I have made another attempt at installing dealii 8.4.1 with PETSc and MPI
First I removed all PETSc and all mpi libraries from the system.
checking with:
898 dpkg -l | grep petsc
899 dpkg -l | grep mpi
petsc an openmpi and mpich and mpich2 were and are gone.
I used downloaded PETSc source and built with:
./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran
--download-mpich
make PETSC_DIR=/home/pgriffin/Documents/Zipstore2/petsc-3.6.4
PETSC_ARCH=arch-linux2-c-debug all
make PETSC_DIR=/home/pgriffin/Documents/Zipstore2/petsc-3.6.4
PETSC_ARCH=arch-linux2-c-debug test
make PETSC_DIR=/home/pgriffin/Documents/Zipstore2/petsc-3.6.4
PETSC_ARCH=arch-linux2-c-debug streams NPMAX=1
ran:
cmake -DCMAKE_INSTALL_PREFIX=/home/pgriffin/mylibs/dealii-8.4.1-PETSc
-DPETSC_DIR=/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug
-DPETSC_ARCH=x86_64 -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_PETSC=ON ../
with
SET(MPI_C_LIBRARIES
"/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpich.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpi.so"
CASHE STRING "")
SET(MPI_C_INCLUDE_PATH
"/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include"
CASHE STRING "")
SET(MPI_CXX_LIBRARIES
"/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichcxx.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpicxx.so"
CASHE STRING "")
SET(MPI_CXX_INCLUDE_PATH
"/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include"
CASHE STRING "")
SET(MPI_Fortran_LIBRARIES
"/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichf90.so"
CASHE STRING "")
SET(MPI_Fortran_INCLUDE_PATH
"/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include"
CASHE STRING "")
appended to setup_deal_ii.cmake.
I could only guess which were the MPI_C_LIBRARIES, MPI_CXX_LIBRARIES,
MPI_Fortran_LIBRARIES which were required from the trail of errors I got.
What is MPI_SEEK_SET?? is that on internal cmake variable?
===========================================================================================================================
The final error I got that is relavant was:
--
-- Include
/home/pgriffin/Documents/Zipstore2/dealii-8.4.1-PETSc/cmake/configure/configure_1_mpi.cmake
-- Found MPI_C:
/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpich.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpi.so;CASHE;STRING;
-- Found MPI_CXX:
/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichcxx.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpicxx.so;CASHE;STRING;
-- Found MPI_Fortran:
/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichf90.so;CASHE;STRING;
-- Performing Test MPI_HAVE_MPI_SEEK_SET
-- Performing Test MPI_HAVE_MPI_SEEK_SET - Failed
-- Found MPI_MPI_H
-- MPI_VERSION: 3.0
-- MPI_LIBRARIES:
/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichcxx.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpicxx.so;CASHE;STRING;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpichf90.so;CASHE;STRING;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpich.so;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/lib/libmpi.so;CASHE;STRING
-- MPI_INCLUDE_DIRS:
/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include;CASHE;STRING;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include;CASHE;STRING
-- MPI_USER_INCLUDE_DIRS:
/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include;CASHE;STRING;/home/pgriffin/Documents/Zipstore2/petsc-3.6.4/arch-linux2-c-debug/include;CASHE;STRING
-- MPI_CXX_FLAGS:
-- MPI_LINKER_FLAGS:
-- Found MPI
-- Could not find a sufficient MPI version: Your MPI implementation must
define MPI_SEEK_SET.
-- DEAL_II_WITH_MPI has unmet external dependencies.
CMake Error at cmake/configure/configure_1_mpi.cmake:38 (MESSAGE):
Could not find any suitable mpi library!
Your MPI implementation must define MPI_SEEK_SET.
Please ensure that an mpi library is installed on your computer
and set CMAKE_CXX_COMPILER to the appropriate mpi wrappers:
$ CXX=".../mpicxx" cmake <...>
$ cmake -DCMAKE_CXX_COMPILER=".../mpicxx" <...>
Or with additional C and Fortran wrappers (recommended!):
$ CC=".../mpicc" CXX=".../mpicxx" F90=".../mpif90" cmake <...>
$ cmake -DCMAKE_C_COMPILER=".../mpicc"\
-DCMAKE_CXX_COMPILER=".../mpicxx"\
-DCMAKE_Fortran_COMPILER=".../mpif90"\
<...>
Call Stack (most recent call first):
build/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1
(FEATURE_MPI_ERROR_MESSAGE)
cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
cmake/macros/macro_configure_feature.cmake:272 (RUN_COMMAND)
cmake/configure/configure_1_mpi.cmake:55 (CONFIGURE_FEATURE)
cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
CMakeLists.txt:119 (VERBOSE_INCLUDE)
-- Configuring incomplete, errors occurred!
