Thanks All!
Martin, after I commented out the line "ADD_FLAGS(DEAL_II_LINKER_FLAGS
"-fuse-ld=gold")" in "cmake/checks/check_01_compiler_features.cmake",
make test, worked. I ran step-17 and saw the speed improvement.
I will try (haven't done it before) to open a bug report on UBUNTU.
I will include your comments, as below, unless I hear from you otherwise.
I'm sure you have defined the problem better than I could!
===========================================================================================
... I can reproduce your error messages on my system (4.4.0-28-generic
#47-Ubuntu SMP Fri Jun 24 10:09:13 UTC 2016 x86_64 x86_64 x86_64
GNU/Linux):
$ cat test.cc
int main() {}
$ mpicxx -fuse-ld=gold test.cc
/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'
collect2: error: ld returned 1 exit status
This clearly is a bug in the OpenMPI implementation shipped by Ubuntu
16.04. I think someone should open a bug on the Ubuntu (or Debian?)
bug tracker but I lack the time to do so right now...
However, it only appears when using the gold linker. If one disables
the gold linker, everything works fine.
$ mpicxx test.cc
$
=============================================================================================
Pete Griffin
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
=====================================================================================================
--
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 [email protected]
<mailto:[email protected]>.
For more options, visit https://groups.google.com/d/optout.
