Hi Zhen
Thanks fo the reply. I have checked in my ~/.bashrc there is not mention of
Boost so Boost library search is unaffected by bashrc
and this is my run_cmake file:
# This file gives some sample cmake invocations. You may wish to
# edit some options that are chosen here.
# For information on how to get cmake, visit this page:
#
https://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Quick-Start
# For information on common options for cmake, visit this page:
#
http://ambermd.org/pmwiki/pmwiki.php/Main/CMake-Common-Options
# (Note that you can change the value of CMAKE_INSTALL_PREFIX from what
# is suggested below, but it cannot coincide with the amber24_src
# folder.)
AMBER_PREFIX=$(dirname $(dirname `pwd`))
if [ `uname -s|awk '{print $1}'` = "Darwin" ]; then
# For macOS:
if [ -x /Applications/CMake.app/Contents/bin/cmake ]; then
cmake=/Applications/CMake.app/Contents/bin/cmake
else
cmake=cmake
fi
$cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=CLANG -DBLA_VENDOR=Apple \
-DMPI=FALSE -DCUDA=FALSE -DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
2>&1 | tee cmake.log
else
# Assuming this is Linux (CentOS) and you are in the Amber build folder
cmake $AMBER_PREFIX/amber24_src \
-DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
-DCOMPILER=GNU \
-DMPI=FALSE \
-DCUDA=FALSE \
-DINSTALL_TESTS=TRUE \
-DDOWNLOAD_MINICONDA=TRUE \
-DTRUST_SYSTEM_LIBS=TRUE \
-DUSE_XTB=ON \
-DXTB_INCLUDE_DIR=$HOME/xtb/build/libxtb.so.6.7.1.p \
-DXTB_LIBRARY=$HOME/.local/lib64/libxtb.so \
-DCMAKE_EXE_LINKER_FLAGS="-Wl,-rpath,$HOME/.local/lib64
-L$HOME/.local/lib64" \
-DCMAKE_SHARED_LINKER_FLAGS="-Wl,-rpath,$HOME/.local/lib64
-L$HOME/.local/lib64" \
2>&1 | tee cmake.log
fi
if [ ! -s cmake.log ]; then
echo ""
echo "Error: No cmake.log file created: you may need to edit run_cmake"
exit 1
fi
echo ""
echo "If errors are reported, search for 'CMake Error' in the cmake.log
file."
echo ""
echo "If the cmake build report looks OK, you should now do the following:"
echo ""
echo " make install"
echo " source $AMBER_PREFIX/amber24/amber.sh"
echo ""
echo "Consider adding the last line to your login startup script, e.g.
~/.bashrc"
echo ""
Best
kriti
On Mon, Oct 27, 2025 at 6:53 PM Li, Zhen <lizhen6.chemistry.msu.edu> wrote:
> Hi Kriti,
>
> This is quite a long error report, but it seems to be related to boost,
> not xTB.
>
> Could you check whether your ~/.bashrc file exports any boost libraries to
> LD_LIBRARY_PATH or sets BOOST_ROOT?
>
> If yes, it is better to comment out those lines (but make sure
> export LD_LIBRARY_PATH="<where boost libraries are>" is still there), log
> out, and log back in to your Linux system. This way, AMBER will handle the
> boost itself.
>
> No guarantee it will work. If you could kindly share your ~/.bashrc and
> $AMBER/build/run_cmake file, that would be helpful. Thanks.
>
> Regards,
> Zhen.
>
>
> _____________________
>
> Zhen Li <http://lizhen62017.wixsite.com/home>, Ph.D.,
>
> The Merz Research Group <http://merzgroup.org>,
>
> Michigan State University,
>
> Cleveland Clinic.
