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glotzerlab / hoomd-blue

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
http://glotzerlab.engin.umich.edu/hoomd-blue
BSD 3-Clause "New" or "Revised" License
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Compile fails with gcc 5.3.1 #122

Closed joaander closed 8 years ago

joaander commented 8 years ago

Original report by Ruggero Cortini (Bitbucket: ruggerocortini, ).

Dear hoomd-blue developers, I am trying to build the package with Fedora 23, which ships with gcc 5.3.1

I am obtaining the following error at linking stage :

[ 72%] Linking CXX executable test_fenebond_force CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function init_unit_test()': test_fenebond_force.cc:(.text+0x42): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function `void std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct<char>(char, char, std::forward_iterator_tag) [clone .isra.204]': test_fenebond_force.cc:(.text+0x11b): undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In functionbool boost::test_tools::tt_detail::check_frwd<boost::test_tools::check_is_close_t, float, float, boost::test_tools::percent_tolerance_t >(boost::test_tools::check_is_close_t, boost::unit_test::lazy_ostream const&, boost::unit_test::basic_cstring, unsigned long, boost::test_tools::tt_detail::tool_level, boost::test_tools::tt_detail::check_type, float const&, char const, float const&, char const, boost::test_tools::percent_tolerance_t const&, char const) [clone .constprop.514]': test_fenebond_force.cc:(.text+0x7b5): undefined reference to std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >::basic_ostringstream(std::_Ios_Openmode)' test_fenebond_force.cc:(.text+0xa14): undefined reference tovtable for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text+0xa1c): undefined reference to `vtable for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text+0xa24): undefined reference to vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >' test_fenebond_force.cc:(.text+0xa46): undefined reference toVTT for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text+0xa4d): undefined reference to `VTT for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function GPUArray<float>::aquire(access_location::Enum, access_mode::Enum, bool) const [clone .constprop.513]': test_fenebond_force.cc:(.text+0xb6a): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text+0xc0f): undefined reference to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text+0xc88): undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In functionGPUArray::aquire(access_location::Enum, access_mode::Enum, bool) const [clone .constprop.512]': test_fenebond_force.cc:(.text+0xe2a): undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' test_fenebond_force.cc:(.text+0xecf): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o:test_fenebond_force.cc:(.text+0xf48): more undefined references to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' follow CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function boost::system::system_error::what() const': test_fenebond_force.cc:(.text._ZNK5boost6system12system_error4whatEv[_ZNK5boost6system12system_error4whatEv]+0x4c): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)' test_fenebond_force.cc:(.text._ZNK5boost6system12system_error4whatEv[_ZNK5boost6system12system_error4whatEv]+0x77): undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const, unsigned long)' test_fenebond_force.cc:(.text._ZNK5boost6system12system_error4whatEv[_ZNK5boost6system12system_error4whatEv]+0xb1): undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const, unsigned long)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function PotentialBond<EvaluatorBondFENE>::getLogValue(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned int)': test_fenebond_force.cc:(.text._ZN13PotentialBondI17EvaluatorBondFENEE11getLogValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEj[_ZN13PotentialBondI17EvaluatorBondFENEE11getLogValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEj]+0xd8): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function boost::detail::sp_counted_impl_p<boost::basic_wrap_stringstream<char> >::dispose()': test_fenebond_force.cc:(.text._ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv[_ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv]+0x31): undefined reference tovtable for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text._ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv[_ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv]+0x39): undefined reference to `vtable for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text._ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv[_ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv]+0x41): undefined reference to vtable for std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >' test_fenebond_force.cc:(.text._ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv[_ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv]+0x63): undefined reference toVTT for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text._ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv[_ZN5boost6detail17sp_counted_impl_pINS_23basic_wrap_stringstreamIcEEE7disposeEv]+0x6a): undefined reference to `VTT for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function boost::exception_detail::error_info_container_impl::diagnostic_information(char const*) const': test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x2b): undefined reference tostd::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::basic_ostringstream(std::_Ios_Openmode)' test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x153): undefined reference to std::__cxx11::basic_stringbuf<char, std::char_traits<char>, std::allocator<char> >::str() const' test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x160): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::swap(std::cxx11::basic_string<char, std::char_traits, std::allocator >&)' test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x18d): undefined reference to vtable for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >' test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x199): undefined reference tovtable for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x1a2): undefined reference to `vtable for std::cxx11::basic_stringbuf<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x1c9): undefined reference to VTT for std::__cxx11::basic_ostringstream<char, std::char_traits<char>, std::allocator<char> >' test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x1d8): undefined reference toVTT for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >' test_fenebond_force.cc:(.text._ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc[_ZNK5boost16exception_detail25error_info_container_impl22diagnostic_informationEPKc]+0x234): undefined reference to `std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function boost::exception_detail::error_info_injector<boost::bad_function_call>::error_info_injector(boost::exception_detail::error_info_injector<boost::bad_function_call> const&)': test_fenebond_force.cc:(.text._ZN5boost16exception_detail19error_info_injectorINS_17bad_function_callEEC2ERKS3_[_ZN5boost16exception_detail19error_info_injectorINS_17bad_function_callEEC5ERKS3_]+0xd): undefined reference tostd::runtime_error::runtime_error(std::runtime_error const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function void boost::throw_exception<boost::bad_function_call>(boost::bad_function_call const&)': test_fenebond_force.cc:(.text._ZN5boost15throw_exceptionINS_17bad_function_callEEEvRKT_[_ZN5boost15throw_exceptionINS_17bad_function_callEEEvRKT_]+0x20): undefined reference tostd::runtime_error::runtime_error(std::runtime_error const&)' test_fenebond_force.cc:(.text._ZN5boost15throw_exceptionINS_17bad_functioncallEEEvRKT[_ZN5boost15throw_exceptionINS_17bad_functioncallEEEvRKT]+0x6a): undefined reference to std::runtime_error::runtime_error(std::runtime_error const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In functionboost::function1<boost::shared_ptr<PotentialBond >, boost::shared_ptr >::operator()(boost::shared_ptr) const': test_fenebond_force.cc:(.text._ZNK5boost9function1INS_10shared_ptrI13PotentialBondI17EvaluatorBondFENEEEENS1I16SystemDefinitionEEEclES7[_ZNK5boost9function1INS_10shared_ptrI13PotentialBondI17EvaluatorBondFENEEEENS1I16SystemDefinitionEEEclES7]+0x8e): undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In functionboost::exception_detail::clone_impl<boost::exception_detail::error_info_injector >::clone() const': test_fenebond_force.cc:(.text._ZNK5boost16exception_detail10clone_implINS0_19error_info_injectorINS_17bad_function_callEEEE5cloneEv[_ZNK5boost16exception_detail10clone_implINS0_19error_info_injectorINS_17bad_function_callEEEE5cloneEv]+0x23): undefined reference to std::runtime_error::runtime_error(std::runtime_error const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In functionstd::cxx11::basic_string<char, std::char_traits, std::allocator > std::operator+<char, std::char_traits, std::allocator >(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)': test_fenebond_force.cc:(.text._ZStplIcSt11char_traitsIcESaIcEENSt7cxx1112basic_stringIT_T0_T1_EERKS8SA[_ZStplIcSt11char_traitsIcESaIcEENSt7cxx1112basic_stringIT_T0_T1_EERKS8SA]+0x2f): undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In functionGPUArray::aquire(access_location::Enum, access_mode::Enum, bool) const': test_fenebond_force.cc:(.text._ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb[_ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb]+0x14b): undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' test_fenebond_force.cc:(.text._ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb[_ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb]+0x202): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text._ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb[_ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb]+0x2d7): undefined reference to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text._ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb[_ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb]+0x33f): undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' test_fenebond_force.cc:(.text._ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb[_ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb]+0x3af): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o:test_fenebond_force.cc:(.text._ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb[_ZNK8GPUArrayIfE6aquireEN15access_location4EnumEN11access_mode4EnumEb]+0x41f): more undefined references to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' follow CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function `PotentialBond::PotentialBond(boost::shared_ptr, std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)': test_fenebond_force.cc:(.text._ZN13PotentialBondI17EvaluatorBondFENEEC2EN5boost10shared_ptrI16SystemDefinitionEERKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN13PotentialBondI17EvaluatorBondFENEEC5EN5boost10shared_ptrI16SystemDefinitionEERKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x29b): 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&)' test_fenebond_force.cc:(.text._ZN13PotentialBondI17EvaluatorBondFENEEC2EN5boost10shared_ptrI16SystemDefinitionEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN13PotentialBondI17EvaluatorBondFENEEC5EN5boost10shared_ptrI16SystemDefinitionEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x37d): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function GPUArray<float4>::resize(unsigned int)': test_fenebond_force.cc:(.text._ZN8GPUArrayI6float4E6resizeEj[_ZN8GPUArrayI6float4E6resizeEj]+0x12c): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function