Build boost from source with manually built gcc compiler in cluster

Question

I am trying to compile Boost 1.79.0 in a cluster using the GCC compiler version 12.1.0 that I have compiled manually since the GCC version of the cluster is very old.

After compiling GCC, I have exported the following paths in a shell script that I source every time in the terminal before installing or running a program. I have manually installed CMake and several programs.

However, I am still struggling with compiling Boost. It is complaining about undefined references in C++11 so I guess there is something that is linked wrongly.

Could anyone provide any suggestions to overcome this issue?

Here is my exports in the shell script:

export PATH=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin:$PATH
export CFLAGS="-I /lustre/home/ucemkmo/Softwares/gcc-12.1.0/include";
export LDFLAGS="-L /lustre/home/ucemkmo/Softwares/gcc-12.1.0/lib64";
export CPPFLAGS="-I /lustre/home/ucemkmo/Softwares/gcc-12.1.0/include";
export CXXFLAGS="-L /lustre/home/ucemkmo/Softwares/gcc-12.1.0/lib64";
export LD_LIBRARY_PATH=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/lib64:$LD_LIBRARY_PATH
export LD_RUN_PATH=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/lib64
export LD="/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/g++"
export MANPATH=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/share/man:$MANPATH
export INFOPATH=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/share/info:$INFOPATH
export INFO_PATH=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/share/info:$INFO_PATH
export AR=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/gcc-ar
export CC=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/gcc
export CXX=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/g++
export LD=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/g++
export CXXCPP="/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/g++ -E"
export FC=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/gfortran
export F77=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/gfortran
export F90=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/gfortran
export COLLECT_GCC=gcc
export COLLECT_LTO_WRAPPER=/lustre/home/ucemkmo/Softwares/gcc-12.1.0/bin/../libexec/gcc/x86_64-unknown-linux-gnu/12.1.0/lto-wrapper
export PATH=/lustre/home/ucemkmo/Softwares/cmake-3.24.0/bin:$PATH
export PATH=/lustre/home/ucemkmo/Softwares/python-3.10.5/3.10.5/bin:$PATH
export PETSC_DIR=/lustre/home/ucemkmo/Softwares/petsc
export PETSC_ARCH=arch-linux-c-opt

Here are the error messages I am receiving during the compilation of Boost v1.79.0:

Building B2 engine..

###
###
### Using 'gcc' toolset.
###
###

g++ (GCC) 12.1.0
Copyright (C) 2022 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.


###
###

> g++ -x c++ -std=c++11 -O2 -s -DNDEBUG builtins.cpp class.cpp command.cpp compile.cpp constants.cpp cwd.cpp debug.cpp debugger.cpp execcmd.cpp execnt.cpp execunix.cpp filesys.cpp filent.cpp fileunix.cpp frames.cpp function.cpp glob.cpp hash.cpp hcache.cpp hdrmacro.cpp headers.cpp jam_strings.cpp jam.cpp jamgram.cpp lists.cpp make.cpp make1.cpp md5.cpp mem.cpp modules.cpp native.cpp object.cpp option.cpp output.cpp parse.cpp pathnt.cpp pathsys.cpp pathunix.cpp regexp.cpp rules.cpp scan.cpp search.cpp startup.cpp subst.cpp sysinfo.cpp timestamp.cpp variable.cpp w32_getreg.cpp modules/order.cpp modules/path.cpp modules/property-set.cpp modules/regex.cpp modules/sequence.cpp modules/set.cpp -o b2
/tmp/cc1S1rUW.o: In function `builtin_normalize_path(frame*, int)':
builtins.cpp:(.text+0x14ea): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
builtins.cpp:(.text+0x1510): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
/tmp/cc8w84jf.o: In function `debug_print_frame_info(_frame_info&)':
debugger.cpp:(.text+0x3d7): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::compare(char const*) const'
/tmp/cc8w84jf.o: In function `debug_frame_read(_IO_FILE*, _frame_info*)':
debugger.cpp:(.text+0x1707): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
/tmp/cceSnutQ.o: In function `var_parse_to_string(VAR_PARSE_GROUP*, bool)':
function.cpp:(.text+0x1683): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
function.cpp:(.text+0x16b5): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
function.cpp:(.text+0x171c): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
function.cpp:(.text+0x1770): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
function.cpp:(.text+0x17b3): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
/tmp/cceSnutQ.o:function.cpp:(.text+0x17d3): more undefined references to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)' follow
/tmp/cceSnutQ.o: In function `var_parse_to_string(VAR_PARSE_VAR const*, bool)':
function.cpp:(.text+0x193f): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
function.cpp:(.text+0x19b0): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
function.cpp:(.text+0x1a2e): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
function.cpp:(.text+0x1ae2): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
function.cpp:(.text+0x1b40): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
function.cpp:(.text+0x1bf3): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
function.cpp:(.text+0x1c3e): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
/tmp/ccwxFfFi.o: In function `errno_printf(char const*, ...)':
output.cpp:(.text+0x69d): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
output.cpp:(.text+0x732): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
output.cpp:(.text+0x7a2): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
output.cpp:(.text+0x8bb): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
output.cpp:(.text+0x8f0): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
output.cpp:(.text+0x92a): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
output.cpp:(.text+0x953): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
output.cpp:(.text+0x9bd): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
output.cpp:(.text+0xa81): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct(unsigned long, char)'
/tmp/cc7flVRU.o: In function `void std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) [clone .isra.0]':
pathsys.cpp:(.text+0x68): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
/tmp/cc7flVRU.o: In function `b2::paths::normalize(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
pathsys.cpp:(.text+0x51d): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
pathsys.cpp:(.text+0x59d): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::rfind(char, unsigned long) const'
pathsys.cpp:(.text+0x5ee): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_erase(unsigned long, unsigned long)'
pathsys.cpp:(.text+0x62d): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
pathsys.cpp:(.text+0x6e7): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_erase(unsigned long, unsigned long)'
pathsys.cpp:(.text+0x711): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_erase(unsigned long, unsigned long)'
pathsys.cpp:(.text+0x761): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_erase(unsigned long, unsigned long)'
/tmp/ccR9xr0R.o: In function `void std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct<char*>(char*, char*, std::forward_iterator_tag) [clone .isra.0]':
startup.cpp:(.text+0x68): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
/tmp/ccR9xr0R.o: In function `void std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_construct<char const*>(char const*, char const*, std::forward_iterator_tag) [clone .isra.0]':
startup.cpp:(.text+0x108): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
/tmp/ccR9xr0R.o: In function `b2::startup::builtin_boost_build(frame*, int)':
startup.cpp:(.text+0x3d2): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
startup.cpp:(.text+0x459): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
startup.cpp:(.text+0x70a): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
startup.cpp:(.text+0x86f): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
startup.cpp:(.text+0x8d2): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
startup.cpp:(.text+0x986): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/tmp/ccR9xr0R.o: In function `b2::startup::bootstrap(frame*)':
startup.cpp:(.text+0x1045): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
startup.cpp:(.text+0x114d): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::rfind(char, unsigned long) const'
startup.cpp:(.text+0x14e5): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
startup.cpp:(.text+0x1517): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
startup.cpp:(.text+0x1658): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
startup.cpp:(.text+0x168a): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
startup.cpp:(.text+0x1852): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
/tmp/ccR9xr0R.o:startup.cpp:(.text+0x1884): more undefined references to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)' follow
/tmp/ccR9xr0R.o: In function `b2::startup::bootstrap(frame*)':
startup.cpp:(.text+0x1a46): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
startup.cpp:(.text+0x1ba6): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
startup.cpp:(.text+0x1c6e): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
startup.cpp:(.text+0x1c93): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
startup.cpp:(.text+0x1ceb): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_create(unsigned long&, unsigned long)'
startup.cpp:(.text+0x1d3e): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_assign(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)'
/tmp/ccR9xr0R.o: In function `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > std::operator+<char, std::char_traits<char>, std::allocator<char> >(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)':
startup.cpp:(.text._ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_[_ZStplIcSt11char_traitsIcESaIcEENSt7__cxx1112basic_stringIT_T0_T1_EERKS8_SA_]+0x42): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_append(char const*, unsigned long)'
/tmp/cceOb6PB.o: In function `cwd_init()':
cwd.cpp:(.text+0x87): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::_M_replace(unsigned long, unsigned long, char const*, unsigned long)'
/tmp/cceOb6PB.o: In function `_GLOBAL__sub_I__Z8cwd_initv':
cwd.cpp:(.text.startup+0xb): undefined reference to `std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >::~basic_string()'
collect2: error: ld returned 1 exit status
> cp b2 bjam
cp: cannot stat ‘b2’: No such file or directory

Failed to build B2 build engine

Answer 1

It seems that you are facing a problem regarding Dual ABIs:

If you get linker errors about undefined references to symbols that involve types in the std::__cxx11 namespace or the tag [abi:cxx11] then it probably indicates that you are trying to link together object files that were compiled with different values for the _GLIBCXX_USE_CXX11_ABI macro. This commonly happens when linking to a third-party library that was compiled with an older version of GCC. If the third-party library cannot be rebuilt with the new ABI then you will need to recompile your code with the old ABI.

In other words, some of the boost dependencies has been compiled using your old gcc. See the full page in gcc documentation, here.