> ------------------------------
> *From:* Kriti Shukla via AMBER <amber.ambermd.org>
> *Sent:* Monday, October 27, 2025 8:09 AM
> *To:* AMBER Mailing List <amber.ambermd.org>
> *Subject:* [AMBER] Error in AMBER24 compilation with xTB
>
> Hello community,
> I have been trying to install amber24 with xTB, snippet from *run_cmake*
> file is like this:
>
> # Assuming this is Linux (CentOS) and you are in the Amber build folder
>
> cmake $AMBER_PREFIX/amber24_src \
> -DCMAKE_INSTALL_PREFIX=$AMBER_PREFIX/amber24 \
> -DCOMPILER=GNU \
> -DMPI=FALSE \
> -DCUDA=FALSE \
> -DINSTALL_TESTS=TRUE \
> -DDOWNLOAD_MINICONDA=TRUE \
> -DTRUST_SYSTEM_LIBS=TRUE \
> -DUSE_XTB=ON \
> -DXTB_INCLUDE_DIR=$HOME/xtb/build/libxtb.so.6.7.1.p \
> -DXTB_LIBRARY=$HOME/.local/lib64/libxtb.so \
> -DCMAKE_EXE_LINKER_FLAGS="-Wl,-rpath,$HOME/.local/lib64
> -L$HOME/.local/lib64" \
> -DCMAKE_SHARED_LINKER_FLAGS="-Wl,-rpath,$HOME/.local/lib64
> -L$HOME/.local/lib64" \
> 2>&1 | tee cmake.log
>
> execution of *run_cmake *completed without any error message but then on
> *make
> install *it stops at 88% with error like this:
> [ 88%] Linking CXX executable metatwist
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `boost::program_options::typed_value<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&) const':
>
> metatwist.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE6xparseERNS_3anyERKSt6vectorIS7_SaIS7_EE]+0x19):
> undefined reference to `boost::program_options::validate(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<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> >*, int)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `boost::program_options::typed_value<std::vector<double,
> std::allocator<double> >, char>::name[abi:cxx11]() const':
>
> metatwist.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorIdSaIdEEcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueISt6vectorIdSaIdEEcE4nameB5cxx11Ev]+0x1e):
> undefined reference to `boost::program_options::arg[abi:cxx11]'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
>
> `boost::program_options::typed_value<std::vector<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >,
> std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > >, char>::name() const':
>
> metatwist.cpp:(.text._ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv[_ZNK5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcE4nameEv]+0x1e):
> undefined reference to `boost::program_options::arg[abi:cxx11]'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `boost::program_options::typed_value<double, char>::name[abi:cxx11]()
> const':
>
> metatwist.cpp:(.text._ZNK5boost15program_options11typed_valueIdcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueIdcE4nameB5cxx11Ev]+0x1e):
> undefined reference to `boost::program_options::arg[abi:cxx11]'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `boost::program_options::typed_value<unsigned long,
> char>::name[abi:cxx11]() const':
>
> metatwist.cpp:(.text._ZNK5boost15program_options11typed_valueImcE4nameB5cxx11Ev[_ZNK5boost15program_options11typed_valueImcE4nameB5cxx11Ev]+0x1e):
> undefined reference to `boost::program_options::arg[abi:cxx11]'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `boost::program_options::typed_value<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >, char>::name() const':
>
> metatwist.cpp:(.text._ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv[_ZNK5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcE4nameEv]+0x1e):
> undefined reference to `boost::program_options::arg[abi:cxx11]'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
>
> `boost::program_options::basic_command_line_parser<char>::extra_parser(boost::function1<std::pair<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&>)':
>
> metatwist.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE[_ZN5boost15program_options25basic_command_line_parserIcE12extra_parserENS_9function1ISt4pairINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ERKSA_EE]+0x3b):
> undefined reference to
>
> `boost::program_options::detail::cmdline::set_additional_parser(boost::function1<std::pair<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&>)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function `main':
> metatwist.cpp:(.text.startup+0x6196): undefined reference to
>
> `boost::program_options::options_description::options_description(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&, unsigned int,
> unsigned int)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
>
> `boost::program_options::basic_command_line_parser<char>::basic_command_line_parser(int,
> char const* const*)':
>
> metatwist.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x168):
> undefined reference to
> `boost::program_options::to_internal(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&)'
>
> metatwist.cpp:(.text._ZN5boost15program_options25basic_command_line_parserIcEC2EiPKPKc[_ZN5boost15program_options25basic_command_line_parserIcEC5EiPKPKc]+0x1ef):
> undefined reference to
>
> `boost::program_options::detail::cmdline::cmdline(std::vector<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >,
> std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > > const&)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `__gnu_cxx::__normal_iterator<char const*, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > >
> boost::re_detail::re_is_set_member<__gnu_cxx::__normal_iterator<char
> const*, std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >, char, boost::regex_traits<char,
> boost::cpp_regex_traits<char> >, unsigned
> int>(__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >, boost::re_detail::re_set_long<unsigned int>
> const*, boost::re_detail::regex_data<char, boost::regex_traits<char,
> boost::cpp_regex_traits<char> > > const&, bool)':
