[Trilinos-Users] stk_util linking errors when building Trilinos master for Albany on OS X 10.11 (El Capitan)
T.J. Corona
tj.corona at kitware.com
Tue Mar 8 11:20:29 EST 2016
Using the following configuration:
cmake \
-D Trilinos_DISABLE_ENABLED_FORWARD_DEP_PACKAGES=ON \
-D CMAKE_INSTALL_PREFIX:PATH=${INSTALL_DIR} \
-D CMAKE_BUILD_TYPE:STRING=RELEASE \
-D BUILD_SHARED_LIBS:BOOL=ON \
-D TPL_ENABLE_MPI:BOOL=ON \
-D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \
-D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
-D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \
-D Teuchos_ENABLE_LONG_LONG_INT:BOOL=ON \
\
-D Trilinos_ENABLE_Teuchos:BOOL=ON \
-D Trilinos_ENABLE_Shards:BOOL=ON \
-D Trilinos_ENABLE_Sacado:BOOL=ON \
-D Trilinos_ENABLE_Epetra:BOOL=ON \
-D Trilinos_ENABLE_EpetraExt:BOOL=ON \
-D Trilinos_ENABLE_Ifpack:BOOL=ON \
-D Trilinos_ENABLE_AztecOO:BOOL=ON \
-D Trilinos_ENABLE_Amesos:BOOL=ON \
-D Trilinos_ENABLE_Anasazi:BOOL=ON \
-D Trilinos_ENABLE_Belos:BOOL=ON \
-D Trilinos_ENABLE_ML:BOOL=ON \
-D Trilinos_ENABLE_Phalanx:BOOL=ON \
-D Trilinos_ENABLE_Intrepid:BOOL=ON \
-D Trilinos_ENABLE_Intrepid2:BOOL=ON \
-D Trilinos_ENABLE_NOX:BOOL=ON \
-D Trilinos_ENABLE_Stratimikos:BOOL=ON \
-D Trilinos_ENABLE_Thyra:BOOL=ON \
-D Trilinos_ENABLE_Rythmos:BOOL=ON \
-D Trilinos_ENABLE_MOOCHO:BOOL=ON \
-D Trilinos_ENABLE_Stokhos:BOOL=ON \
-D Trilinos_ENABLE_Piro:BOOL=ON \
-D Trilinos_ENABLE_Teko:BOOL=ON \
\
-D Trilinos_ENABLE_STKIO:BOOL=ON \
-D Trilinos_ENABLE_STKMesh:BOOL=ON \
-D TPL_ENABLE_Boost:BOOL=ON \
-D Boost_INCLUDE_DIRS:FILEPATH="$BOOST_DIR/include" \
-D Boost_LIBRARY_DIRS:FILEPATH="$BOOST_DIR/lib" \
-D TPL_ENABLE_BoostLib:BOOL=ON \
-D BoostLib_INCLUDE_DIRS:FILEPATH="$BOOST_DIR/include" \
-D BoostLib_LIBRARY_DIRS:FILEPATH="$BOOST_DIR/lib" \
\
-D Trilinos_ENABLE_SEACASIoss:BOOL=ON \
-D Trilinos_ENABLE_SEACASExodus:BOOL=ON \
-D TPL_ENABLE_Netcdf:BOOL=ON \
-D Netcdf_INCLUDE_DIRS:PATH="$NETCDF_DIR/../include" \
-D Netcdf_LIBRARY_DIRS:PATH="$NETCDF_DIR/lib" \
-D TPL_ENABLE_HDF5:BOOL=ON \
-D HDF5_INCLUDE_DIRS:PATH="$HDF5_DIR/include" \
-D HDF5_LIBRARY_DIRS:PATH="$HDF5_DIR/lib" \
\
-D Trilinos_ENABLE_Tpetra:BOOL=ON \
-D Trilinos_ENABLE_Kokkos:BOOL=ON \
-D Trilinos_ENABLE_Ifpack2:BOOL=ON \
-D Trilinos_ENABLE_Amesos2:BOOL=ON \
-D Trilinos_ENABLE_Zoltan2:BOOL=ON \
-D Trilinos_ENABLE_MueLu:BOOL=ON \
-D Amesos2_ENABLE_KLU2:BOOL=ON \
\
-D Trilinos_ENABLE_EXPLICIT_INSTANTIATION:BOOL=ON \
-D Tpetra_INST_INT_LONG_LONG:BOOL=ON \
-D Tpetra_INST_INT_INT:BOOL=ON \
-D Tpetra_INST_DOUBLE:BOOL=ON \
-D Tpetra_INST_FLOAT:BOOL=OFF \
-D Tpetra_INST_COMPLEX_FLOAT:BOOL=OFF \
-D Tpetra_INST_COMPLEX_DOUBLE:BOOL=OFF \
-D Tpetra_INST_INT_LONG:BOOL=OFF \
-D Tpetra_INST_INT_UNSIGNED:BOOL=OFF \
\
-D Trilinos_ENABLE_Kokkos:BOOL=ON \
-D Trilinos_ENABLE_KokkosCore:BOOL=ON \
-D Phalanx_KOKKOS_DEVICE_TYPE:STRING="SERIAL" \
-D Phalanx_INDEX_SIZE_TYPE:STRING="INT" \
-D Phalanx_SHOW_DEPRECATED_WARNINGS:BOOL=OFF \
-D Kokkos_ENABLE_Serial:BOOL=ON \
-D Kokkos_ENABLE_OpenMP:BOOL=OFF \
-D Kokkos_ENABLE_Pthread:BOOL=OFF \
-D TPL_ENABLE_SuperLU:STRING=ON \
-D SuperLU_INCLUDE_DIRS:STRING="${SUPERLU_DIR}/include" \
-D SuperLU_LIBRARY_DIRS:STRING="${SUPERLU_DIR}/lib" \
\
../
I receive the following error:
[ 19%] Linking CXX shared library libstk_util_env.dylib
Undefined symbols for architecture x86_64:
"null_streambuf::null_streambuf()", referenced from:
stk::EnvData::EnvData() in EnvData.cpp.o
"null_streambuf::~null_streambuf()", referenced from:
stk::EnvData::EnvData() in EnvData.cpp.o
stk::EnvData::~EnvData() in EnvData.cpp.o
"stk::get_heap_used()", referenced from:
stk::diag::Trace::Trace(stk::diag::Writer&, char const*, int, bool) in Trace.cpp.o
stk::diag::Trace::~Trace() in Trace.cpp.o
"stk::all_reduce_impl(ompi_communicator_t*, unsigned long const*, unsigned long*, unsigned int, ompi_op_t*)", referenced from:
stk::get_memory_high_water_mark_across_processors(ompi_communicator_t*, unsigned long&, unsigned long&, unsigned long&) in memory_util.cpp.o
stk::get_memory_available_across_processors(ompi_communicator_t*, unsigned long&, unsigned long&, unsigned long&) in memory_util.cpp.o
"stk::all_write_string(ompi_communicator_t*, std::__1::basic_ostream<char, std::__1::char_traits<char> >&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
sierra::Env::output_flush() in Env.cpp.o