See also
"/home/pgriffin/Documents/Zipstore2/dealii-8.4.1-PETSc/build/CMakeFiles/CMakeOutput.log".
See also
"/home/pgriffin/Documents/Zipstore2/dealii-8.4.1-PETSc/build/CMakeFiles/CMakeError.log".
On Sunday, July 10, 2016 at 10:54:54 PM UTC-4, Pete Griffin wrote:
>
> I am trying to get PETSc running with dealii-8.4.1. (on Ubuntu 16.04)
> Reading the documentation it looks
> like I don't need to have MPI. (???) I downloaded petsc-3.6.4 and most
> recently compiled it with:
>
> ./configure --with-cc=gcc --with-cxx=g++ --with-fc=gfortran
> --download-fblaslapack --with-mpi=0
>
> This resulted in the following being created in
> petsc-3.6.4/arch-linux2-c-debug:
>
> ls -R lib
>
> lib:
> libfblas.a libflapack.a libpetsc.so libpetsc.so.3.6 libpetsc.so.3.6.4
> petsc pkgconfig
>
> lib/petsc:
> conf
>
> lib/petsc/conf:
> configure.log error.log files make.log PETScConfig.cmake
> petscvariables reconfigure-arch-linux2-c-debug.py
> configure.log.bkp fblaslapack gmake.log modules petscrules
> RDict.db test.log
>
> lib/petsc/conf/modules:
> petsc
>
> lib/petsc/conf/modules/petsc:
> 3.6.4
>
> lib/pkgconfig:
> PETSc.pc
>
> and
>
> ls -R include/
>
> include/:
> mpi.mod petscdef.mod petscdm.mod petscksp.mod
> petscpcdef.mod petscsys.mod
> petscaodef.mod petscdmcomposite.mod petscfix.h
> petscmachineinfo.h petscpc.mod petsctsdef.mod
> petscao.mod petscdmdadef.mod petscisdef.mod petscmatdef.mod
> petscsnesdef.mod petscts.mod
> petscconf.h petscdmda.mod petscis.mod petscmat.mod
> petscsnes.mod petscvecdef.mod
> petscconfiginfo.h petscdmdef.mod petsckspdef.mod petsc.mod
> petscsysdef.mod petscvec.mod
>
> Originally I compiled without the --with-mpi=0 and mpi libraries were
> created. The MPI version
> did not work! Since I am running on a single computer MPI was not needed
> and tried without it.
>
>
> =================================================================================================
>
> The basic error is, with full details below:
>
> -- Found PETSC
> -- Could not find a sufficient PETSc installation: PETSc has to be
> configured with the same MPI configuration as deal.II.
> -- DEAL_II_WITH_PETSC has unmet external dependencies.
> CMake Error at cmake/configure/configure_3_petsc.cmake:110 (MESSAGE):
>
>
> Could not find the petsc library!
>
> Could not find a sufficient PETSc installation:
>
> PETSc has to be configured with the same MPI configuration as deal.II,
> but
> found:
>
> DEAL_II_WITH_MPI = OFF
> PETSC_WITH_MPI = (NOT FALSE)
> ....
>
>
> I assume the -DDEAL_II_WITH_MPI=OFF switch would work since I created
> PETsc with
> --with-mpi=0 and since mpi files were not created.
>
>
>
> Thanks, Pete Griffin
>
>
>
> =================================================================================================
> THE RESULTS OF cmake for dealii were as follows:
>
> =================================================================================================
>
> $ cd dealii-8.4.1-PETSc/
> /dealii-8.4.1-PETSc$ mkdir build
> /dealii-8.4.1-PETSc$ cd build
>
> =================================================================================================
> /dealii-8.4.1-PETSc/build$ cmake
> -DCMAKE_INSTALL_PREFIX=/home/pgriffin/mylibs/dealii-8.4.1-PETSc
> -DPETSC_DIR=/petsc-3.6.4/arch-linux2-c-debug/lib -DPETSC_ARCH=x86_64
> -DDEAL_II_WITH_MPI=OFF -DDEAL_II_WITH_PETSC=ON ../
>
> =================================================================================================
> -- This is CMake 3.5.1
> --
> -- Include /dealii-8.4.1-PETSc/cmake/setup_external_macros.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_enable_if_supported.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_find_file.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_setup_target.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_insource_setup_target.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_add_flags.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_add_dependencies.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_invoke_autopilot.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_push_cmake_required.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_enable_language_optional.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_filter_system_libraries.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_purge_feature.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_switch_library_preference.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_remove_duplicates.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_check_cxx_compiler_bug.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_query_git_information.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_clear_cmake_required.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_set_if_empty.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_expand_instantiations.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_reset_cmake_required.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_replace_flag.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_register_feature.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_find_package.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_find_system_library.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_package_handle.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_verbose_include.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_add_library.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_item_matches.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_configure_feature.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_to_string.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_pickup_tests.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_to_string_and_add_prefix.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_strip_flag.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_initialize_cached_variables.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_add_definitions.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_find_path.cmake
> -- Include
> /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_find_library.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_deal_ii_add_test.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_check_mpi_interface.cmake
> -- Include /dealii-8.4.1-PETSc/cmake/macros/macro_enable_if_links.cmake
> --
> -- Include /dealii-8.4.1-PETSc/cmake/setup_cached_variables.cmake
> -- The CXX compiler identification is GNU 5.3.1
> -- The C compiler identification is GNU 5.3.1
> -- Check for working CXX compiler: /usr/bin/c++
> -- Check for working CXX compiler: /usr/bin/c++ -- works
> -- Detecting CXX compiler ABI info
> -- Detecting CXX compiler ABI info - done
> -- Detecting CXX compile features
> -- Detecting CXX compile features - done
> -- Check for working C compiler: /usr/bin/cc
> -- Check for working C compiler: /usr/bin/cc -- works
> -- Detecting C compiler ABI info
> -- Detecting C compiler ABI info - done
> -- Detecting C compile features
> -- Detecting C compile features - done
> -- The Fortran compiler identification is GNU 5.3.1
> -- Check for working Fortran compiler: /usr/bin/gfortran
> -- Check for working Fortran compiler: /usr/bin/gfortran -- works
> -- Detecting Fortran compiler ABI info
> -- Detecting Fortran compiler ABI info - done
> -- Checking whether /usr/bin/gfortran supports Fortran 90
> -- Checking whether /usr/bin/gfortran supports Fortran 90 -- yes
> --
> -- Include /dealii-8.4.1-PETSc/cmake/setup_deal_ii.cmake
> --
> -- Include /dealii-8.4.1-PETSc/cmake/setup_compiler_flags.cmake
> --
> -- Include /dealii-8.4.1-PETSc/cmake/setup_compiler_flags_gnu.cmake
> -- Performing Test DEAL_II_HAVE_FLAG_pedantic
> -- Performing Test DEAL_II_HAVE_FLAG_pedantic - Success
> -- Performing Test DEAL_II_HAVE_FLAG_fpic
> -- Performing Test DEAL_II_HAVE_FLAG_fpic - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wl__as_needed
> -- Performing Test DEAL_II_HAVE_FLAG_Wl__as_needed - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wall
> -- Performing Test DEAL_II_HAVE_FLAG_Wall - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wextra
> -- Performing Test DEAL_II_HAVE_FLAG_Wextra - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wpointer_arith
> -- Performing Test DEAL_II_HAVE_FLAG_Wpointer_arith - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wwrite_strings