GPUArray<float4>::resize(unsigned int, unsigned int)': test_fenebond_force.cc:(.text._ZN8GPUArrayI6float4E6resizeEjj[_ZN8GPUArrayI6float4E6resizeEjj]+0xfd): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function GPUArray<unsigned int>::allocate()': test_fenebond_force.cc:(.text._ZN8GPUArrayIjE8allocateEv[_ZN8GPUArrayIjE8allocateEv]+0x155): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text._ZN8GPUArrayIjE8allocateEv[_ZN8GPUArrayIjE8allocateEv]+0x24a): undefined reference to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function PotentialBondGPU<EvaluatorBondFENE, &(gpu_compute_fene_forces(bond_args_t const&, float4 const*, unsigned int*))>::PotentialBondGPU(boost::shared_ptr<SystemDefinition>, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': test_fenebond_force.cc:(.text._ZN16PotentialBondGPUI17EvaluatorBondFENEXadL_Z23gpu_compute_fene_forcesRK11bond_args_tPK6float4PjEEEC2EN5boost10shared_ptrI16SystemDefinitionEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE[_ZN16PotentialBondGPUI17EvaluatorBondFENEXadL_Z23gpu_compute_fene_forcesRK11bond_args_tPK6float4PjEEEC5EN5boost10shared_ptrI16SystemDefinitionEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE]+0x79e): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o:test_fenebond_force.cc:(.text._ZN8GPUArrayIjE6resizeEj[_ZN8GPUArrayIjE6resizeEj]+0x130): more undefined references to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' follow CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function std::_Rb_tree<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, ProfileDataElem>, std::_Select1st<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, ProfileDataElem> >, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, ProfileDataElem> > >::_M_get_insert_unique_pos(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': test_fenebond_force.cc:(.text._ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15ProfileDataElemESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE24_M_get_insert_unique_posERS7_[_ZNSt8_Rb_treeINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt4pairIKS5_15ProfileDataElemESt10_Select1stIS9_ESt4lessIS5_ESaIS9_EE24_M_get_insert_unique_posERS7_]+0x98): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function std::map<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, ProfileDataElem, std::less<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::allocator<std::pair<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const, ProfileDataElem> > >::operator[](std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': test_fenebond_force.cc:(.text._ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6_EEEixERSA_[_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6_EEEixERSA_]+0xce): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' test_fenebond_force.cc:(.text._ZNSt3mapINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6EEEixERSA[_ZNSt3mapINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6EEEixERSA]+0x22a): undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::__cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' test_fenebond_force.cc:(.text._ZNSt3mapINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6EEEixERSA[_ZNSt3mapINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6EEEixERSA]+0x247): undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' test_fenebond_force.cc:(.text._ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6EEEixERSA[_ZNSt3mapINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6EEEixERSA]+0x2c4): undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o:test_fenebond_force.cc:(.text._ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6_EEEixERSA_[_ZNSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE15ProfileDataElemSt4lessIS5_ESaISt4pairIKS5_S6_EEEixERSA_]+0x33b): more undefined references tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&) const' follow CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > >::_M_insert_aux(__gnu_cxx::__normal_iterator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >*, std::vector<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > > > >, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)': test_fenebond_force.cc:(.text._ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS5_S7_EERKS5_[_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS5_S7_EERKS5_]+0xa8): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text._ZNSt6vectorINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9gnu_cxx17normal_iteratorIPS5_S7EERKS5[_ZNSt6vectorINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9gnu_cxx17normal_iteratorIPS5_S7EERKS5]+0xee): 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&)' test_fenebond_force.cc:(.text._ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS5_S7_EERKS5_[_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS5_S7_EERKS5_]+0xfe): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text._ZNSt6vectorINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9gnu_cxx17normal_iteratorIPS5_S7EERKS5[_ZNSt6vectorINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9gnu_cxx17normal_iteratorIPS5_S7EERKS5]+0x10e): 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&)' test_fenebond_force.cc:(.text._ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS5_S7_EERKS5_[_ZNSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9__gnu_cxx17__normal_iteratorIPS5_S7_EERKS5_]+0x11e): undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o:test_fenebond_force.cc:(.text._ZNSt6vectorINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9gnu_cxx17normal_iteratorIPS5_S7EERKS5[_ZNSt6vectorINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS5_EE13_M_insert_auxEN9gnu_cxx17normal_iteratorIPS5_S7EERKS5]+0x12e): more undefined references 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&)' follow CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In functionPotentialBond::computeForces(unsigned int)': test_fenebond_force.cc:(.text._ZN13PotentialBondI17EvaluatorBondFENEE13computeForcesEj[_ZN13PotentialBondI17EvaluatorBondFENEE13computeForcesEj]+0x545): undefined reference to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' test_fenebond_force.cc:(.text._ZN13PotentialBondI17EvaluatorBondFENEE13computeForcesEj[_ZN13PotentialBondI17EvaluatorBondFENEE13computeForcesEj]+0xa34): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text._ZN13PotentialBondI17EvaluatorBondFENEE13computeForcesEj[_ZN13PotentialBondI17EvaluatorBondFENEE13computeForcesEj]+0x100a): undefined reference to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o: In function PotentialBondGPU<EvaluatorBondFENE, &(gpu_compute_fene_forces(bond_args_t const&, float4 const*, unsigned int*))>::computeForces(unsigned int)': test_fenebond_force.cc:(.text._ZN16PotentialBondGPUI17EvaluatorBondFENEXadL_Z23gpu_compute_fene_forcesRK11bond_args_tPK6float4PjEEE13computeForcesEj[_ZN16PotentialBondGPUI17EvaluatorBondFENEXadL_Z23gpu_compute_fene_forcesRK11bond_args_tPK6float4PjEEE13computeForcesEj]+0x7a7): undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' test_fenebond_force.cc:(.text._ZN16PotentialBondGPUI17EvaluatorBondFENEXadL_Z23gpu_compute_fene_forcesRK11bond_args_tPK6float4PjEEE13computeForcesEj[_ZN16PotentialBondGPUI17EvaluatorBondFENEXadL_Z23gpu_compute_fene_forcesRK11bond_args_tPK6float4PjEEE13computeForcesEj]+0x82d): undefined reference to `std::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' CMakeFiles/test_fenebond_force.dir/test_fenebond_force.cc.o:test_fenebond_force.cc:(.text._ZN16PotentialBondGPUI17EvaluatorBondFENEXadL_Z23gpu_compute_fene_forcesRK11bond_args_tPK6float4PjEEE13computeForcesEj[_ZN16PotentialBondGPUI17EvaluatorBondFENEXadL_Z23gpu_compute_fene_forcesRK11bond_args_tPK6float4PjEEE13computeForcesEj]+0x8ab): more undefined references to std::runtime_error::runtime_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' follow ../../libhoomd/hoomd.so: undefined reference toVTT for std::cxx11::basic_istringstream<char, std::char_traits, std::allocator >' ../../libhoomd/hoomd.so: undefined reference to std::basic_istream<char, std::char_traits<char> >& std::operator>><char, std::char_traits<char>, std::allocator<char> >(std::basic_istream<char, std::char_traits<char> >&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)' ../../libhoomd/hoomd.so: undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::resize(unsigned long, char)' ../../libhoomd/hoomd.so: undefined reference to typeinfo for std::ios_base::failure[abi:cxx11]' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_iostreams.so: undefined reference tostd::ios_base::failure[abi:cxx11]::what() const@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_python.so: undefined reference to `std::range_error::range_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_mutate(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference toVTT for std::cxx11::basic_stringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_filesystem.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find_first_not_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_iostreams.so: undefined reference tostd::ios_base::failure[abi:cxx11]::~cxx11()@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to `std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to `std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::basic_ostringstream(std::_Ios_Openmode)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::~basic_string()@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find_last_not_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_filesystem.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace_aux(unsigned long, unsigned long, unsigned long, char)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_assign(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to typeinfo for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::basic_istream<char, std::char_traits >& std::operator>><char, std::char_traits, std::allocator >(std::basic_istream<char, std::char_traits >&, std::cxx11::basic_string<char, std::char_traits, std::allocator >&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_thread.so.1.58.0: undefined reference to std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference tostd::cxx11::basic_stringstream<char, std::char_traits, std::allocator >::~basic_stringstream()@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to std::logic_error::logic_error(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference tovtable for std::ios_base::failure[abi:cxx11]' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to `std::basic_istream<wchar_t, std::char_traits >& std::getline<wchar_t, std::char_traits, std::allocator >(std::basic_istream<wchar_t, std::char_traits >&, std::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >&, wchar_t)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference to std::ios_base::failure[abi:cxx11]::what() const' ../../libhoomd/hoomd.so: undefined reference tostd::runtime_error::runtime_error(std::runtime_error const&)' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/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' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_append(char const, unsigned long)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()' ../../libhoomd/hoomd.so: undefined reference tostd::cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::str(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_iostreams.so: undefined reference to std::ios_base::failure[abi:cxx11]::cxx11(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference totypeinfo for std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_iostreams.so: undefined reference to `std::ios_base::failure[abi:cxx11]::cxx11(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_filesystem.