Upgrade docker containers

[chapman39]

• Create images from radiuss-docker instead of axom-docker
• Upgrade compilers to clang15 and gcc13
• Upgrade OS to ubuntu22
• Update Doxyfile.in to 1.9.1

[codecov-commenter]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 86.91%. Comparing base (7672d33) to head (c9abf44).

Additional details and impacted files

@@             Coverage Diff             @@
##           develop    #1074      +/-   ##
===========================================
- Coverage    88.85%   86.91%   -1.94%     
===========================================
  Files          155      159       +4     
  Lines        12581    15412    +2831     
===========================================
+ Hits         11179    13396    +2217     
- Misses        1402     2016     +614     

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[chapman39]

@samuelpmish @white238 @jamiebramwell I'm not sure if anyone's familiar with this error, but I'm having trouble how to approach it

[ 17%] Linking CXX static library ../../../../lib/libserac_contact.a
cd /home/serac/serac/_serac_build_and_test_2024_02_26_16_51_55/build-gcc@13.1.0/src/serac/physics/contact && /usr/local/bin/cmake -P CMakeFiles/serac_contact.dir/cmake_clean_target.cmake
cd /home/serac/serac/_serac_build_and_test_2024_02_26_16_51_55/build-gcc@13.1.0/src/serac/physics/contact && /usr/local/bin/cmake -E cmake_link_script CMakeFiles/serac_contact.dir/link.txt --verbose=1
/usr/bin/ar qc ../../../../lib/libserac_contact.a CMakeFiles/serac_contact.dir/contact_data.cpp.o CMakeFiles/serac_contact.dir/contact_interaction.cpp.o
/usr/bin/ranlib ../../../../lib/libserac_contact.a
make[2]: Leaving directory '/home/serac/serac/_serac_build_and_test_2024_02_26_16_51_55/build-gcc@13.1.0'
[ 17%] Built target serac_contact
In file included from /usr/include/c++/13/bits/stl_uninitialized.h:63,
                 from /usr/include/c++/13/memory:69,
                 from /home/serac/serac/src/serac/infrastructure/../../serac/mesh/mesh_utils_base.hpp:16,
                 from /home/serac/serac/src/serac/infrastructure/../../serac/mesh/mesh_utils.hpp:16,
                 from /home/serac/serac/src/serac/mesh/mesh_utils.cpp:7:
In static member function ‘static _Up* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(_Tp*, _Tp*, _Up*) [with _Tp = const double; _Up = double; bool _IsMove = false]’,
    inlined from ‘_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = const double*; _OI = double*]’ at /usr/include/c++/13/bits/stl_algobase.h:506:30,
    inlined from ‘_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = const double*; _OI = double*]’ at /usr/include/c++/13/bits/stl_algobase.h:533:42,
    inlined from ‘_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = const double*; _OI = double*]’ at /usr/include/c++/13/bits/stl_algobase.h:540:31,
    inlined from ‘_OI std::copy(_II, _II, _OI) [with _II = const double*; _OI = double*]’ at /usr/include/c++/13/bits/stl_algobase.h:633:7,
    inlined from ‘static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const double*; _ForwardIterator = double*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:147:27,
    inlined from ‘_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = const double*; _ForwardIterator = double*]’ at /usr/include/c++/13/bits/stl_uninitialized.h:185:15,
    inlined from ‘_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, allocator<_Tp>&) [with _InputIterator = const double*; _ForwardIterator = double*; _Tp = double]’ at /usr/include/c++/13/bits/stl_uninitialized.h:373:37,
    inlined from ‘void std::vector<_Tp, _Alloc>::_M_assign_aux(_ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = const double*; _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/vector.tcc:345:35,
    inlined from ‘std::vector<_Tp, _Alloc>& std::vector<_Tp, _Alloc>::operator=(std::initializer_list<_Tp>) [with _Tp = double; _Alloc = std::allocator<double>]’ at /usr/include/c++/13/bits/stl_vector.h:787:21,
    inlined from ‘serac::mesh::InputOptions FromInlet<serac::mesh::InputOptions>::operator()(const axom::inlet::Container&)’ at /home/serac/serac/src/serac/mesh/mesh_utils.cpp:494:58:
/usr/include/c++/13/bits/stl_algobase.h:437:30: error: ‘void* __builtin_memcpy(void*, const void*, long unsigned int)’ forming offset 24 is out of the bounds [0, 24] [-Werror=array-bounds=]
  437 |             __builtin_memmove(__result, __first, sizeof(_Tp) * _Num);
      |             ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

It's failing only gcc13-release. https://dev.azure.com/llnl-serac/serac/_build/results?buildId=10908&view=logs&j=8418a147-cefe-5fbf-eb11-e069d1299bbe&t=02db9b20-7613-5b66-5602-b48459f634fd&l=463

Edit: I figured it out.

[chapman39]

May be worth bringing this up to radiuss-docker, if they end up building clang with mpich.

[white238]

@davidbeckingsale would you like this to go into the base radiuss image? The mpich wrappers add link time optimization flags which then fails in the non-gcc compilers due to it being very specific.

[chapman39]

Strumpack works on docker containers now

[white238]

Thanks @chapman39 ! Did this pass the style check w/o any changes? That would be amazing since it was so version dependent before.

[white238]

@chapman39 can you fix the following warning:

CMake Warning at cmake/blt/cmake/SetupCodeChecks.cmake:695 (message):
  blt_add_clangformat_target: clang-format '10'' is required, found '15.0.7'.
  Disabling 'style' build target.
Call Stack (most recent call first):
  cmake/blt/cmake/SetupCodeChecks.cmake:206 (blt_add_clangformat_target)
  cmake/SeracMacros.cmake:50 (blt_add_code_checks)
  CMakeLists.txt:167 (serac_add_code_checks)

serac/CMakeLists.txt

Line 104 in 7672d33

set(BLT_REQUIRED_CLANGFORMAT_VERSION "10" CACHE STRING "")

[jamiebramwell]

Thanks @chapman39 !