>
> metatwist.cpp:(.text._ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x339):
> undefined reference to
>
> `boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary[abi:cxx11](char
> const*, char const*) const'
>
> metatwist.cpp:(.text._ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SH_SH_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x54d):
> undefined reference to
>
> `boost::re_detail::cpp_regex_traits_implementation<char>::transform[abi:cxx11](char
> const*, char const*) const'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `__gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > >
> boost::re_detail::re_is_set_member<__gnu_cxx::__normal_iterator<char*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >, char, boost::regex_traits<char,
> boost::cpp_regex_traits<char> >, unsigned
> int>(__gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > >,
> __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > >,
> boost::re_detail::re_set_long<unsigned int> const*,
> boost::re_detail::regex_data<char, boost::regex_traits<char,
> boost::cpp_regex_traits<char> > > const&, bool)':
>
> metatwist.cpp:(.text._ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SG_SG_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SG_SG_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x339):
> undefined reference to
>
> `boost::re_detail::cpp_regex_traits_implementation<char>::transform_primary[abi:cxx11](char
> const*, char const*) const'
>
> metatwist.cpp:(.text._ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SG_SG_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb[_ZN5boost9re_detail16re_is_set_memberIN9__gnu_cxx17__normal_iteratorIPcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEjEET_SG_SG_PKNS0_11re_set_longIT2_EERKNS0_10regex_dataIT0_T1_EEb]+0x54d):
> undefined reference to
>
> `boost::re_detail::cpp_regex_traits_implementation<char>::transform[abi:cxx11](char
> const*, char const*) const'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > const&
>
> boost::program_options::validators::get_single_string<char>(std::vector<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >,
> std::allocator<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > > const&, bool)':
>
> metatwist.cpp:(.text._ZN5boost15program_options10validators17get_single_stringIcEERKNSt7__cxx1112basic_stringIT_St11char_traitsIS5_ESaIS5_EEERKSt6vectorIS9_SaIS9_EEb[_ZN5boost15program_options10validators17get_single_stringIcEERKNSt7__cxx1112basic_stringIT_St11char_traitsIS5_ESaIS5_EEERKSt6vectorIS9_SaIS9_EEb]+0x98):
> undefined reference to
>
> `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
>
> metatwist.cpp:(.text._ZN5boost15program_options10validators17get_single_stringIcEERKNSt7__cxx1112basic_stringIT_St11char_traitsIS5_ESaIS5_EEERKSt6vectorIS9_SaIS9_EEb[_ZN5boost15program_options10validators17get_single_stringIcEERKNSt7__cxx1112basic_stringIT_St11char_traitsIS5_ESaIS5_EEERKSt6vectorIS9_SaIS9_EEb]+0xac):
> undefined reference to
>
> `boost::program_options::error_with_option_name::error_with_option_name(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&, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&, int)'
>
> metatwist.cpp:(.text._ZN5boost15program_options10validators17get_single_stringIcEERKNSt7__cxx1112basic_stringIT_St11char_traitsIS5_ESaIS5_EEERKSt6vectorIS9_SaIS9_EEb[_ZN5boost15program_options10validators17get_single_stringIcEERKNSt7__cxx1112basic_stringIT_St11char_traitsIS5_ESaIS5_EEERKSt6vectorIS9_SaIS9_EEb]+0x168):
> undefined reference to
>
> `boost::program_options::validation_error::get_template[abi:cxx11](boost::program_options::validation_error::kind_t)'
>
> metatwist.cpp:(.text._ZN5boost15program_options10validators17get_single_stringIcEERKNSt7__cxx1112basic_stringIT_St11char_traitsIS5_ESaIS5_EEERKSt6vectorIS9_SaIS9_EEb[_ZN5boost15program_options10validators17get_single_stringIcEERKNSt7__cxx1112basic_stringIT_St11char_traitsIS5_ESaIS5_EEERKSt6vectorIS9_SaIS9_EEb]+0x17c):
> undefined reference to
>
> `boost::program_options::error_with_option_name::error_with_option_name(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&, std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&, int)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function `void
> boost::program_options::validate<double, char>(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&, double*, long)':
>
> metatwist.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0xaa):
> undefined reference to
>
> `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function `void
> boost::program_options::validate<unsigned long, char>(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&, unsigned long*,
> long)':
>
> metatwist.cpp:(.text._ZN5boost15program_options8validateImcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l[_ZN5boost15program_options8validateImcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPT_l]+0xa8):
> undefined reference to
>
> `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function `void
> boost::program_options::validate<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> >, char>(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > >*, int)':
>
> metatwist.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0xb6):
> undefined reference to `boost::program_options::validate(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<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> >*, int)'
>
> metatwist.cpp:(.text._ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi[_ZN5boost15program_options8validateINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEEvRNS_3anyERKSt6vectorINS3_IT0_S4_ISB_ESaISB_EEESaISE_EEPSA_IT_SaISJ_EEi]+0x371):
> undefined reference to
>
> `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function `void
> boost::program_options::validate<double, char>(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&,
> std::vector<double, std::allocator<double> >*, int)':
>
> metatwist.cpp:(.text._ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi[_ZN5boost15program_options8validateIdcEEvRNS_3anyERKSt6vectorINSt7__cxx1112basic_stringIT0_St11char_traitsIS7_ESaIS7_EEESaISB_EEPS4_IT_SaISG_EEi]+0x2bf):
> undefined reference to
>
> `boost::program_options::invalid_option_value::invalid_option_value(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function `bool
> boost::regex_search<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >,
> std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > > >, char, boost::regex_traits<char,
> boost::cpp_regex_traits<char> > >(__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >, __gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >,
> boost::match_results<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >,
> std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > > > >&, boost::basic_regex<char,
> boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&,
> boost::regex_constants::_match_flags, __gnu_cxx::__normal_iterator<char
> const*, std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >)':
>
> metatwist.cpp:(.text._ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_[_ZN5boost12regex_searchIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISB_EEEcNS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEEEbT_SJ_RNS_13match_resultsISJ_T0_EERKNS_11basic_regexIT1_T2_EENS_15regex_constants12_match_flagsESJ_]+0x11d):
> undefined reference to
> `boost::re_detail::perl_matcher<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >,
> std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > > >, boost::regex_traits<char,
> boost::cpp_regex_traits<char> > >::construct_init(boost::basic_regex<char,
> boost::regex_traits<char, boost::cpp_regex_traits<char> > > const&,
> boost::regex_constants::_match_flags)'
> CMakeFiles/metatwist.dir/metatwist.cpp.o: In function
> `boost::re_detail::perl_matcher<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >,
> std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > > >, boost::regex_traits<char,
> boost::cpp_regex_traits<char> > >::match_match()':
>
> metatwist.cpp:(.text._ZN5boost9re_detail12perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv[_ZN5boost9re_detail12perl_matcherIN9__gnu_cxx17__normal_iteratorIPKcNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEESaINS_9sub_matchISC_EEENS_12regex_traitsIcNS_16cpp_regex_traitsIcEEEEE11match_matchEv]+0x282):
> undefined reference to
> `boost::match_results<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >,
> std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > > >
> >::maybe_assign(boost::match_results<__gnu_cxx::__normal_iterator<char
> const*, std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > >,
> std::allocator<boost::sub_match<__gnu_cxx::__normal_iterator<char const*,
> std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> > > > > > const&)'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE]+0x30):
> undefined reference to
>
> `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE]+0x38):
> undefined reference to
>
> `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[_ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE]+0x30):
> undefined reference to
>
> `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[_ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE]+0x38):
> undefined reference to
>
> `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[_ZTVN5boost15program_options16validation_errorE]+0x30):
> undefined reference to
>
> `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[_ZTVN5boost15program_options20invalid_option_valueE]+0x30):
> more undefined references to
>
> `boost::program_options::error_with_option_name::substitute_placeholders(std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > const&) const' follow
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEcEE]+0x38):
> undefined reference to
>
> `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE[_ZTVN5boost15program_options11typed_valueINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcEE]+0x38):
> undefined reference to
>
> `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueIdcEE[_ZTVN5boost15program_options11typed_valueIdcEE]+0x38):
> undefined reference to
>
> `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueISt6vectorIdSaIdEEcEE[_ZTVN5boost15program_options11typed_valueISt6vectorIdSaIdEEcEE]+0x38):
> undefined reference to
>
> `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
>
> CMakeFiles/metatwist.dir/metatwist.cpp.o:(.rodata._ZTVN5boost15program_options11typed_valueImcEE[_ZTVN5boost15program_options11typed_valueImcEE]+0x38):
> undefined reference to
>
> `boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
> std::vector<std::__cxx11::basic_string<char, std::char_traits<char>,
> std::allocator<char> >, std::allocator<std::__cxx11::basic_string<char,
> std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
> collect2: error: ld returned 1 exit status
> make[2]: *** [AmberTools/src/moft/metatwist] Error 1
> make[1]: *** [AmberTools/src/moft/CMakeFiles/metatwist.dir/all] Error 2
> make: *** [all] Error 2
>
> I am unable to understand this.
>
> Your guidance will be helpful.
>
> Thank you
> --
> Kriti Shukla
> Research Scholar
> Department of Chemistry
> Indian Institute of Technology, Kharagpur
> India. 721302
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
>
> https://urldefense.com/v3/__http://lists.ambermd.org/mailman/listinfo/amber__;!!HXCxUKc!wmMlM6XihnAkJnFCD1hOOLuR87A2a9mz498zjAADfgKGfS46NTxelBluyv7_3Z1idS7Ttd9_AT1hTPL6Sxm9ZKI$
>
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Received on Mon Oct 27 2025 - 23:30:02 PDT
