Compile error: long unsigned int offset 8 out of bound

[NooraAz]

I'm compiling rosetta with extras=mpi and mode=release.
The GCC version is 8.5.
Settings are site.settings.release.
system info:

Operating System: Red Hat Enterprise Linux 8.8 (Ootpa)
CPE OS Name: cpe:/o:redhat:enterprise_linux:8::baseos
Kernel: Linux 4.18.0-477.27.1.el8_8.x86_64
Architecture: x86-64

and I get this error:

In file included from /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../include/c++/13.1.0/bits/stl_uninitialized.h:63,
                 from /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../include/c++/13.1.0/memory:69,
                 from src/utility/pointer/std/owning_ptr.hh:20,
                 from src/utility/pointer/owning_ptr.hh:15,
                 from src/protocols/antibody/AntibodyCDRGrafter.fwd.hh:19,
                 from src/protocols/antibody/AntibodyCDRGrafter.hh:18,
                 from src/protocols/antibody/AntibodyCDRGrafter.cc:14:
In static member function 'static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = long unsigned int; _Up = long unsigned int; bool _IsMove = false]',
    inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux
-gnu/13.1.0/../../../../include/c++/13.1.0/bits/stl_algobase.h:506:30,
    inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux
-gnu/13.1.0/../../../../include/c++/13.1.0/bits/stl_algobase.h:533:42,
    inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = long unsigned int*; _OI = long unsigned int*]' at /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux-
gnu/13.1.0/../../../../include/c++/13.1.0/bits/stl_algobase.h:540:31,
    inlined from '_OI std::copy(_II, _II, _OI) [with _II = long unsigned int*; _OI = long unsigned int*]' at /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../include/
c++/13.1.0/bits/stl_algobase.h:633:7,
    inlined from 'std::vector<bool, _Alloc>::iterator std::vector<bool, _Alloc>::_M_copy_aligned(const_iterator, const_iterator, iterator) [with _Alloc = std::allocator<bool>]' at /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3
uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../include/c++/13.1.0/bits/stl_bvector.h:1303:28,
    inlined from 'void std::vector<bool, _Alloc>::_M_fill_insert(iterator, size_type, bool) [with _Alloc = std::allocator<bool>]' at /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux-gnu/13.
1.0/../../../../include/c++/13.1.0/bits/vector.tcc:879:34,
    inlined from 'std::vector<bool, _Alloc>::iterator std::vector<bool, _Alloc>::insert(const_iterator, size_type, const bool&) [with _Alloc = std::allocator<bool>]' at /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjv
bu2w/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../include/c++/13.1.0/bits/stl_bvector.h:1203:16,
    inlined from 'void std::vector<bool, _Alloc>::resize(size_type, bool) [with _Alloc = std::allocator<bool>]' at /gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../in
clude/c++/13.1.0/bits/stl_bvector.h:1249:10,
    inlined from 'void protocols::antibody::AntibodyCDRGrafter::set_cdr_only(protocols::antibody::CDRNameEnum)' at src/protocols/antibody/AntibodyCDRGrafter.cc:315:23:
/gpfs/packages/spack/spack-rhel8/opt/spack/linux-rhel8-broadwell/gcc-8.5.0/gcc-13.1.0-pcukou32lkbpveja3uuimh2lbpjvbu2w/lib/gcc/x86_64-pc-linux-gnu/13.1.0/../../../../include/c++/13.1.0/bits/stl_algobase.h:437:30: error: 'void* __builtin_memmove(void*, const void*, long unsigned int)
' forming offset 8 is out of the bounds [0, 8] [-Werror=array-bounds=]
  437 |             __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
      |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Thanks for your help.

[everyday847]

Tricky to debug because of all the inlined functions, but the issue is that the function set_cdr_only sets the value for an index in an array, and it seems to be objecting to the array bounds. I don't know if there is a difference in how utility::vector1< bool > extends std::vector< bool > -- versus other vector< T > -- because it's weird that the boundary 8 is not okay. (It's basically checking "oh, this function could take an enum of value 8, but that would not work in this function." That would be true if the vector were zero indexed, but it isn't?

[NooraAz]

just a note, when I was compiling with cxx11thread and gcc 12 I was getting the same error which was resolved by downgrading gcc to 8.5. But I can't see how it can be related to GCC version, and now I'm on 8.5 anyway.

[NooraAz]

This is also default version from main repo. so I haven't modified any codes.

[vmullig]

I don't know if it's relevant or not, but one piece of information to keep in mind is that std::vector<bool> is a weird special case in the STL. Where std::vector<T> ordinarily guarantees that every element in the vector is addressable (occupying at least one byte), std::vector<bool> is packed, with each element occupying one bit rather than one byte. Again, that could be a red herring; I'm not sure.

[NooraAz]

Adding #include <cstdint> to main/source/src/utility/io/tarparser.hh solved the issue.