Compiler segfaulting when compiling gmml

[gitoliver]

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::vectorMolecularModeling::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::vectorMolecularModeling::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::vectorGlycan::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->mono_neighbors_.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::vectorGlycan::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....

[gitoliver]

[ 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,

[gitoliver]

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::Edgecds::Residue, std::default_delete<glygraph::Edgecds::Residue >}; std::__tuple_element_t<__i, std::tuple<_Elements ...> > = glygraph::Edgecds::Residue]’:
/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::Edgecds::Residue; _Dp = std::default_delete<glygraph::Edgecds::Residue >; std::__uniq_ptr_impl<_Tp, _Dp>::pointer = glygraph::Edgecds::Residue]’
/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::Edgecds::Residue; _Dp = std::default_delete<glygraph::Edgecds::Residue >; std::unique_ptr<_Tp, _Dp>::pointer = glygraph::Edgecds::Residue]’
/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); }

[gitoliver]

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,

[gitoliver]

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

[gitoliver]

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