> -- Performing Test DEAL_II_HAVE_FLAG_Wwrite_strings - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wsynth
> -- Performing Test DEAL_II_HAVE_FLAG_Wsynth - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wsign_compare
> -- Performing Test DEAL_II_HAVE_FLAG_Wsign_compare - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wswitch
> -- Performing Test DEAL_II_HAVE_FLAG_Wswitch - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Woverloaded_virtual
> -- Performing Test DEAL_II_HAVE_FLAG_Woverloaded_virtual - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wlong_long
> -- Performing Test DEAL_II_HAVE_FLAG_Wlong_long - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wdeprecated_declarations
> -- Performing Test DEAL_II_HAVE_FLAG_Wdeprecated_declarations - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wliteral_suffix
> -- Performing Test DEAL_II_HAVE_FLAG_Wliteral_suffix - Success
> -- Performing Test DEAL_II_HAVE_FLAG_funroll_loops
> -- Performing Test DEAL_II_HAVE_FLAG_funroll_loops - Success
> -- Performing Test DEAL_II_HAVE_FLAG_funroll_all_loops
> -- Performing Test DEAL_II_HAVE_FLAG_funroll_all_loops - Success
> -- Performing Test DEAL_II_HAVE_FLAG_fstrict_aliasing
> -- Performing Test DEAL_II_HAVE_FLAG_fstrict_aliasing - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Og
> -- Performing Test DEAL_II_HAVE_FLAG_Og - Success
> -- Performing Test DEAL_II_HAVE_FLAG_ggdb
> -- Performing Test DEAL_II_HAVE_FLAG_ggdb - Success
> --
> -- Include /dealii-8.4.1-PETSc/bundled/setup_bundled.cmake
> --
> -- Include
> /dealii-8.4.1-PETSc/cmake/checks/check_01_compiler_features.cmake
> -- Performing Test DEAL_II_COMPILER_USE_VECTOR_ARITHMETICS
> -- Performing Test DEAL_II_COMPILER_USE_VECTOR_ARITHMETICS - Success
> -- Performing Test DEAL_II_VECTOR_ITERATOR_IS_POINTER_OK
> -- Performing Test DEAL_II_VECTOR_ITERATOR_IS_POINTER_OK - Success
> -- Test successful, do not define DEAL_II_VECTOR_ITERATOR_IS_POINTER
> -- Performing Test DEAL_II_HAVE_BUILTIN_EXPECT
> -- Performing Test DEAL_II_HAVE_BUILTIN_EXPECT - Success
> -- Performing Test DEAL_II_HAVE_VERBOSE_TERMINATE
> -- Performing Test DEAL_II_HAVE_VERBOSE_TERMINATE - Success
> -- Performing Test DEAL_II_HAVE_GLIBC_STACKTRACE
> -- Performing Test DEAL_II_HAVE_GLIBC_STACKTRACE - Success
> -- Performing Test DEAL_II_HAVE_FLAG_rdynamic
> -- Performing Test DEAL_II_HAVE_FLAG_rdynamic - Success
> -- Performing Test DEAL_II_HAVE_LIBSTDCXX_DEMANGLER
> -- Performing Test DEAL_II_HAVE_LIBSTDCXX_DEMANGLER - Success
> -- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_PRETTY_FUNCTION
> -- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_PRETTY_FUNCTION - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wa__compress_debug_sections
> -- Performing Test DEAL_II_HAVE_FLAG_Wa__compress_debug_sections - Success
> -- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED
> -- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED - Success
> -- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_ALWAYS_INLINE
> -- Performing Test DEAL_II_COMPILER_HAS_ATTRIBUTE_ALWAYS_INLINE - Success
> -- Performing Test DEAL_II_COMPILER_HAS_DIAGNOSTIC_PRAGMA
> -- Performing Test DEAL_II_COMPILER_HAS_DIAGNOSTIC_PRAGMA - Success
> -- Performing Test DEAL_II_COMPILER_HAS_FUSE_LD_GOLD
> -- Performing Test DEAL_II_COMPILER_HAS_FUSE_LD_GOLD - Success
> --
> -- Include /dealii-8.4.1-PETSc/cmake/checks/check_01_cpu_features.cmake
> -- Check if the system is big endian
> -- Searching 16 bit integer
> -- Looking for sys/types.h
> -- Looking for sys/types.h - found
> -- Looking for stdint.h
> -- Looking for stdint.h - found
> -- Looking for stddef.h
> -- Looking for stddef.h - found
> -- Check size of unsigned short
> -- Check size of unsigned short - done
> -- Using unsigned short
> -- Check if the system is big endian - little endian
> -- Performing Test DEAL_II_HAVE_SSE2
> -- Performing Test DEAL_II_HAVE_SSE2 - Success
> -- Performing Test DEAL_II_HAVE_AVX
> -- Performing Test DEAL_II_HAVE_AVX - Failed
> -- Performing Test DEAL_II_HAVE_AVX512
> -- Performing Test DEAL_II_HAVE_AVX512 - Failed
> -- Performing Test DEAL_II_HAVE_OPENMP_SIMD
> -- Performing Test DEAL_II_HAVE_OPENMP_SIMD - Success