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' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::cxx11::numpunct const& std::use_facet<std::__cxx11::numpunct >(std::locale const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_python.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_construct(unsigned long, char)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::copy(char, unsigned long, unsigned long) const' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_serialization.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::resize(unsigned long, wchar_t)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference tovtable for std::cxx11::basic_istringstream<char, std::char_traits, std::allocator >' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_python.so: undefined reference to `std::invalid_argument::invalid_argument(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to std::logic_error::logic_error(std::logic_error const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_filesystem.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, wchar_t const*, unsigned long)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/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' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::runtime_error::runtime_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const' ../../libhoomd/hoomd.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::reserve(unsigned long)' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to vtable for std::__cxx11::basic_stringstream<char, std::char_traits<char>, std::allocator<char> >@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::resize(unsigned long, char)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference to `std::cxx11::basic_istringstream<char, std::char_traits, std::allocator >::~basic_istringstream()' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_filesystem.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find(char, unsigned long) const@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference tostd::ios_base::failure[abi:cxx11]::~cxx11()' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_python.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::_M_construct(unsigned long, wchar_t)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::find_last_of(char const, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_mutate(unsigned long, unsigned long, char const, unsigned long)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to `std::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/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' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference tostd::cxx11::basic_string<wchar_t, std::char_traits, std::allocator >::compare(wchar_t const*) const@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference to std::ios_base::failure[abi:cxx11]::~cxx11()' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_iostreams.so: undefined reference tostd::ios_base::failure[abi:cxx11]::~cxx11()@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::_M_replace(unsigned long, unsigned long, char const, unsigned long)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference to std::ios_base::failure[abi:cxx11]::cxx11(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::__cxx11::basic_string<char, std::char_traits, std::allocator >::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::_M_sync(char, unsigned long, unsigned long)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_filesystem.so: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::find_first_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::cxx11::basic_ostringstream<char, std::char_traits, std::allocator >::~basic_ostringstream()@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_iostreams.so: undefined reference to vtable for std::ios_base::failure[abi:cxx11]@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference tostd::cxx11::basic_string<char, std::char_traits, std::allocator >::find(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to `std::logic_error::logic_error(std::cxx11::basic_string<char, std::char_traits, std::allocator > const&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_program_options.so: undefined reference to std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>, std::allocator<wchar_t> >::~basic_string()@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tostd::basic_istream<char, std::char_traits >& std::getline<char, std::char_traits, std::allocator >(std::basic_istream<char, std::char_traits >&, std::__cxx11::basic_string<char, std::char_traits, std::allocator >&, char)@GLIBCXX_3.4.21' ../../libhoomd/hoomd.so: undefined reference to `std::cxx11::basic_string<char, std::char_traits, std::allocator >::compare(unsigned long, unsigned long, char const*) const' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_thread.so.1.58.0: undefined reference to std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::swap(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&)@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference tovtable for std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >@GLIBCXX_3.4.21' /usr/lib/gcc/x86_64-redhat-linux/5.3.1/../../../../lib64/libboost_unit_test_framework.so: undefined reference to `std::__cxx11::basic_stringbuf<char, std::char_traits, std::allocator >::str() const@GLIBCXX_3.4.21' collect2: error: ld returned 1 exit status test/unit/CMakeFiles/test_fenebond_force.dir/build.make:119: recipe for target 'test/unit/test_fenebond_force' failed make[2]: [test/unit/test_fenebond_force] Error 1 CMakeFiles/Makefile2:2061: recipe for target 'test/unit/CMakeFiles/test_fenebond_force.dir/all' failed make[1]: [test/unit/CMakeFiles/test_fenebond_force.dir/all] Error 2 Makefile:138: recipe for target 'all' failed make: *** [all] Error 2

