmp/testCXXCompiler.cxx
>>>
>>>
>>> Linking CXX executable cmTC_8341d
>>>
>>> ~/local_opt/cmake/bin/cmake -E cmake_link_script
>>> CMakeFiles/cmTC_8341d.dir/link.txt --verbose=1
>>>
>>>
>>>
>>> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/bin64/mpicxx
>>> -rdynamic CMakeFiles/cmTC_8341d.dir/testCXXCompiler.cxx.o -o cmTC_8341d
>>>
>>>
>>>
>>> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/intel64/lib/release_mt/libmpi.so:
>>> error: undefined reference to 'pthread_sigmask'
>>>
>>>
>>>
>>> /share/apps/software/Compiler/intel/2017.1.132-GCC-6.3.0-2.27/impi/2017.1.132/intel64/lib/release_mt/libmpi.so:
>>> error: undefined reference to 'pthread_create'
>>>
>>>
>>> When compiling it with OpenMPI using the same GCC it works. I added
>>> -pthread and -lpthread to all possible linker flag locations (i.e.
>>> DEAL_II_LINKER_FLAGS and DEAL_II_CXX_FLAGS), but the error persists.
>>> Compiling an example program with mpicxx -lpthread works. Additional tests
>>> show that the OpenMPI-version of mpicxx works fine with -pthread and with
>>> -lpthread, but the Intel MPI-version of mpicxx only works with -lpthread.
>>> Is there a fix I could apply so that the test passes?
>>> Thanks!
>>>
>>
>>
--
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