> --
> -- Include /dealii-8.4.1-PETSc/cmake/checks/check_01_cxx_features.cmake
> -- Performing Test DEAL_II_HAVE_FLAG_stdcxx14
> -- Performing Test DEAL_II_HAVE_FLAG_stdcxx14 - Success
> -- Using C++ version flag "-std=c++14"
> -- Performing Test DEAL_II_HAVE_CXX14_MAKE_UNIQUE
> -- Performing Test DEAL_II_HAVE_CXX14_MAKE_UNIQUE - Success
> -- Performing Test DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK
> -- Performing Test DEAL_II_HAVE_CXX14_CLANGAUTODEBUG_BUG_OK - Success
> -- Using C++ version flag "-std=c++14"
> -- Performing Test DEAL_II_HAVE_CXX11_ARRAY
> -- Performing Test DEAL_II_HAVE_CXX11_ARRAY - Success
> -- Performing Test DEAL_II_HAVE_CXX11_CONDITION_VARIABLE
> -- Performing Test DEAL_II_HAVE_CXX11_CONDITION_VARIABLE - Success
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL - Success
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_GCCBUG35569_OK
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_GCCBUG35569_OK - Success
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK
> -- Performing Test DEAL_II_HAVE_CXX11_FUNCTIONAL_LLVMBUG20084_OK - Success
> -- Performing Test DEAL_II_HAVE_CXX11_SHARED_PTR
> -- Performing Test DEAL_II_HAVE_CXX11_SHARED_PTR - Success
> -- Performing Test DEAL_II_HAVE_CXX11_THREAD
> -- Performing Test DEAL_II_HAVE_CXX11_THREAD - Success
> -- Performing Test DEAL_II_HAVE_CXX11_MUTEX
> -- Performing Test DEAL_II_HAVE_CXX11_MUTEX - Success
> -- Performing Test DEAL_II_HAVE_CXX11_TUPLE
> -- Performing Test DEAL_II_HAVE_CXX11_TUPLE - Success
> -- Performing Test DEAL_II_HAVE_CXX11_TYPE_TRAITS
> -- Performing Test DEAL_II_HAVE_CXX11_TYPE_TRAITS - Success
> -- Performing Test DEAL_II_HAVE_CXX11_MACOSXC99BUG_OK
> -- Performing Test DEAL_II_HAVE_CXX11_MACOSXC99BUG_OK - Success
> -- Performing Test DEAL_II_HAVE_CXX11_ICCNUMERICLIMITSBUG_OK
> -- Performing Test DEAL_II_HAVE_CXX11_ICCNUMERICLIMITSBUG_OK - Success
> -- Performing Test DEAL_II_HAVE_CXX11_ICCLIBSTDCPP47CXX11BUG_OK
> -- Performing Test DEAL_II_HAVE_CXX11_ICCLIBSTDCPP47CXX11BUG_OK - Success
> -- DEAL_II_WITH_CXX11 successfully set up
> -- DEAL_II_WITH_CXX14 successfully set up
> -- Performing Test DEAL_II_HAVE_CXX11_IS_TRIVIALLY_COPYABLE
> -- Performing Test DEAL_II_HAVE_CXX11_IS_TRIVIALLY_COPYABLE - Success
> -- Performing Test DEAL_II_HAVE_STD_ISNAN
> -- Performing Test DEAL_II_HAVE_STD_ISNAN - Success
> -- Performing Test DEAL_II_HAVE_ISNAN
> -- Performing Test DEAL_II_HAVE_ISNAN - Success
> -- Performing Test DEAL_II_HAVE_UNDERSCORE_ISNAN
> -- Performing Test DEAL_II_HAVE_UNDERSCORE_ISNAN - Failed
> -- Performing Test DEAL_II_HAVE_ISFINITE
> -- Performing Test DEAL_II_HAVE_ISFINITE - Success
> -- Performing Test DEAL_II_HAVE_FP_EXCEPTIONS
> -- Performing Test DEAL_II_HAVE_FP_EXCEPTIONS - Success
> -- Performing Test DEAL_II_HAVE_COMPLEX_OPERATOR_OVERLOADS
> -- Performing Test DEAL_II_HAVE_COMPLEX_OPERATOR_OVERLOADS - Failed
> --
> -- Include /dealii-8.4.1-PETSc/cmake/checks/check_02_system_features.cmake
> -- Looking for C++ include sys/resource.h
> -- Looking for C++ include sys/resource.h - found
> -- Looking for C++ include sys/time.h
> -- Looking for C++ include sys/time.h - found
> -- Looking for C++ include sys/times.h
> -- Looking for C++ include sys/times.h - found
> -- Looking for times
> -- Looking for times - found
> -- Looking for C++ include sys/types.h
> -- Looking for C++ include sys/types.h - found
> -- Looking for C++ include unistd.h
> -- Looking for C++ include unistd.h - found
> -- Looking for gethostname
> -- Looking for gethostname - found
> -- Looking for getpid
> -- Looking for getpid - found
> -- Performing Test m_LIBRARY
> -- Performing Test m_LIBRARY - Success
> -- Looking for jn
> -- Looking for jn - found
> --
> -- Include /dealii-8.4.1-PETSc/cmake/checks/check_03_compiler_bugs.cmake
> -- Performing Test DEAL_II_WRETURN_TYPE_CONST_QUALIFIER_BUG_OK
> -- Performing Test DEAL_II_WRETURN_TYPE_CONST_QUALIFIER_BUG_OK - Success
> -- Test successful, do not define DEAL_II_WRETURN_TYPE_CONST_QUALIFIER_BUG
> -- Performing Test DEAL_II_TEMPL_SPEC_FRIEND_BUG_OK
> -- Performing Test DEAL_II_TEMPL_SPEC_FRIEND_BUG_OK - Success
> -- Test successful, do not define DEAL_II_TEMPL_SPEC_FRIEND_BUG
