installing Auryn using cmake

This section contains questions related to the compilation of Auryn on different platforms.
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james_4424
Posts: 3
Joined: Thu Apr 07, 2016 8:20 am

installing Auryn using cmake

Post by james_4424 »

Hi I am new to Auryn, and try to install it on my Ubuntu laptop as per instruction on https://github.com/fzenke/auryn/tree/74 ... 28e0598fbd

However when I run cmake:
cmake ../ -DCMAKE_BUILD_TYPE=Release && make

I get the below error:

CMake Error at src/CMakeLists.txt:7 (TARGET_INCLUDE_DIRECTORIES):
Unknown CMake command "TARGET_INCLUDE_DIRECTORIES".


-- Configuring incomplete, errors occurred!


I am not sure how I should proceed. Please advise.
User avatar
zenke
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Posts: 156
Joined: Tue Oct 14, 2014 11:34 am
Location: Basel, CH
Contact:

Re: installing Auryn using cmake

Post by zenke »

Hi,
this looks as if your version of cmake is too old. Which cmake version do you have installed? If I remember correctly you need a cmake version >2.8.11. I added this now in the config file requirements such that one should get a more meaningful error message next time.
Cheers,
F
james_4424
Posts: 3
Joined: Thu Apr 07, 2016 8:20 am

Re: installing Auryn using cmake

Post by james_4424 »

Hi,

I have installed the newest cmake version and managed to proceed further, before running into errors, which i presumed are related to boost. I have boost installed on my machine, so am not sure what is wrong, below being the error during make:

Code: Select all

[ 71%] Linking CXX executable sim_isp_orig
/usr/bin/ld: warning: libmpi.so.0, needed by /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libboost_mpi-mt.so, may conflict with libmpi.so.1
/usr/bin/ld: warning: libmpi_cxx.so.0, needed by /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libboost_mpi-mt.so, may conflict with libmpi_cxx.so.1
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
sim_isp_orig.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x2c): undefined reference to `boost::program_options::validation_error::get_template(boost::program_options::validation_error::kind_t)'
sim_isp_orig.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x44): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::program_options::error_with_option_name::~error_with_option_name()':
sim_isp_orig.cpp:(.text._ZN5boost15program_options22error_with_option_nameD2Ev[_ZN5boost15program_options22error_with_option_nameD5Ev]+0x7): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >::~clone_impl()':
sim_isp_orig.cpp:(.text._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEED1Ev[boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >::~clone_impl()]+0x57): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>::~error_info_injector()':
sim_isp_orig.cpp:(.text._ZN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEED2Ev[_ZN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEED5Ev]+0x2c): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >::~clone_impl()':
sim_isp_orig.cpp:(.text._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEED0Ev[boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >::~clone_impl()]+0x57): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::program_options::basic_parsed_options<char> boost::program_options::parse_command_line<char>(int, char const* const*, boost::program_options::options_description const&, int, boost::function1<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
sim_isp_orig.cpp:(.text._ZN5boost15program_options18parse_command_lineIcEENS0_20basic_parsed_optionsIT_EEiPKPKS3_RKNS0_19options_descriptionEiNS_9function1ISt4pairISsSsERKSsEE[boost::program_options::basic_parsed_options<char> boost::program_options::parse_command_line<char>(int, char const* const*, boost::program_options::options_description const&, int, boost::function1<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)]+0x3d5): undefined reference to `boost::program_options::detail::cmdline::get_canonical_option_prefix()'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `void boost::serialization::throw_exception<boost::archive::archive_exception>(boost::archive::archive_exception const&)':
sim_isp_orig.cpp:(.text._ZN5boost13serialization15throw_exceptionINS_7archive17archive_exceptionEEEvRKT_[void boost::serialization::throw_exception<boost::archive::archive_exception>(boost::archive::archive_exception const&)]+0x1d): undefined reference to `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception const&)'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error const&)':
sim_isp_orig.cpp:(.text._ZN5boost15program_options16validation_errorC2ERKS1_[_ZN5boost15program_options16validation_errorC5ERKS1_]+0x2c): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[vtable for boost::program_options::validation_error]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[vtable for boost::program_options::validation_error]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error>]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error>]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >]+0x28): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[vtable for boost::program_options::invalid_option_value]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[vtable for boost::program_options::invalid_option_value]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >]+0x28): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTIN5boost15program_options16validation_errorE[typeinfo for boost::program_options::validation_error]+0x10): undefined reference to `typeinfo for boost::program_options::error_with_option_name'
../src/libauryn.a(System.cpp.o): In function `boost::archive::detail::common_iarchive<boost::archive::binary_iarchive>::vload(boost::archive::class_name_type&)':
System.cpp:(.text._ZN5boost7archive6detail15common_iarchiveINS0_15binary_iarchiveEE5vloadERNS0_15class_name_typeE[boost::archive::detail::common_iarchive<boost::archive::binary_iarchive>::vload(boost::archive::class_name_type&)]+0x1): undefined reference to `boost::archive::basic_binary_iarchive<boost::archive::binary_iarchive>::load_override(boost::archive::class_name_type&)'
../src/libauryn.a(SpikingGroup.cpp.o): In function `boost::archive::detail::common_iarchive<boost::archive::text_iarchive>::vload(boost::archive::class_name_type&)':
SpikingGroup.cpp:(.text._ZN5boost7archive6detail15common_iarchiveINS0_13text_iarchiveEE5vloadERNS0_15class_name_typeE[boost::archive::detail::common_iarchive<boost::archive::text_iarchive>::vload(boost::archive::class_name_type&)]+0x1): undefined reference to `boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load_override(boost::archive::class_name_type&)'
collect2: ld returned 1 exit status
make[2]: *** [examples/sim_isp_orig] Error 1
make[1]: *** [examples/CMakeFiles/sim_isp_orig.dir/all] Error 2
make: *** [all] Error 2
thanks for your help!