I guess there is some issue with compatibility with the compiler?

joaander commented 8 years ago

HOOMD is not tested on GCC 5.x yet, nor with the C++11 stdlib.

Do these only occur in the unit tests and not hoomd.so? If so, you can disable unit test builds with cmake -DBUILD_TESTING=off.

joaander commented 8 years ago

Will add preliminary support for gcc 5x in v2.0.

joaander commented 8 years ago

Original comment by Matthew Spellings (Bitbucket: mspells, GitHub: klarh).

FWIW, compilation works fine for me with gcc 5.2.0 (on commit 1a8e0d9e ).

joaander commented 8 years ago

I haven't spun up a Fedora 23 VM to confirm, but I suspect that the issue results from boost being built with C++11 and hoomd not. Which is odd, because I think the default for gcc5 is --std=gnu++14.

Regardless, commit:fe93729f7 (off the currently experimental 2.0 branch) fixes compile errors with --std=c++11 on gcc-4.9. Perhaps next week I will install a Fedora 23 VM and see if I can reproduce this issue.

joaander commented 8 years ago

I was looking at the wrong gcc docs. The default is gnu++98 for gcc 5.3: https://gcc.gnu.org/onlinedocs/gcc-5.3.0/gcc/Standards.html#Standards

joaander commented 8 years ago

OK, I have a Fedora 23 VM and installed the packages:

Judging by the package list, it appears there is a full python2 stack as well.

I configure hoomd with: cmake -DCMAKE_CXX_FLAGS="--std=c++11" (on the cxx11 branch). It builds and passes all tests (CPU, no mpi).

Even when I build without --std=c++11, it builds and tests run fine. I'm not fully understanding what steps are needed to reproduce this. It appears that the boost that dnf installs in Fedora 23 is not linked to c++11. I don't understand because your error log clearly indicates that libboost_unit_test_framework.so is looking for symbols in the cxx11 namespace.

joaander commented 8 years ago

Cannot reproduce.