> -- Performing Test DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG_OK
> -- Performing Test DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG_OK - Success
> -- Test successful, do not define DEAL_II_MEMBER_ARRAY_SPECIALIZATION_BUG
> -- Performing Test DEAL_II_MEMBER_VAR_SPECIALIZATION_BUG_OK
> -- Performing Test DEAL_II_MEMBER_VAR_SPECIALIZATION_BUG_OK - Success
> -- Test successful, do not define DEAL_II_MEMBER_VAR_SPECIALIZATION_BUG
> -- Performing Test DEAL_II_EXPLICIT_CONSTRUCTOR_BUG
> -- Performing Test DEAL_II_EXPLICIT_CONSTRUCTOR_BUG - Failed
> -- Performing Test DEAL_II_CONST_MEMBER_DEDUCTION_BUG_OK
> -- Performing Test DEAL_II_CONST_MEMBER_DEDUCTION_BUG_OK - Success
> -- Test successful, do not define DEAL_II_CONST_MEMBER_DEDUCTION_BUG
> -- Performing Test DEAL_II_TYPE_QUALIFIER_BUG_OK
> -- Performing Test DEAL_II_TYPE_QUALIFIER_BUG_OK - Success
> -- Test successful, do not define DEAL_II_TYPE_QUALIFIER_BUG
> -- Performing Test DEAL_II_BOOST_BIND_COMPILER_BUG_OK
> -- Performing Test DEAL_II_BOOST_BIND_COMPILER_BUG_OK - Failed
> -- Test unsuccessful, define DEAL_II_BOOST_BIND_COMPILER_BUG
> -- Performing Test DEAL_II_BIND_NO_CONST_OP_PARENTHESES_OK
> -- Performing Test DEAL_II_BIND_NO_CONST_OP_PARENTHESES_OK - Success
> -- Test successful, do not define DEAL_II_BIND_NO_CONST_OP_PARENTHESES
> -- Performing Test DEAL_II_ICC_SFINAE_BUG_OK
> -- Performing Test DEAL_II_ICC_SFINAE_BUG_OK - Success
> -- Test successful, do not define DEAL_II_ICC_SFINAE_BUG
> --
> -- Include /dealii-8.4.1-PETSc/cmake/checks/check_03_generator_bugs.cmake
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_1_bzip2.cmake
> -- Could NOT find BZip2 (missing: BZIP2_LIBRARIES BZIP2_INCLUDE_DIR)
> -- BZIP2_LIBRARIES: *** Required variable "_bzip2_libraries" set to
> NOTFOUND ***
> -- BZIP2_INCLUDE_DIRS: *** Required variable "BZIP2_INCLUDE_DIR" set to
> NOTFOUND ***
> -- Could NOT find BZIP2
> -- DEAL_II_WITH_BZIP2 has unmet external dependencies.
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_1_lapack.cmake
> -- Looking for Fortran sgemm
> -- Looking for Fortran sgemm - found
> -- Looking for pthread.h
> -- Looking for pthread.h - found
> -- Looking for pthread_create
> -- Looking for pthread_create - not found
> -- Looking for pthread_create in pthreads
> -- Looking for pthread_create in pthreads - not found
> -- Looking for pthread_create in pthread
> -- Looking for pthread_create in pthread - found
> -- Found Threads: TRUE
> -- A library with BLAS API found.
> -- Looking for Fortran cheev
> -- Looking for Fortran cheev - found
> -- A library with LAPACK API found.
> -- Performing Test gfortran_LIBRARY
> -- Performing Test gfortran_LIBRARY - Success
> -- Performing Test quadmath_LIBRARY
> -- Performing Test quadmath_LIBRARY - Success
> -- Performing Test c_LIBRARY
> -- Performing Test c_LIBRARY - Success
> -- LAPACK_LIBRARIES:
> /usr/lib/liblapack.so;/usr/lib/libblas.so;/usr/lib/libblas.so;gfortran;m;quadmath;m;c
> -- LAPACK_LINKER_FLAGS:
> -- Found LAPACK
> -- Performing Test DEAL_II_HAVE_FLAG_pthread
> -- Performing Test DEAL_II_HAVE_FLAG_pthread - Success
> -- Performing Test LAPACK_SYMBOL_CHECK
> -- Performing Test LAPACK_SYMBOL_CHECK - Success
> -- DEAL_II_WITH_LAPACK successfully set up with external dependencies.
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_1_mpi.cmake
> -- DEAL_II_WITH_MPI is set to off.
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_1_threads.cmake
> -- TBB_LIBRARY not found! Call:
> -- FIND_LIBRARY(TBB_LIBRARY NAMES tbb HINTS PATH_SUFFIXES lib lib64
> lib)
> -- TBB_DEBUG_LIBRARY not found! Call:
> -- FIND_LIBRARY(TBB_DEBUG_LIBRARY NAMES tbb_debug HINTS PATH_SUFFIXES
> lib lib64 lib)
> -- TBB_INCLUDE_DIR not found! Call:
> -- FIND_PATH(TBB_INCLUDE_DIR tbb/tbb_stddef.h HINTS PATH_SUFFIXES
> include include/tbb tbb)
> -- TBB_LIBRARIES: *** Required variable "TBB_LIBRARY" set to NOTFOUND ***
> -- TBB_INCLUDE_DIRS: *** Required variable "TBB_INCLUDE_DIR" set to
> NOTFOUND ***
> -- TBB_USER_INCLUDE_DIRS: *** Required variable "TBB_INCLUDE_DIR" set to
> NOTFOUND ***
> -- Could NOT find TBB
> -- DEAL_II_WITH_THREADS has unmet external dependencies.