yansong
User avatar
zenke
Site Admin
Posts: 156
Joined: Tue Oct 14, 2014 11:34 am
Location: Basel, CH
Contact:

Re: installing Auryn using cmake

Post by zenke »

Hmmm,
interesting. Yup that looks like a linker error. Seems as if the linker cannot find boost.
Can you give some more info on the libs you are using? Are you using the Ubuntu packages of boost or did you compile boost from source. Which MPI implementation are you using? My best 2nd guess right now is that your boost version was compiled with a different MPI version than you are trying to link against, but if you are using the default packages, that should not be the case...
Can you confirm that you have only one MPI implementation and one boost library installed? Otherwise cmake might be confused about that too.
Any warnings concerning boost in the cmake output? Maybe also check in CMakeFiles/CMakeOutput.log to be sure.

The initial output of cmake should look similar to this:

Code: Select all

zenke@arthur ~/auryn/build/arch $ ./bootstrap.sh 
-- Boost version: 1.54.0
-- Found the following Boost libraries:
--   mpi
--   serialization
--   program_options
--   date_time
-- Configuring done
-- Generating done
-- Build files have been written to: /home/zenke/auryn/build/arch
Bye,
F
User avatar
zenke
Site Admin
Posts: 156
Joined: Tue Oct 14, 2014 11:34 am
Location: Basel, CH
Contact:

Re: installing Auryn using cmake

Post by zenke »

Hi,
just wondering if you had any luck with compiling the code.
Best,
F
james_4424
Posts: 3
Joined: Thu Apr 07, 2016 8:20 am

Re: installing Auryn using cmake

Post by james_4424 »

Hi,

I think you are right, as I have my version of boost installed (boost 1.6.0), and they probably have a different MPI, and hence the problem. The below is the output when I run cmake again, sorry for its length. I am new to this and not sure how best to overcome this, so here goes:

