Error from shark-importer when compiling SHARK

[WR136a1]

Hi,

I was trying to run SHARK for my research, but I keep failing at compiling when linking shark-importer because of this error;

[ 95%] Linking CXX executable shark-importer /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/cmake -E cmake_link_script CMakeFiles/shark-importer.dir/link.txt --verbose=1 /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/x86_64-conda_cos6-linux-gnu-c++ -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/include -O3 -DNDEBUG -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib -Wl,-rpath-link,/mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib -L/mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib -rdynamic CMakeFiles/shark-importer.dir/src/importer/descendants.cpp.o CMakeFiles/shark-importer.dir/src/importer/main.cpp.o CMakeFiles/shark-importer.dir/src/importer/reader.cpp.o CMakeFiles/shark-importer.dir/src/importer/velociraptor.cpp.o -o shark-importer -Wl,-rpath,/mnt/2nddrive/mjh/Intern/Shark/shark-1.2.0/build: libshark.so -lgsl -lgslcblas -lhdf5_cpp -lhdf5 -lrt /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_log.a /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_filesystem.a /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_atomic.a /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_chrono.a /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_date_time.a /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_regex.a /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_thread.a -lpthread /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_program_options.a /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/lib/libboost_system.a -lpthread -lz -ldl -lm -lgomp -lpthread -lz -ldl -lm -lgomp /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/shark-importer.dir/src/importer/main.cpp.o: in function boost::log::v2_mt_posix::aux::record_pump<boost::log::v2_mt_posix::sources::severity_logger_mt<boost::log::v2_mt_posix::trivial::severity_level> >::~record_pump()': main.cpp:(.text._ZN5boost3log11v2_mt_posix3aux11record_pumpINS1_7sources18severity_logger_mtINS1_7trivial14severity_levelEEEED2Ev[_ZN5boost3log11v2_mt_posix3aux11record_pumpINS1_7sources18severity_logger_mtINS1_7trivial14severity_levelEEEED5Ev]+0x37): undefined reference toboost::log::v2_mt_posix::core::push_record_move(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5boost3log11v2_mt_posix3aux11record_pumpINS1_7sources18severity_logger_mtINS1_7trivial14severity_levelEEEED2Ev[_ZN5boost3log11v2_mt_posix3aux11record_pumpINS1_7sources18severity_logger_mtINS1_7trivial14severity_levelEEEED5Ev]+0x44): undefined reference to boost::log::v2_mt_posix::aux::stream_provider<char>::release_compound(boost::log::v2_mt_posix::aux::stream_provider<char>::stream_compound*)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5boost3log11v2_mt_posix3aux11record_pumpINS1_7sources18severity_logger_mtINS1_7trivial14severity_levelEEEED2Ev[_ZN5boost3log11v2_mt_posix3aux11record_pumpINS1_7sources18severity_logger_mtINS1_7trivial14severity_levelEEEED5Ev]+0x5d): undefined reference toboost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/shark-importer.dir/src/importer/main.cpp.o: in function void shark::Options::load<int>(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int&, bool) const': main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x78): undefined reference toboost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x85): undefined reference to boost::log::v2_mt_posix::core::get_logging_enabled() const' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0xe3): undefined reference toboost::log::v2_mt_posix::sources::aux::get_severity_level()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x104): undefined reference to boost::log::v2_mt_posix::core::open_record(boost::log::v2_mt_posix::attribute_set const&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x393): undefined reference toboost::log::v2_mt_posix::core::push_record_move(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x39c): undefined reference to `boost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x3ae): undefined reference to boost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x3c1): undefined reference toboost::log::v2_mt_posix::aux::stream_provider::allocate_compound(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x93b): undefined reference to boost::log::v2_mt_posix::record_view::public_data::destroy(boost::log::v2_mt_posix::record_view::public_data const*)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b[_ZNK5shark7Options4loadIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_b]+0x9b4): undefined reference toboost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/shark-importer.dir/src/importer/main.cpp.o: in function void shark::Options::load<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&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >&, bool) const': main.cpp:(.text._ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0x7c): undefined reference toboost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0x89): undefined reference to `boost::log::v2_mt_posix::core::get_logging_enabled() const' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0x19b): undefined reference to `boost::log::v2_mt_posix::sources::aux::get_severity_level()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0x1bc): undefined reference to boost::log::v2_mt_posix::core::open_record(boost::log::v2_mt_posix::attribute_set const&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0x443): undefined reference toboost::log::v2_mt_posix::core::push_record_move(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0x44c): undefined reference to `boost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0x45e): undefined reference to `boost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0x471): undefined reference to `boost::log::v2_mt_posix::aux::stream_provider::allocate_compound(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0xa1b): undefined reference to boost::log::v2_mt_posix::record_view::public_data::destroy(boost::log::v2_mt_posix::record_view::public_data const*)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b[_ZNK5shark7Options4loadINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_b]+0xae9): undefined reference toboost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/shark-importer.dir/src/importer/main.cpp.o: in function shark::importer::ImporterParameters::ImporterParameters(shark::Options const&)': main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x1c1): undefined reference toboost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x1ce): undefined reference to boost::log::v2_mt_posix::core::get_logging_enabled() const' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x2d3): undefined reference toboost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x2e0): undefined reference to boost::log::v2_mt_posix::core::get_logging_enabled() const' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x543): undefined reference toboost::log::v2_mt_posix::sources::aux::get_severity_level()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x564): undefined reference to boost::log::v2_mt_posix::core::open_record(boost::log::v2_mt_posix::attribute_set const&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x803): undefined reference toboost::log::v2_mt_posix::core::push_record_move(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x80c): undefined reference to `boost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x81e): undefined reference to boost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x831): undefined reference toboost::log::v2_mt_posix::aux::stream_provider::allocate_compound(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x8bb): undefined reference to boost::log::v2_mt_posix::sources::aux::get_severity_level()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x8df): undefined reference toboost::log::v2_mt_posix::core::open_record(boost::log::v2_mt_posix::attribute_set const&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0xb83): undefined reference to boost::log::v2_mt_posix::core::push_record_move(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0xb8c): undefined reference toboost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0xba1): undefined reference to boost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0xbb4): undefined reference toboost::log::v2_mt_posix::aux::stream_provider::allocate_compound(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x16af): undefined reference to `boost::log::v2_mt_posix::record_view::public_data::destroy(boost::log::v2_mt_posix::record_view::public_data const)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x1734): undefined reference to boost::log::v2_mt_posix::record_view::public_data::destroy(boost::log::v2_mt_posix::record_view::public_data const*)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x178a): undefined reference toboost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: main.cpp:(.text._ZN5shark8importer18ImporterParametersC2ERKNS_7OptionsE[_ZN5shark8importer18ImporterParametersC5ERKNS_7OptionsE]+0x18b2): undefined reference to `boost::log::v2_mt_posix::aux::stream_provider::release_compound(boost::log::v2_mt_posix::aux::stream_provider::stream_compound)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld generated: undefined reference to boost::log::v2_mt_posix::sources::aux::get_severity_level()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld generated: undefined reference toboost::log::v2_mt_posix::core::open_record(boost::log::v2_mt_posix::attribute_set const&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld generated: undefined reference to boost::log::v2_mt_posix::record_view::public_data::destroy(boost::log::v2_mt_posix::record_view::public_data const*)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld generated: undefined reference toboost::log::v2_mt_posix::aux::stream_provider::allocate_compound(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld generated: undefined reference to boost::log::v2_mt_posix::core::push_record_move(boost::log::v2_mt_posix::record&)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld generated: undefined reference toboost::log::v2_mt_posix::trivial::logger::get()' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld generated: undefined reference to boost::log::v2_mt_posix::aux::stream_provider<char>::release_compound(boost::log::v2_mt_posix::aux::stream_provider<char>::stream_compound*)' /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /mnt/2nddrive/mjh/Intern/Anaconda/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld generated: undefined reference toboost::log::v2_mt_posix::core::get_logging_enabled() const' collect2: error: ld returned 1 exit status make[2]: [CMakeFiles/shark-importer.dir/build.make:173: shark-importer] Error 1 make[2]: Leaving directory '/mnt/2nddrive/mjh/Intern/Shark/shark-1.2.0/build' make[1]: [CMakeFiles/Makefile2:99: CMakeFiles/shark-importer.dir/all] Error 2 make[1]: Leaving directory '/mnt/2nddrive/mjh/Intern/Shark/shark-1.2.0/build' make: *** [Makefile:149: all] Error 2

