Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in GLIBC #115

Open
lh12565 opened this issue May 20, 2022 · 0 comments
Open

Error in GLIBC #115

lh12565 opened this issue May 20, 2022 · 0 comments

Comments

@lh12565
Copy link

lh12565 commented May 20, 2022

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!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant