Compiler segfaulting when compiling gmml

The "fix" is to just compile again. It never happens twice. Does seem to be related to compiling the Glycan/oligosaccharide class. Making note of it here. Not sure how frequent it is inside the dev env, happens relatively frequently (every other build sometimes, then nothing for a run of 20 or so builds) on my bare metal builds. Those numbers are extremely vague I wasn't tracking. [ 8%] Building CXX object CMakeFiles/gmml.dir/src/Glycan/glycosidiclinkage.cc.o [ 9%] Building CXX object CMakeFiles/gmml.dir/src/Glycan/monosaccharide.cc.o [ 9%] Building CXX object CMakeFiles/gmml.dir/src/Glycan/oligosaccharide.cc.o /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/GeometryTopology/grid.cc: In constructor ‘GeometryTopology::Grid::Grid(MolecularModeling::Assembly, GeometryTopology::Coordinate, GeometryTopology::Coordinate, double, double)’: /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/GeometryTopology/grid.cc:19:128: warning: unused parameter ‘ion_radius’ [-Wunused-parameter] 19 | Grid::Grid(MolecularModeling::Assembly assembly, GeometryTopology::Coordinate min, GeometryTopology::Coordinate max, double ion_radius, double ion_charge) | ~^~~~ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/monosaccharide.cc: In copy constructor ‘Glycan::Monosaccharide::Monosaccharide(const Glycan::Monosaccharide&)’: /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/monosaccharide.cc:22:54: warning: unused parameter ‘mono’ [-Wunused-parameter] 22 | Monosaccharide::Monosaccharide(const Monosaccharide &mono) | ~~~~^~ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/monosaccharide.cc: In constructor ‘Glycan::Monosaccharide::Monosaccharide(std::string, std::vector<MolecularModeling::Atom>&, MolecularModeling::Assembly, std::string)’: /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/monosaccharide.cc:92:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 92 | for(int i = 0; i < orientations.size(); i++) | ^~~~~~~ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/monosaccharide.cc:27:170: warning: unused parameter ‘CCD_Path’ [-Wunused-parameter] 27 | Monosaccharide::Monosaccharide(std::string cycle_atoms_str, std::vector<MolecularModeling::Atom>& cycle_atoms, MolecularModeling::Assembly this_assembly, std::string CCD_Path) | ~~^~ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/oligosaccharide.cc: In member function ‘void Glycan::Oligosaccharide::Print(std::ostream&)’: /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/oligosaccharide.cc:51:51: warning: unused parameter ‘out’ [-Wunused-parameter] 51 | void Glycan::Oligosaccharide::Print(std::ostream& out) | ~~~~~~^~~ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/monosaccharide.cc: In member function ‘void Glycan::Monosaccharide::CheckMonoNaming(std::string, std::string)’: /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/monosaccharide.cc:1878:58: warning: unused parameter ‘original_residue’ [-Wunused-parameter] 1878 | void Glycan::Monosaccharide::CheckMonoNaming(std::string original_residue, std::string original_residue_id) | ~~^~~~~~ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/monosaccharide.cc:1878:88: warning: unused parameter ‘original_residue_id’ [-Wunused-parameter] 1878 | void Glycan::Monosaccharide::CheckMonoNaming(std::string original_residue, std::string original_residue_id) | ~~^~~~~ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/oligosaccharide.cc: In member function ‘void Glycan::Oligosaccharide::indexMono(Glycan::Monosaccharide, int, std::vector<Glycan::Monosaccharide>&)’: /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/oligosaccharide.cc:1481:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::pair<Glycan::GlycosidicLinkage, Glycan::Monosaccharide> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare] 1481 | for(int i = 0; i < thisMono->mononeighbors.size(); i++) | ^~~~~~~~ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/oligosaccharide.cc:1301:6: internal compiler error: Segmentation fault 1301 | void Glycan::Oligosaccharide::indexMono(Glycan::Monosaccharide thisMono, int thisIndex, std::vector<Glycan::Monosaccharide> &branchedMonos) | ^~ 0x7f38078da08f ??? /build/glibc-SzIz7B/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0 0x7f38078bb082 __libc_start_main ../csu/libc-start.c:308 Please submit a full bug report, with preprocessed source if appropriate. Please include the complete backtrace with any bug report. See file:///usr/share/doc/gcc-9/README.Bugs for instructions. make[3]: [CMakeFiles/gmml.dir/build.make:505: CMakeFiles/gmml.dir/src/Glycan/oligosaccharide.cc.o] Error 1 make[3]: Waiting for unfinished jobs....

[ 8%] Building CXX object CMakeFiles/gmml.dir/src/InternalPrograms/glycosylationSiteFinder.cpp.o [ 9%] Building CXX object CMakeFiles/gmml.dir/src/MolecularMetadata/glycoprotein.cpp.o /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/InternalPrograms/functionsForGMML.cpp: In function ‘void gmml::WritePDBFile(MolecularModeling::Assembly&, std::string, std::string, bool)’: /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/InternalPrograms/functionsForGMML.cpp:19:9: warning: deleting object of polymorphic class type ‘PdbFileSpace::PdbFile’ which has non-virtual destructor might cause undefined behavior [-Wdelete-non-virtual-dtor] 19 | delete outputPdbFile; | ^~~~~ during IPA pass: icf /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/MolecularMetadata/glycoprotein.cpp:119:1: internal compiler error: Segmentation fault 119 | } | ^ 0x7f80c451f08f ??? /build/glibc-SzIz7B/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0 0x7f80c4500082 __libc_start_main ../csu/libc-start.c:308 Please submit a full bug report,

In file included from /usr/include/c++/9/functional:54, from /usr/include/c++/9/pstl/glue_algorithm_defs.h:13, from /usr/include/c++/9/algorithm:71, from /usr/include/c++/9/regex:38, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/MolecularModeling/TemplateGraph/GraphStructure/include/././../../AbstractObject/includes/Labels.hpp:4, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/MolecularModeling/TemplateGraph/GraphStructure/include/././../../AbstractObject/includes/AbstractObject.hpp:4, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/MolecularModeling/TemplateGraph/GraphStructure/include/././GenericGraphObject.hpp:6, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/MolecularModeling/TemplateGraph/GraphStructure/include/./Edge.hpp:5, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/MolecularModeling/TemplateGraph/GraphStructure/include/Node.hpp:5, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/CentralDataStructure/atom.hpp:8, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/CentralDataStructure/residue.hpp:4, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/CentralDataStructure/molecule.hpp:4, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/CentralDataStructure/assembly.hpp:4, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/CentralDataStructure/ensemble.hpp:4, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/InputSet/PdbFile/pdbFile.hpp:18, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/Glycan/ontologyGmmlInterface.hpp:5, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/ontologyGmmlInterface.cpp:1: /usr/include/c++/9/tuple: In instantiation of ‘constexpr std::tuple_element_t<i, std::tuple<_Elements ...> >& std::get(const std::tuple<_Elements ...>&) [with long unsigned int i = 0; _Elements = {glygraph::Edge*, std::default_delete<glygraph::Edge >}; std::tuple_element_t<i, std::tuple<_Elements ...> > = glygraph::Edge*]’: /usr/include/c++/9/bits/unique_ptr.h:154:53: required from ‘std::uniq_ptr_impl<_Tp, _Dp>::pointer std::uniq_ptr_impl<_Tp, _Dp>::_M_ptr() const [with _Tp = glygraph::Edge; _Dp = std::default_delete<glygraph::Edge >; std::__uniq_ptr_impl<_Tp, _Dp>::pointer = glygraph::Edge]’ /usr/include/c++/9/bits/unique_ptr.h:361:28: required from ‘std::unique_ptr<_Tp, _Dp>::pointer std::unique_ptr<_Tp, _Dp>::get() const [with _Tp = glygraph::Edge; _Dp = std::default_delete<glygraph::Edge >; std::unique_ptr<_Tp, _Dp>::pointer = glygraph::Edge]’ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/MolecularModeling/TemplateGraph/GraphStructure/include/Node.hpp:464:46: required from ‘void glygraph::Node::removeOutEdge(glygraph::Edge*) [with T = cds::Residue]’ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/MolecularModeling/TemplateGraph/GraphStructure/include/Node.hpp:178:9: required from ‘glygraph::Node::~Node() [with T = cds::Residue]’ /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/includes/CentralDataStructure/residue.hpp:19:15: required from here /usr/include/c++/9/tuple:1327:36: internal compiler error: Segmentation fault 1327 | { return std::get_helper<__i>(__t); }

In file included from /usr/include/c++/9/bits/stl_algobase.h:59, from /usr/include/c++/9/vector:60, from /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/oligosaccharide.cc:4: /usr/include/c++/9/bits/stl_multimap.h: In instantiation of ‘class std::multimap<std::cxx11::basic_string, std::__cxx11::basic_string >’: /home/oliver/Programs/GLYCAM_Dev_Env/V_2/Web_Programs/gems/gmml/src/Glycan/../../includes/MolecularModeling/../GeometryTopology/../MolecularModeling/oligosaccharidedetectionatom.hpp:101:34: required from here /usr/include/c++/9/bits/stl_multimap.h:358:21: internal compiler error: Segmentation fault 358 | begin() const _GLIBCXX_NOEXCEPT | ^~~~~ 0x7fa48a91a08f ??? /build/glibc-SzIz7B/glibc-2.31/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0 0x7fa48a8fb082 libc_start_main ../csu/libc-start.c:308 Please submit a full bug report,

Again just recompiling will "fix" the compiler segfault, but this was an interesting one. First time I've seen it when compiling tests: Testing 005.overlaps.cc... In file included from /usr/include/c++/8/bits/stl_algobase.h:61, from /usr/include/c++/8/bits/char_traits.h:39, from /usr/include/c++/8/string:40, from /programs/gems/gmml/includes/common.hpp:4, from /programs/gems/gmml/includes/gmml.hpp:4, from tests/005.overlaps.cc:1: /usr/include/c++/8/bits/cpp_type_traits.h: In instantiation of ‘_Iterator std::miter_base(_Iterator) [with _Iterator = boost::token_iterator<boost::char_separator, __gnu_cxx::normal_iterator<const char, std::cxx11::basic_string >, std::__cxx11::basic_string >]’: /usr/include/c++/8/bits/stl_algobase.h:455:26: required from ‘_OI std::copy(_II, _II, _OI) [with _II = boost::token_iterator<boost::char_separator, gnu_cxx::__normal_iterator<const char, std::cxx11::basic_string >, std::cxx11::basic_string >; _OI = std::cxx11::basic_string*]’ /usr/include/c++/8/bits/vector.tcc:308:29: required from ‘void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = boost::token_iterator<boost::char_separator, gnu_cxx::normal_iterator<const char*, std::__cxx11::basic_string >, std::cxx11::basic_string >; _Tp = std::cxx11::basic_string; _Alloc = std::allocator<std::cxx11::basic_string >]’ /usr/include/c++/8/bits/stl_vector.h:1512:4: required from ‘void std::vector<_Tp, _Alloc>::_M_assign_dispatch(_InputIterator, _InputIterator, std::false_type) [with _InputIterator = boost::token_iterator<boost::char_separator, gnu_cxx::normal_iterator<const char*, std::__cxx11::basic_string >, std::cxx11::basic_string >; _Tp = std::cxx11::basic_string; _Alloc = std::allocator<std::cxx11::basic_string >]’ /usr/include/c++/8/bits/stl_vector.h:656:4: required from ‘void std::vector<_Tp, _Alloc>::assign(_InputIterator, _InputIterator) [with _InputIterator = boost::token_iterator<boost::char_separator, gnu_cxx::__normal_iterator<const char*, std::cxx11::basic_string >, std::cxx11::basic_string >; = void; _Tp = std::cxx11::basic_string; _Alloc = std::allocator<std::__cxx11::basic_string >]’ /programs/gems/gmml/includes/utils.hpp:118:57: required from here /usr/include/c++/8/bits/cpp_type_traits.h:420:20: internal compiler error: Segmentation fault { return __it; } ^ Please submit a full bug report, with preprocessed source if appropriate. See file:///usr/share/doc/gcc-8/README.Bugs for instructions. Test FAILED! Exit Code: 1

This is the function it failed on. This is defined elsewhere with the same name so that could be it.