-- Boost version: 1.60.0
-- Found the following Boost libraries:
-- mpi
-- serialization
-- program_options
-- date_time
-- Configuring done
-- Generating done
-- Build files have been written to: /home/yansong/programs/auryn/build
[ 70%] Built target auryn
[ 71%] Linking CXX executable sim_isp_orig
/usr/bin/ld: warning: libmpi.so.0, needed by /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libboost_mpi-mt.so, may conflict with libmpi.so.1
/usr/bin/ld: warning: libmpi_cxx.so.0, needed by /usr/lib/gcc/x86_64-linux-gnu/4.6/../../../../lib/libboost_mpi-mt.so, may conflict with libmpi_cxx.so.1
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error::kind_t, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)':
sim_isp_orig.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x2c): undefined reference to `boost::program_options::validation_error::get_template(boost::program_options::validation_error::kind_t)'
sim_isp_orig.cpp:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x44): undefined reference to `boost::program_options::error_with_option_name::error_with_option_name(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::program_options::error_with_option_name::~error_with_option_name()':
sim_isp_orig.cpp:(.text._ZN5boost15program_options22error_with_option_nameD2Ev[_ZN5boost15program_options22error_with_option_nameD5Ev]+0x7): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >::~clone_impl()':
sim_isp_orig.cpp:(.text._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEED1Ev[boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >::~clone_impl()]+0x57): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>::~error_info_injector()':
sim_isp_orig.cpp:(.text._ZN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEED2Ev[_ZN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEED5Ev]+0x2c): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >::~clone_impl()':
sim_isp_orig.cpp:(.text._ZN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEED0Ev[boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >::~clone_impl()]+0x57): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::program_options::basic_parsed_options<char> boost::program_options::parse_command_line<char>(int, char const* const*, boost::program_options::options_description const&, int, boost::function1<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)':
sim_isp_orig.cpp:(.text._ZN5boost15program_options18parse_command_lineIcEENS0_20basic_parsed_optionsIT_EEiPKPKS3_RKNS0_19options_descriptionEiNS_9function1ISt4pairISsSsERKSsEE[boost::program_options::basic_parsed_options<char> boost::program_options::parse_command_line<char>(int, char const* const*, boost::program_options::options_description const&, int, boost::function1<std::pair<std::basic_string<char, std::char_traits<char>, std::allocator<char> >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > >, std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&>)]+0x3d5): undefined reference to `boost::program_options::detail::cmdline::get_canonical_option_prefix()'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `void boost::serialization::throw_exception<boost::archive::archive_exception>(boost::archive::archive_exception const&)':
sim_isp_orig.cpp:(.text._ZN5boost13serialization15throw_exceptionINS_7archive17archive_exceptionEEEvRKT_[void boost::serialization::throw_exception<boost::archive::archive_exception>(boost::archive::archive_exception const&)]+0x1d): undefined reference to `boost::archive::archive_exception::archive_exception(boost::archive::archive_exception const&)'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o: In function `boost::program_options::validation_error::validation_error(boost::program_options::validation_error const&)':
sim_isp_orig.cpp:(.text._ZN5boost15program_options16validation_errorC2ERKS1_[_ZN5boost15program_options16validation_errorC5ERKS1_]+0x2c): undefined reference to `vtable for boost::program_options::error_with_option_name'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[vtable for boost::program_options::validation_error]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost15program_options16validation_errorE[vtable for boost::program_options::validation_error]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error>]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options16validation_errorEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::validation_error>]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >]+0x28): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options16validation_errorEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::validation_error> >]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[vtable for boost::program_options::invalid_option_value]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost15program_options20invalid_option_valueE[vtable for boost::program_options::invalid_option_value]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>]+0x20): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail19error_info_injectorINS_15program_options20invalid_option_valueEEE[vtable for boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value>]+0x30): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >]+0x28): undefined reference to `boost::program_options::error_with_option_name::what() const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTVN5boost16exception_detail10clone_implINS0_19error_info_injectorINS_15program_options20invalid_option_valueEEEEE[vtable for boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >]+0x38): undefined reference to `boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/sim_isp_orig.dir/sim_isp_orig.cpp.o:(.rodata._ZTIN5boost15program_options16validation_errorE[typeinfo for boost::program_options::validation_error]+0x10): undefined reference to `typeinfo for boost::program_options::error_with_option_name'
../src/libauryn.a(System.cpp.o): In function `boost::archive::detail::common_iarchive<boost::archive::binary_iarchive>::vload(boost::archive::class_name_type&)':
System.cpp:(.text._ZN5boost7archive6detail15common_iarchiveINS0_15binary_iarchiveEE5vloadERNS0_15class_name_typeE[boost::archive::detail::common_iarchive<boost::archive::binary_iarchive>::vload(boost::archive::class_name_type&)]+0x1): undefined reference to `boost::archive::basic_binary_iarchive<boost::archive::binary_iarchive>::load_override(boost::archive::class_name_type&)'
../src/libauryn.a(SpikingGroup.cpp.o): In function `boost::archive::detail::common_iarchive<boost::archive::text_iarchive>::vload(boost::archive::class_name_type&)':
SpikingGroup.cpp:(.text._ZN5boost7archive6detail15common_iarchiveINS0_13text_iarchiveEE5vloadERNS0_15class_name_typeE[boost::archive::detail::common_iarchive<boost::archive::text_iarchive>::vload(boost::archive::class_name_type&)]+0x1): undefined reference to `boost::archive::text_iarchive_impl<boost::archive::text_iarchive>::load_override(boost::archive::class_name_type&)'
collect2: ld returned 1 exit status
make[2]: *** [examples/sim_isp_orig] Error 1
make[1]: *** [examples/CMakeFiles/sim_isp_orig.dir/all] Error 2
make: *** [all] Error 2
User avatar
zenke
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Re: installing Auryn using cmake

Post by zenke »

Hey there,
could you give some more information about the Ubuntu version and the packages you are using? Which Linux distribution/version are you using? Which MPI libraries are installed? Ubuntu relies per default on OpenMPI, but MPICH2 is optimally also available. Did you compile the libraries manually? Did you install them via the package managing software? Normally, you can rely on the packages shipped through the standard repositories to install boost and MPI and they will work together. The story might change a bit if you install them manually or you have different versions installed. Boost normally automatically detects which version of MPI you are using, but might get "confused" if two different libs are installed at compile time...

I am currently using Ubuntu Trusty with Boost version: 1.54.0 and libopenmpi 1.6. Both installed from standard Trusty repositories.

PS.: Did you run "make clean" before reattempting to compile the libraries?
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zenke
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Re: installing Auryn using cmake

Post by zenke »

Any news on this? I hope you managed to compile the library.
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