Closed sogoogos closed 6 years ago
alfbr
commented
6 years ago Currently we do not support any proprietary compilers, simply because nobody put up the necessary resources to do it. Most of us probably do not even have a license to the Intel compiler, and hence may have a hard time reproducing your issues. You will probably find that help is more readily available if you use gcc instead.
blattms
commented
6 years ago Just check with your system administrator. Usually they have gcc/g++ available as a fallback on clusters anyway.
sogoogos
commented
6 years ago Actually, I was using gcc initially then it did not work. The administrator said to use the intel compiler....
I could not even build opm-common with gcc due to the following error. It looks like Boost issue. I tried both Boost already installed in the system and the one I manually installed, but both of them did not work.
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /bin/cc
-- Check for working C compiler: /bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /bin/c++
-- Check for working CXX compiler: /bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- CMake version: 2.8.12.2
-- Linux distribution: CentOS Linux 7 (Core)
-- Target architecture: x86_64
-- Found Git: /opt/apps/git/2.9.0/bin/git (found version "2.9.0")
-- Source code repository: git 8ab7beb
-- GNU C++ compiler version: 4.8.5
-- Linker: ld 2.25.1-32.base.el7_4.2
-- Checking to see if CXX compiler accepts flag -Wl,--enable-new-dtags
-- Checking to see if CXX compiler accepts flag -Wl,--enable-new-dtags - yes
-- Precompiled headers: disabled
-- Build type: Release
-- Checking to see if CXX compiler accepts flag -mtune=native
-- Checking to see if CXX compiler accepts flag -mtune=native - yes
-- All warnings enabled: -Wall
-- OpenMP: disabled
-- Looking for include file pthread.h
-- Looking for include file 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
-- Checking to see if CXX compiler accepts flag -pthread
-- Checking to see if CXX compiler accepts flag -pthread - yes
-- Could NOT find CppCheck (missing: CPPCHECK_PROGRAM)
-- Disabling clang-check as CMAKE_EXPORT_COMPILE_COMMANDS is not enabled
-- Performing Test HAVE_C99
-- Performing Test HAVE_C99 - Success
-- Found C99: -std=c99
-- Checking to see if CXX compiler accepts flag -std=c++14
-- Checking to see if CXX compiler accepts flag -std=c++14 - no
-- Checking to see if CXX compiler accepts flag -std=c++11
-- Checking to see if CXX compiler accepts flag -std=c++11 - yes
-- Performing Test HAVE_FINAL
-- Performing Test HAVE_FINAL - Success
-- Performing Test HAVE_TYPE_TRAITS
-- Performing Test HAVE_TYPE_TRAITS - Success
-- Performing Test HAVE_SHARED_PTR
-- Performing Test HAVE_SHARED_PTR - Success
-- Performing Test HAVE_UNIQUE_PTR
-- Performing Test HAVE_UNIQUE_PTR - Success
-- Performing Test HAVE_NULLPTR
-- Performing Test HAVE_NULLPTR - Success
-- Performing Test HAVE_CONSTEXPR
-- Performing Test HAVE_CONSTEXPR - Success
-- Performing Test HAVE_ARRAY
-- Performing Test HAVE_ARRAY - Success
-- Performing Test HAVE_INTEGRAL_CONSTANT
-- Performing Test HAVE_INTEGRAL_CONSTANT - Success
-- Looking for C++ include tuple
-- Looking for C++ include tuple - found
-- Looking for C++ include tr1/tuple
-- Looking for C++ include tr1/tuple - found
-- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE
-- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE - Success
-- Performing Test HAS_ATTRIBUTE_UNUSED
-- Performing Test HAS_ATTRIBUTE_UNUSED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED
-- Performing Test HAS_ATTRIBUTE_DEPRECATED - Success
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG
-- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG - Success
-- Performing Test HAVE_STATIC_ASSERT
-- Performing Test HAVE_STATIC_ASSERT - Success
-- Performing Test HAVE_AUTO
-- Performing Test HAVE_AUTO - Success
-- Performing Test HAVE_VARIADIC_TEMPLATES
-- Performing Test HAVE_VARIADIC_TEMPLATES - Success
-- Performing Test HAVE_VARIADIC_CONSTRUCTOR_SFINAE
-- Performing Test HAVE_VARIADIC_CONSTRUCTOR_SFINAE - Success
-- Performing Test HAVE_RVALUE_REFERENCES
-- Performing Test HAVE_RVALUE_REFERENCES - Success
-- Looking for C++ include tr1/type_traits
-- Looking for C++ include tr1/type_traits - found
-- Boost version: 1.64.0
-- Found the following Boost libraries:
-- system
-- unit_test_framework
-- Generating debug symbols: -ggdb3
-- Looking for strip utility
-- Looking for strip utility - found
-- Performing Test HAVE_DYNAMIC_BOOST_TEST
-- Performing Test HAVE_DYNAMIC_BOOST_TEST - Failed
-- Writing config file "/work/02552/sogoogos/rmine/OPM_20180221/opm-common/cmake-build-release/config.h"...