I first thought this problem was similar to the previous issue( #1 ) since the problem occured in the same place, shark-importer. I installed boost, gsl, and HDF5 in the conda environment, and from the code result it seems that the code has found the right compiler, so it seems not to be an interoperability problem shown in the previous issue. Until now I still don't have any clue what is wrong with my settings.

Could you please give me any advice to solve this problem? I attached the CMakeError.log file in case you need it CMakeError.log .

Thank you.

[rtobar]

@WR136a1 thanks for getting in touch, and sorry for not being to respond earlier, it's been a busy time.

This looks like a problem with your boost installation, which cannot be found. It could be possible that cmake is trying to use your system's boost installation rather than anaconda's, but that's a guess at this point. I can say with confidence though that this is not shark-importer in particular that is failing; if we removed it the same problem would happen when building the main shark executable.

Could you provide more information about your installation? Please provide:

• Linux version.
• If this is an HPC system, which modules you have loaded (and their versions)
• cmake, boost, anaconda versions
• cmake output when running for the first time
• The output of make, but add VERBOSE=1 to get a full dump of what the compiler is doing

I think that should be enough as a first start.

[WR136a1]

@rtobar Luckily, I successfully built SHARK after creating a new conda environment and re-installing all the packages. Thank you for your help.

However, now I have another question about the code, which I couldn't find an answer through the paper and SHARK documentation website. I see that there are two outputs about the black hole accretion rate ; bh_accretion_rate_hh and bh_accretion_rate_sb. I understand what those data mean, but still not clear about how to calculate the accretion rate of the central black hole at the snapshot from this two data. Is there any other data specifies whether the galaxy is in the hot halo mode or starburst mode at the snapshot? Or should I sum those two data to calculate the black hole accretion rate? Also, since this question is quite unrelated to the original issue I have posted, if you think I should post this question somewhere else please let me know where should I ask this kind of questions.

Thank you.

[cdplagos]

You just need to sum the two accretion rates to get the total one of the back hole.