> -- Performing Test DEAL_II_HAVE_MT_POSIX_BARRIERS
> -- Performing Test DEAL_II_HAVE_MT_POSIX_BARRIERS - Success
> -- Performing Test DEAL_II_HAVE_FLAG_Wparentheses
> -- Performing Test DEAL_II_HAVE_FLAG_Wparentheses - Success
> -- DEAL_II_WITH_THREADS successfully set up with bundled packages.
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_1_zlib.cmake
> -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.2.8")
> -- ZLIB_VERSION: 1.2.8
> -- ZLIB_LIBRARIES: /usr/lib/x86_64-linux-gnu/libz.so
> -- ZLIB_INCLUDE_DIRS: /usr/include
> -- Found ZLIB
> -- DEAL_II_WITH_ZLIB successfully set up with external dependencies.
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_2_metis.cmake
> -- METIS_LIBRARY not found! Call:
> -- FIND_LIBRARY(METIS_LIBRARY NAMES metis HINTS PATH_SUFFIXES lib
> lib64 lib build/Linux-x86_64/libmetis)
> -- PARMETIS_LIBRARY not found! Call:
> -- FIND_LIBRARY(PARMETIS_LIBRARY NAMES parmetis HINTS NO_DEFAULT_PATH
> NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH NO_SYSTEM_ENVIRONMENT_PATH
> NO_CMAKE_SYSTEM_PATH NO_CMAKE_FIND_ROOT_PATH)
> -- METIS_INCLUDE_DIR not found! Call:
> -- FIND_PATH(METIS_INCLUDE_DIR metis.h HINTS PATH_SUFFIXES metis
> include/metis include)
> -- METIS_LIBRARIES: *** Required variable "METIS_LIBRARY" set to
> NOTFOUND ***
> -- METIS_INCLUDE_DIRS: *** Required variable "METIS_INCLUDE_DIR" set to
> NOTFOUND ***
> -- METIS_USER_INCLUDE_DIRS: *** Required variable "METIS_INCLUDE_DIR"
> set to NOTFOUND ***
> -- Could NOT find METIS
> -- DEAL_II_WITH_METIS has unmet external dependencies.
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_2_trilinos.cmake
> -- EPETRA_CONFIG_H not found! Call:
> -- FIND_FILE(EPETRA_CONFIG_H Epetra_config.h HINTS NO_DEFAULT_PATH
> NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH NO_SYSTEM_ENVIRONMENT_PATH
> NO_CMAKE_SYSTEM_PATH NO_CMAKE_FIND_ROOT_PATH)
> -- SACADO_CONFIG_H not found! Call:
> -- FIND_FILE(SACADO_CONFIG_H Sacado_config.h HINTS NO_DEFAULT_PATH
> NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH NO_SYSTEM_ENVIRONMENT_PATH
> NO_CMAKE_SYSTEM_PATH NO_CMAKE_FIND_ROOT_PATH)
> -- SACADO_CMATH_HPP not found! Call:
> -- FIND_FILE(SACADO_CMATH_HPP Sacado_cmath.hpp HINTS NO_DEFAULT_PATH
> NO_CMAKE_ENVIRONMENT_PATH NO_CMAKE_PATH NO_SYSTEM_ENVIRONMENT_PATH
> NO_CMAKE_SYSTEM_PATH NO_CMAKE_FIND_ROOT_PATH)
> -- TRILINOS_LIBRARIES:
> -- TRILINOS_INCLUDE_DIRS: *** Required variable "Trilinos_INCLUDE_DIRS"
> empty ***
> -- TRILINOS_USER_INCLUDE_DIRS: *** Required variable
> "Trilinos_INCLUDE_DIRS" empty ***
> -- Could NOT find TRILINOS
> -- DEAL_II_WITH_TRILINOS has unmet external dependencies.
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_2_umfpack.cmake
> -- Found UMFPACK_INCLUDE_DIR
> -- Found AMD_INCLUDE_DIR
> -- Found SuiteSparse_config_INCLUDE_DIR
> -- Found UMFPACK_LIBRARY
> -- Found AMD_LIBRARY
> -- Found CHOLMOD_LIBRARY
> -- Found COLAMD_LIBRARY
> -- Found CCOLAMD_LIBRARY
> -- Found CAMD_LIBRARY
> -- Found SuiteSparse_config_LIBRARY
> -- Performing Test LAPACK_SUITESPARSECONFIG_WITH_PIC
> -- Performing Test LAPACK_SUITESPARSECONFIG_WITH_PIC - Failed
> -- Performing Test rt_LIBRARY
> -- Performing Test rt_LIBRARY - Success
> -- UMFPACK_VERSION: 5.7.1
> -- UMFPACK_LIBRARIES:
> /usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/liblapack.so;/usr/lib/libblas.so;gfortran;quadmath;m;c;rt
> -- UMFPACK_INCLUDE_DIRS:
> /usr/include/suitesparse;/usr/include/suitesparse;/usr/include/suitesparse
> -- UMFPACK_USER_INCLUDE_DIRS:
> /usr/include/suitesparse;/usr/include/suitesparse;/usr/include/suitesparse
> -- UMFPACK_LINKER_FLAGS:
> -- Found UMFPACK
> -- DEAL_II_WITH_UMFPACK successfully set up with external dependencies.