-- This build defaults to installing in /work/02552/sogoogos/rmine/foo_20180221
-- Found Doxygen: /bin/doxygen (found version "1.8.5")
-- Writing version information to local header project-version.h
-- Configuring done
-- Generating done
-- Build files have been written to: /work/02552/sogoogos/rmine/OPM_20180221/opm-common/cmake-build-release
----------------------------
Linking CXX static library lib/libopmcommon.a
[ 64%] Built target opmcommon
Scanning dependencies of target test_OpmLog
Scanning dependencies of target test_SimulationDataContainer
[ 72%] [ 72%] Building CXX object CMakeFiles/test_SimulationDataContainer.dir/tests/test_SimulationDataContainer.cpp.o
Building CXX object CMakeFiles/test_OpmLog.dir/tests/test_OpmLog.cpp.o
Linking CXX executable bin/test_SimulationDataContainer
/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
CMakeFiles/test_SimulationDataContainer.dir/tests/test_SimulationDataContainer.cpp.o: In function `boost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long)':
test_SimulationDataContainer.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x20): undefined reference to `boost::unit_test::ut_detail::normalize_test_case_name(boost::unit_test::basic_cstring<char const>)'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_timer.so.1.64.0: undefined reference to `VTT for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_system.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::str() const@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_timer.so.1.64.0: undefined reference to `vtable for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_istringstream()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(char const*)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `typeinfo for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::rfind(char, unsigned long) const@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::_M_sync(char*, unsigned long, unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(char const*)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_system.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::append(char const*)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_system.so: undefined reference to `operator delete(void*, unsigned long)@CXXABI_1.3.9'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::basic_istringstream(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::_Ios_Openmode)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/test_SimulationDataContainer] Error 1
make[1]: *** [CMakeFiles/test_SimulationDataContainer.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
Linking CXX executable bin/test_OpmLog
/usr/lib/gcc/x86_64-redhat-linux/4.8.5/../../../../lib64/crt1.o: In function `_start':
(.text+0x20): undefined reference to `main'
CMakeFiles/test_OpmLog.dir/tests/test_OpmLog.cpp.o: In function `boost::unit_test::make_test_case(boost::function<void ()> const&, boost::unit_test::basic_cstring<char const>, boost::unit_test::basic_cstring<char const>, unsigned long)':
test_OpmLog.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x20): undefined reference to `boost::unit_test::ut_detail::normalize_test_case_name(boost::unit_test::basic_cstring<char const>)'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_timer.so.1.64.0: undefined reference to `VTT for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_system.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::operator=(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&&)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::str() const@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::basic_stringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_timer.so.1.64.0: undefined reference to `vtable for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_istringstream()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `vtable for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(char const*)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `typeinfo for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::reserve(unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `VTT for std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::rfind(char, unsigned long) const@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::_M_sync(char*, unsigned long, unsigned long)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(char const*)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_system.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::append(char const*)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_ostringstream()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_system.so: undefined reference to `operator delete(void*, unsigned long)@CXXABI_1.3.9'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_istringstream<char, std::char_traits<char>, std::allocator<char> >::basic_istringstream(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::_Ios_Openmode)@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21'
/opt/apps/gcc7_1/boost/1.64/lib/libboost_unit_test_framework.so: undefined reference to `std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
collect2: error: ld returned 1 exit status
make[2]: *** [bin/test_OpmLog] Error 1
make[1]: *** [CMakeFiles/test_OpmLog.dir/all] Error 2
make: *** [all] Error 2I close this and post the issue in opm-common page.
atgeirr
commented
6 years ago To your opm-output problem, I have only one suggestion: try changing line 36 of Solution.hpp from
Solution() = default;to
Solution() noexcept = default;I have no idea if that helps, since gcc and clang accepts the code as is.