/*! \fn
  * Split a line (series of characters) with the given delimiter
  * @param line Input string in order to be split by the given delimiter
  * @param delim Series of delimiters (each delimiter character is followed by the next one in a single string variable) in order to split the given string
  * @return Vector of elements of the given string that have been split by the given delimiter(s)
  */
inline std::vector<std::string> Split(std::string line, std::string delim)
{
    boost::char_separator<char> separator(delim.c_str());
    boost::tokenizer< boost::char_separator<char> > tokens(line, separator);
    std::vector<std::string> vectorTokens = std::vector<std::string>();
    **vectorTokens.assign(tokens.begin(), tokens.end());**
    return vectorTokens;
}

Line 118 is bolded. Tho the origin could be just the crazy include cascade that comes from including gmml.hpp

It's happening in the tests sometimes, again just recompiling and it's fine. Again it's gmml.hpp showing up:

webdev@oliver-gw-grpc-delegator:/programs/gems/gmml/tests$ bash compile_run_tests.bash -j10

#### Beginning GMML tests ####
Number of tests found:  25
Number of testing jobs: 10

mkdir: created directory './tempTestOutputs'

Beginning test: ./000.test.buildBySequenceOldWay.sh
Beginning test: ./002.test.createAssemblyWritePDB.sh
Beginning test: ./003.test.SuperimpositionEigen.sh
Beginning test: ./004.test.PDBpreprocessor.sh
Beginning test: ./005.test.Overlaps.sh
Beginning test: ./006.test.BFMP-RingShapeCalculation.sh
Beginning test: ./007.test.DetectSugars.sh
Beginning test: ./008.test.PDB2GlycamAndSubgraphMatching.sh
Beginning test: ./009.test.Reorder_and_Label_Sequence.sh
Beginning test: ./010.test.buildBySequenceRotamer.sh

Testing 009.reorderSequence.cc (Sequence reordering and labeling)... In file included from /programs/gems/gmml/includes/gmml.hpp:165,
                 from tests/009.reorderSequence.cc:1:
/programs/gems/gmml/includes/Resolver/PdbPreprocessor/pdbpreprocessor.hpp:471:9: internal compiler error: Segmentation fault
  471 |         }
      |         ^
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-10/README.Bugs> for instructions.
Test FAILED! (comparison of results)
Exit Code: 1

Beginning test: ./011.test.writeResNumbers.sh

Testing 003.superimpositionEigen.cc... In file included from /programs/gems/gmml/includes/gmml.hpp:165,
                 from tests/003.superimpositionEigen.cc:1:
/programs/gems/gmml/includes/Resolver/PdbPreprocessor/pdbpreprocessor.hpp:471:9: internal compiler error: Segmentation fault
  471 |         }
      |         ^
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-10/README.Bugs> for instructions.
Test FAILED!
Exit Code: 1

Beginning test: ./012.test.AddSolventNeutralize.sh

Testing 010.buildBySequenceRotamer.cc... Test FAILED! structure.pdb file different from tests/correct_outputs/010.buildBySequenceRotamer.pdb
Exit Code: 1

Beginning test: ./014.test.SequenceParser.sh

Testing 005.overlaps.cc... during GIMPLE pass: local-fnsummary
tests/005.overlaps.cc: In function ‘void __static_initialization_and_destruction_0(int, int)’:
tests/005.overlaps.cc:16:1: internal compiler error: Segmentation fault
   16 | }
      | ^
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-10/README.Bugs> for instructions.
Test FAILED!
Exit Code: 1

GLYCAM-Web / gmml

Compiler segfaulting when compiling gmml #145