> --
> -- Include /dealii-8.4.1-PETSc/cmake/configure/configure_3_petsc.cmake
> -- Found PETSC_LIBRARY
> -- Found PETSC_INCLUDE_DIR_ARCH
> -- Found PETSC_INCLUDE_DIR_COMMON
> -- PETSC_PETSCVARIABLES not found! Call:
> -- FIND_FILE(PETSC_PETSCVARIABLES NAMES petscvariables HINTS
> /petsc-3.6.4/arch-linux2-c-debug/lib/x86_64
> /petsc-3.6.4/arch-linux2-c-debug/lib PATH_SUFFIXES conf)
> -- PETSC_VERSION: 3.6.2.0
> -- PETSC_LIBRARIES: /petsc-3.6.4/arch-linux2-c-debug/lib/libpetsc.so
> -- PETSC_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
> -- PETSC_USER_INCLUDE_DIRS: /usr/include/petsc;/usr/include/petsc
> -- Found PETSC
> -- Could not find a sufficient PETSc installation: PETSc has to be
> configured with the same MPI configuration as deal.II.
> -- DEAL_II_WITH_PETSC has unmet external dependencies.
> CMake Error at cmake/configure/configure_3_petsc.cmake:110 (MESSAGE):
>
>
> Could not find the petsc library!
>
> Could not find a sufficient PETSc installation:
>
> PETSc has to be configured with the same MPI configuration as deal.II,
> but
> found:
>
> DEAL_II_WITH_MPI = OFF
> PETSC_WITH_MPI = (NOT FALSE)
>
>
>
> Please ensure that the petsc library version 3.0.0 or newer is installed
> on
> your computer and is configured with the same mpi options as deal.II
>
> If the library is not at a default location, either provide some hints
>
> for the autodetection:
>
> PETSc installed with --prefix=<...> to a destination:
>
> $ PETSC_DIR="..." cmake <...>
> $ cmake -DPETSC_DIR="..." <...>
>
> PETSc compiled in source tree:
>
> $ PETSC_DIR="..." PETSC_ARCH="..." cmake <...>
> $ cmake -DPETSC_DIR="..." -DPETSC_ARCH="..." <...>
>
> or set the relevant variables by hand in ccmake.
>
>
>
> Call Stack (most recent call first):
> build/CMakeFiles/CMakeTmp/macro_configure_feature.tmp:1
> (FEATURE_PETSC_ERROR_MESSAGE)
> cmake/macros/macro_configure_feature.cmake:76 (INCLUDE)
> cmake/macros/macro_configure_feature.cmake:272 (RUN_COMMAND)
> cmake/configure/configure_3_petsc.cmake:129 (CONFIGURE_FEATURE)
> cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
> CMakeLists.txt:119 (VERBOSE_INCLUDE)
>
>
> -- Configuring incomplete, errors occurred!
> See also "/dealii-8.4.1-PETSc/build/CMakeFiles/CMakeOutput.log".
> See also "/dealii-8.4.1-PETSc/build/CMakeFiles/CMakeError.log".
>
>
> =======================================================================================================================
> Originally I tried (and numerous other combinations):
>
> sudo apt-get install libpetsc3.6.2-dev
> and
> sudo apt-get install libopenmpi-dev
>
> all work well til:
>
> make test
>
> when a number of errors including:
>
> /usr/lib/openmpi/lib/libmpi_cxx.so: error: undefined reference to
> 'opal_list_item_t_class'
> /usr/lib/openmpi/lib/libmpi_cxx.so: error: undefined reference to
> 'opal_class_initialize'
>
> CMakeFiles/Makefile2:3087: recipe for target
> 'tests/quick_tests/CMakeFiles/step.debug.dir/all' failed
> CMakeFiles/Makefile2:3384: recipe for target
> 'tests/quick_tests/CMakeFiles/step.debug.run.dir/rule' failed
> Makefile:1111: recipe for target 'step.debug.run' failed
>
> CMakeFiles/Makefile2:3571: recipe for target
> 'tests/quick_tests/CMakeFiles/step.release.dir/all' failed
>
> resulted.
>
>
> sudo apt-get install libmpich-dev
> with
> sudo apt-get install libpetsc3.6.2-dev
> also had problems
>
>
> =====================================================================================================
>
>
--
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