blattms
commented
6 years ago -- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 ... /opt/apps/gcc7_1/boost/1.64/lib/libboost_timer.so.1.64.0: undefined reference to `VTT for std::__cxx11::basic_stringstream<char, std::char_traits
, std::allocator >@GLIBCXX_3.4.21'
Could it be possible that boost was compiled with gcc version 7.1? At least the path suggests this. Maybe you need to load the correct gcc/g++ version first?
module avail might list newer versions.
module load gcc_version would load gcc_version.
and please use the correct order (first the compiler,then mpi, then other libs, etc.)
atgeirr
commented
6 years ago Please move discussion to OPM/opm-common#336
sogoogos
commented
6 years ago @atgeirr Thank you for your suggestion, but unfortunately I got the same error with the change: Solution() noexcept = default;
Hello, I had the following problem when I was trying to build opm-output in a cluster Stampede2 (https://www.tacc.utexas.edu/systems/stampede2). I was able to build all the modules (dune-common dune-istl dune-geometry dune-grid libecl opm-common opm-parser opm-grid opm-material opm-output ewoms opm-simulators) in my local macbook in the same way. However, it did not somehow work in the cluster with Intel compiler. Can you tell what the problem is here?
Configuration message (cmake $OPM_CMAKE_OPTIONS ..)
-- The C compiler identification is Intel 17.0.0.20170411 -- The CXX compiler identification is Intel 17.0.0.20170411 -- Check for working C compiler: /opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicc -- Check for working C compiler: /opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx -- Check for working CXX compiler: /opt/intel/compilers_and_libraries_2017.4.196/linux/mpi/intel64/bin/mpicxx -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Performing Test HAVE_C99 -- Performing Test HAVE_C99 - Success -- Found C99: -std=c99
-- Checking to see if CXX compiler accepts flag -std=c++14 -- Checking to see if CXX compiler accepts flag -std=c++14 - yes -- Performing Test HAVE_FINAL -- Performing Test HAVE_FINAL - Success -- Performing Test HAVE_TYPE_TRAITS -- Performing Test HAVE_TYPE_TRAITS - Success -- Performing Test HAVE_SHARED_PTR -- Performing Test HAVE_SHARED_PTR - Success -- Performing Test HAVE_UNIQUE_PTR -- Performing Test HAVE_UNIQUE_PTR - Success -- Performing Test HAVE_NULLPTR -- Performing Test HAVE_NULLPTR - Success -- Performing Test HAVE_CONSTEXPR -- Performing Test HAVE_CONSTEXPR - Success -- Performing Test HAVE_ARRAY -- Performing Test HAVE_ARRAY - Success -- Performing Test HAVE_INTEGRAL_CONSTANT -- Performing Test HAVE_INTEGRAL_CONSTANT - Success -- Looking for C++ include tuple -- Looking for C++ include tuple - found -- Looking for C++ include tr1/tuple -- Looking for C++ include tr1/tuple - found -- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE -- Performing Test HAVE_ATTRIBUTE_ALWAYS_INLINE - Success -- Performing Test HAS_ATTRIBUTE_DEPRECATED -- Performing Test HAS_ATTRIBUTE_DEPRECATED - Success -- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG -- Performing Test HAS_ATTRIBUTE_DEPRECATED_MSG - Success -- Performing Test HAVE_STATIC_ASSERT -- Performing Test HAVE_STATIC_ASSERT - Success -- Performing Test HAVE_AUTO -- Performing Test HAVE_AUTO - Success -- Performing Test HAVE_VARIADIC_TEMPLATES -- Performing Test HAVE_VARIADIC_TEMPLATES - Success -- Performing Test HAVE_VARIADIC_CONSTRUCTOR_SFINAE -- Performing Test HAVE_VARIADIC_CONSTRUCTOR_SFINAE - Success -- Performing Test HAVE_RVALUE_REFERENCES -- Performing Test HAVE_RVALUE_REFERENCES - Success -- Looking for C++ include tr1/type_traits -- Looking for C++ include tr1/type_traits - found -- Boost version: 1.64.0 -- Found the following Boost libraries: -- unit_test_framework -- Found opm-common: /work/02552/sogoogos/rmine/OPM_20180221/opm-common/cmake-build-release/lib/libopmcommon.a