"stk::parallel_machine_rank(ompi_communicator_t*)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
stk::aggregate_messages(ompi_communicator_t*, std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char const*) in RuntimeMessage.cpp.o
"stk::parallel_machine_size(ompi_communicator_t*)", referenced from:
stk::get_memory_high_water_mark_across_processors(ompi_communicator_t*, unsigned long&, unsigned long&, unsigned long&) in memory_util.cpp.o
stk::get_memory_available_across_processors(ompi_communicator_t*, unsigned long&, unsigned long&, unsigned long&) in memory_util.cpp.o
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
stk::aggregate_messages(ompi_communicator_t*, std::__1::basic_ostringstream<char, std::__1::char_traits<char>, std::__1::allocator<char> >&, char const*) in RuntimeMessage.cpp.o
"stk::diag::Writer::pop()", referenced from:
stk::diag::pop(stk::diag::Writer&) in Trace.cpp.o
"stk::diag::Writer::push()", referenced from:
stk::diag::push(stk::diag::Writer&) in Trace.cpp.o
"stk::diag::Writer::dendl()", referenced from:
stk::diag::dendl(stk::diag::Writer&) in Trace.cpp.o
"stk::diag::Writer::operator<<(stk::diag::Writer& (*)(stk::diag::Writer&))", referenced from:
stk::diag::Trace::Trace(stk::diag::Writer&, char const*, int, bool) in Trace.cpp.o
stk::diag::Trace::~Trace() in Trace.cpp.o
"stk::diag::operator<<(stk::diag::Writer&, char const*)", referenced from:
stk::diag::Trace::Trace(stk::diag::Writer&, char const*, int, bool) in Trace.cpp.o
stk::diag::Trace::~Trace() in Trace.cpp.o
stk::diag::Trace::verbose_print(stk::diag::Writer&) const in Trace.cpp.o
"stk::diag::operator<<(stk::diag::Writer&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
stk::diag::Trace::~Trace() in Trace.cpp.o
"stk::Marshal::Marshal(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal::Marshal(unsigned int)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Bootstrap::Bootstrap(void (*)())", referenced from:
__GLOBAL__sub_I_RuntimeMessage.cpp in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator<<<std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(stk::Marshal&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator<<<std::type_info>(stk::Marshal&, std::type_info const&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator<<<int>(stk::Marshal&, int const&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator<<<long>(stk::Marshal&, long const&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator<<<unsigned long>(stk::Marshal&, unsigned long const&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator>><std::type_info const>(stk::Marshal&, std::type_info const&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator>><std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > >(stk::Marshal&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> >&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator>><int>(stk::Marshal&, int&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator>><long>(stk::Marshal&, long&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"stk::Marshal& stk::operator>><unsigned long>(stk::Marshal&, unsigned long&)", referenced from:
stk::report_deferred_messages(ompi_communicator_t*) in RuntimeMessage.cpp.o
"sierra::SignalHandler::add_handler(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, sierra::Callback<void>&)", referenced from:
stk::util::Scheduler::set_signal(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in Scheduler.cpp.o
"sierra::SignalHandler::check_signal_name(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&)", referenced from:
stk::util::Scheduler::set_signal(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in Scheduler.cpp.o
"sierra::SignalHandler::instance()", referenced from:
stk::util::Scheduler::set_signal(std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in Scheduler.cpp.o
"sierra::Env::HUP_received()", referenced from:
sierra::Env::is_shutdown_requested() in Env.cpp.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make[2]: *** [packages/stk/stk_util/stk_util/environment/libstk_util_env.12.7.dylib] Error 1
make[1]: *** [packages/stk/stk_util/stk_util/environment/CMakeFiles/stk_util_env.dir/all] Error 2
make: *** [all] Error 2
Any help would be greatly appreciated!
Thomas J. Corona
Kitware, Inc.
R&D Engineer
21 Corporate Drive
Clifton Park, NY 12065-8662
Phone: 518-881-4443
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