Error in GLIBC #115
Description
Hi, my system is CentOS7. when I install the coordgen, there is an error as follows:
make -j install
[ 85%] Building CXX object example_dir/CMakeFiles/example.dir/example.cpp.o
[ 90%] Linking CXX executable example
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /NAS/lh/software/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /NAS/lh/software/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
make[2]: *** [example_dir/example] Error 1
make[1]: *** [example_dir/CMakeFiles/example.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 95%] Linking CXX executable test_smilesparser
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_smilesparser.dir/test_smilesparser.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_smilesparser.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x38): undefined reference to `boost::unit_test::ut_detail::normalize_test_case_name[abi:cxx11](boost::unit_test::basic_cstring<char const>)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/local/boost/lib/libboost_unit_test_framework.so.1.79.0: undefined reference to `memcpy@GLIBC_2.14'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /NAS/lh/software/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /NAS/lh/software/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
make[2]: *** [test/test_smilesparser] Error 1
make[1]: *** [test/CMakeFiles/test_smilesparser.dir/all] Error 2
[100%] Linking CXX executable test_coordgen
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.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_coordgen.cpp:(.text._ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m[_ZN5boost9unit_test14make_test_caseERKNS_8functionIFvvEEENS0_13basic_cstringIKcEES8_m]+0x38): undefined reference to `boost::unit_test::ut_detail::normalize_test_case_name[abi:cxx11](boost::unit_test::basic_cstring<char const>)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o: in function `mol_from_mae_block(schrodinger::mae::Block&)':
test_coordgen.cpp:(.text._Z18mol_from_mae_blockRN11schrodinger3mae5BlockE+0x84): undefined reference to `schrodinger::mae::Block::getIndexedBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: test_coordgen.cpp:(.text._Z18mol_from_mae_blockRN11schrodinger3mae5BlockE+0x600): undefined reference to `schrodinger::mae::Block::getIndexedBlock(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o: in function `ClearWedgesTest::test_method()':
test_coordgen.cpp:(.text._ZN15ClearWedgesTest11test_methodEv+0xdd): undefined reference to `schrodinger::mae::Reader::Reader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: test_coordgen.cpp:(.text._ZN15ClearWedgesTest11test_methodEv+0x10b): undefined reference to `schrodinger::mae::Reader::next(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o: in function `testMinimizedRingsShape::test_method()':
test_coordgen.cpp:(.text._ZN23testMinimizedRingsShape11test_methodEv+0xdd): undefined reference to `schrodinger::mae::Reader::Reader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: test_coordgen.cpp:(.text._ZN23testMinimizedRingsShape11test_methodEv+0x10b): undefined reference to `schrodinger::mae::Reader::next(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o: in function `testGetDoubleBondConstraints::test_method()':
test_coordgen.cpp:(.text._ZN28testGetDoubleBondConstraints11test_methodEv+0x103): undefined reference to `schrodinger::mae::Reader::Reader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: test_coordgen.cpp:(.text._ZN28testGetDoubleBondConstraints11test_methodEv+0x131): undefined reference to `schrodinger::mae::Reader::next(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o: in function `SampleTest::test_method()':
test_coordgen.cpp:(.text._ZN10SampleTest11test_methodEv+0xe0): undefined reference to `schrodinger::mae::Reader::Reader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: test_coordgen.cpp:(.text._ZN10SampleTest11test_methodEv+0x10e): undefined reference to `schrodinger::mae::Reader::next(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o: in function `DisableMetalZOBs::test_method()':
test_coordgen.cpp:(.text._ZN16DisableMetalZOBs11test_methodEv+0xe0): undefined reference to `schrodinger::mae::Reader::Reader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: test_coordgen.cpp:(.text._ZN16DisableMetalZOBs11test_methodEv+0x10e): undefined reference to `schrodinger::mae::Reader::next(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o: in function `terminalMetalZOBs::test_method()':
test_coordgen.cpp:(.text._ZN17terminalMetalZOBs11test_methodEv+0xe0): undefined reference to `schrodinger::mae::Reader::Reader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: test_coordgen.cpp:(.text._ZN17terminalMetalZOBs11test_methodEv+0x10e): undefined reference to `schrodinger::mae::Reader::next(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: CMakeFiles/test_coordgen.dir/test_coordgen.cpp.o: in function `TemplateTest::test_method()':
test_coordgen.cpp:(.text._ZN12TemplateTest11test_methodEv+0x1ca): undefined reference to `schrodinger::mae::Reader::Reader(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, unsigned long)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: test_coordgen.cpp:(.text._ZN12TemplateTest11test_methodEv+0x2ac): undefined reference to `schrodinger::mae::Reader::next(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /usr/local/boost/lib/libboost_unit_test_framework.so.1.79.0: undefined reference to `memcpy@GLIBC_2.14'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /NAS/lh/software/miniconda3/lib/libstdc++.so: undefined reference to `aligned_alloc@GLIBC_2.16'
/NAS/lh/software/miniconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /NAS/lh/software/miniconda3/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17'
collect2: error: ld returned 1 exit status
make[2]: *** [test/test_coordgen] Error 1
make[1]: *** [test/CMakeFiles/test_coordgen.dir/all] Error 2
make: *** [all] Error 2
It seems my glibc is too old. I can't change the version without authorization. Can conda solve this problem here?
Thanks!