-- Could NOT find CJSON (missing: CJSON_INCLUDE_DIRS HAVE_CJSON) -- Found opm-parser: /work/02552/sogoogos/rmine/OPM_20180221/opm-parser/cmake-build-release/lib/libopmparser.a
-- CMake version: 2.8.12.2 -- Linux distribution: CentOS Linux 7 (Core) -- Target architecture: x86_64 -- Found Git: /opt/apps/git/2.9.0/bin/git (found version "2.9.0") -- Source code repository: git 165d5cc% -- Linker: ld 2.26.20160125 -- Precompiled headers: disabled -- Build type: Release -- OpenMP: disabled -- Looking for include file pthread.h -- Looking for include file pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - found -- Found Threads: TRUE
-- Could NOT find CppCheck (missing: CPPCHECK_PROGRAM) -- Disabling clang-check as CMAKE_EXPORT_COMPILE_COMMANDS is not enabled -- Performing Test HAVE_DYNAMIC_BOOST_TEST -- Performing Test HAVE_DYNAMIC_BOOST_TEST - Success -- Writing config file "/work/02552/sogoogos/rmine/OPM_20180221/opm-output/cmake-build-release/config.h"... -- This build defaults to installing in /work/02552/sogoogos/rmine/foo_20180221 -- Found Doxygen: /bin/doxygen (found version "1.8.5") -- Writing version information to local header project-version.h -- Configuring done -- Generating done -- Build files have been written to: /work/02552/sogoogos/rmine/OPM_20180221/opm-output/cmake-build-release
Building message (make $OPM_MAKE_OPTIONS)
Scanning dependencies of target update-version Scanning dependencies of target datafiles [ 2%] [ 5%] Updating version information Generating tests/summary_deck_non_constant_porosity.DATA [ 8%] Generating tests/FIRST_SIM.DATA [ 8%] Built target update-version [ 11%] Generating tests/summary_deck.DATA Scanning dependencies of target opmoutput [ 14%] Generating tests/group_group.DATA [ 17%] Generating tests/testblackoilstate3.DATA [ 20%] Generating tests/testrft.DATA [ 22%] Generating tests/table_deck.DATA [ 25%] Making "tests" data available in output tree [ 25%] Built target datafiles [ 31%] [ 31%] Building CXX object CMakeFiles/opmoutput.dir/opm/test_util/summaryIntegrationTest.cpp.o Building CXX object CMakeFiles/opmoutput.dir/opm/test_util/summaryRegressionTest.cpp.o [ 34%] Building CXX object CMakeFiles/opmoutput.dir/opm/test_util/summaryComparator.cpp.o [ 37%] Building CXX object CMakeFiles/opmoutput.dir/opm/test_util/EclFilesComparator.cpp.o [ 40%] Building CXX object CMakeFiles/opmoutput.dir/opm/output/eclipse/EclipseGridInspector.cpp.o [ 42%] Building CXX object CMakeFiles/opmoutput.dir/opm/output/eclipse/EclipseIO.cpp.o [ 45%] Building CXX object CMakeFiles/opmoutput.dir/opm/output/eclipse/LinearisedOutputTable.cpp.o In file included from /work/02552/sogoogos/rmine/OPM_20180221/opm-output/opm/output/eclipse/EclipseIO.hpp(35), from /work/02552/sogoogos/rmine/OPM_20180221/opm-output/opm/output/eclipse/EclipseIO.cpp(27): /work/02552/sogoogos/rmine/OPM_20180221/opm-output/opm/output/data/Solution.hpp(38): error: cannot determine the exception specification of the default constructor due to a circular dependency using Base::map; ^
[ 48%] Building CXX object CMakeFiles/opmoutput.dir/opm/output/eclipse/RestartIO.cpp.o compilation aborted for /work/02552/sogoogos/rmine/OPM_20180221/opm-output/opm/output/eclipse/EclipseIO.cpp (code 2) make[2]: [CMakeFiles/opmoutput.dir/opm/output/eclipse/EclipseIO.cpp.o] Error 2 make[2]: Waiting for unfinished jobs.... In file included from /work/02552/sogoogos/rmine/OPM_20180221/opm-output/opm/output/eclipse/RestartIO.hpp(34), from /work/02552/sogoogos/rmine/OPM_20180221/opm-output/opm/output/eclipse/RestartIO.cpp(30): /work/02552/sogoogos/rmine/OPM_20180221/opm-output/opm/output/data/Solution.hpp(38): error: cannot determine the exception specification of the default constructor due to a circular dependency using Base::map; ^
compilation aborted for /work/02552/sogoogos/rmine/OPM_20180221/opm-output/opm/output/eclipse/RestartIO.cpp (code 2) make[2]: [CMakeFiles/opmoutput.dir/opm/output/eclipse/RestartIO.cpp.o] Error 2 make[1]: [CMakeFiles/opmoutput.dir/all] Error 2 make: *** [all] Error 2