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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