Dear VOTCA developers and users,
I am trying to install the VOTCA software with build.sh on Centos system
but encountered some errors. Before install votca, I have installed all the
dependencies: Boost, Git, GSL, FFTW3, EXPAT, PkgConfig, SQLITE3, Doxygen,
Gromacs. The gcc version is 6.1.0 and the current boost version is 1.53.0.
The installation command I used is:
./build.sh --prefix /usr/local/votca/
-DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/
-DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so --dev tools csg
kmc moo ctp ctp-tutorials ctp-manual
With this building command, I got the following error information:
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::~basic_string()@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::logic_error::logic_error(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>,
std::allocator<wchar_t> >::~basic_string()@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`operator delete(void*, unsigned long)@CXXABI_1.3.9'
/usr/local/lib/libboost_program_options.so: 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)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::find(char const*, unsigned long, unsigned long)
const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_filesystem.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> >::rfind(char, unsigned long) const@GLIBCXX_3.4.21'
collect2: ld returned 1 exit status
make[2]: *** [src/tools/votca_property] Error 1
make[1]: *** [src/tools/CMakeFiles/votca_property.dir/all] Error 2
make: *** [all] Error 2
When searching from the previous discussions, I found that I may need to
specify the Boost path. As a result, I tried:
./build.sh --prefix /usr/local/votca/
-DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/
-DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so
-DBoost_INCLUDE_DIR=/usr/local/include/boost/
-DBoost_PROGRAM_OPTIONS_LIBRARY=/usr/local/lib/libboost_program_options.so
-DBoost_FILESYSTEM_LIBRARY=/usr/local/lib/libboost_filesystem.so --dev
tools csg kmc moo ctp ctp-tutorials ctp-manual
This time, votca can not find the boost package? I have no idea why it can
not find boost since I have specified the path to it!
For more information, I have attached the entire on screen printed
information and the cmake error file. The file names with "_noBoostPath"
correspond to the first building command (no boost path is specified) while
the file names with "_withBoostPath" correspond to the second building
command.
By the way, when using the second building command, votca find both GSL and
MKL libraries, so I have also tried to disable the mkl library with
-DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON, but not change happens.
Thank you very much for your kind help!
With best regards,
Shiyun
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[32;01mThis is VOTCA build.sh, version 2.1.3[0m
Install prefix is '/usr/local/votca/'
[34;01mUsing 29 jobs for make/ninja[0m
[32;01mWorking on tools[0m
[34;01mSource dir (tools) is already there - skipping checkout[0m
[34;01mcmake -DCMAKE_INSTALL_PREFIX='/usr/local/votca/'
-DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/
-DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so
-DCMAKE_DISABLE_FIND_PACKAGE_MKL=ON -DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .[0m
-- Found Git: /usr/local/bin/bin/git (found version "2.3.0")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Boost version: 1.53.0
-- Found the following Boost libraries:
-- program_options
-- filesystem
-- system
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Checking for module 'gsl'
-- Found gsl, version 2.3
-- Found GSL: /usr/local/lib/libgsl.so
-- Looking for gsl_linalg_QR_decomp in /usr/local/lib/libgsl.so;
-- Looking for gsl_linalg_QR_decomp in /usr/local/lib/libgsl.so; - not found
-- Found GSLCBLAS: /usr/local/lib/libgslcblas.so
-- Looking for cblas_dsyrk in /usr/local/lib/libgslcblas.so;
-- Looking for cblas_dsyrk in /usr/local/lib/libgslcblas.so; - found
-- Looking for gsl_linalg_QR_lssolve in
/usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so;
-- Looking for gsl_linalg_QR_lssolve in
/usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so; - found
-- Checking for module 'fftw3'
-- No package 'fftw3' found
-- Found FFTW3: /usr/local/fftw_shared/lib/libfftw3.so
-- Looking for fftw_plan_r2r_1d in /usr/local/fftw_shared/lib/libfftw3.so;
-- Looking for fftw_plan_r2r_1d in /usr/local/fftw_shared/lib/libfftw3.so; -
found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Checking for module 'expat'
-- Found expat, version 2.2.0
-- Found EXPAT: /usr/lib64/libexpat.so
-- Checking for module 'sqlite3'
-- No package 'sqlite3' found
-- Found SQLITE3: /usr/lib64/libsqlite3.so
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Found Doxygen: /usr/bin/doxygen (found version "1.6.1")
--
-- The following OPTIONAL packages have been found:
* Git
* GSL
* FFTW3
* EXPAT
* PkgConfig
* SQLITE3
* Doxygen
-- The following REQUIRED packages have been found:
* Threads
* Boost (required version >= 1.39.0)
-- Configuring done
-- Generating done
-- Build files have been written to: /home/xiong/votca/src/tools
[32;01mcleaning tools[0m
[32;01mbuidling tools[0m
[ 0%] Built target votca_tools_manpages
[ 0%] Built target gitversion
Scanning dependencies of target votca_tools
[ 2%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/akimaspline.cc.o
[ 5%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/application.cc.o
[ 7%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/colors.cc.o
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src/libtools/CMakeFiles/votca_tools.dir/correlate.cc.o
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src/libtools/CMakeFiles/votca_tools.dir/crosscorrelate.cc.o
[ 15%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/cubicspline.cc.o
[ 17%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/datacollection.cc.o
[ 20%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/globals.cc.o
[ 23%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/histogram.cc.o
[ 25%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/histogramnew.cc.o
[ 28%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/linalg.cc.o
[ 33%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/mutex.cc.o
[ 30%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linspline.cc.o
[ 35%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/parcer.cc.o
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src/libtools/CMakeFiles/votca_tools.dir/rangeparser.cc.o
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src/libtools/CMakeFiles/votca_tools.dir/propertyiomanipulator.cc.o
[ 53%] Building CXX object src/libtools/CMakeFiles/votca_tools.dir/random2.cc.o
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src/libtools/CMakeFiles/votca_tools.dir/tokenizer.cc.o
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src/libtools/CMakeFiles/votca_tools.dir/statement.cc.o
[ 74%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/cholesky.cc.o
[ 76%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/eigensystems.cc.o
[ 79%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/qrsolve.cc.o
[ 82%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/invert.cc.o
[ 84%] Building CXX object
src/libtools/CMakeFiles/votca_tools.dir/linalg/gsl/svd.cc.o
[ 87%] Linking CXX shared library libvotca_tools.so
[ 89%] Built target votca_tools
[ 92%] Building CXX object
src/tools/CMakeFiles/votca_property.dir/votca_property.cc.o
[ 94%] Linking CXX executable votca_property
CMakeFiles/votca_property.dir/votca_property.cc.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)':
votca_property.cc:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x34):
undefined reference to
`boost::program_options::validation_error::get_template(boost::program_options::validation_error::kind_t)'
votca_property.cc:(.text._ZN5boost15program_options16validation_errorC2ENS1_6kind_tERKSsS4_i[_ZN5boost15program_options16validation_errorC5ENS1_6kind_tERKSsS4_i]+0x4a):
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/votca_property.dir/votca_property.cc.o: In function
`boost::program_options::typed_value<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&,
std::vector<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&) const':
votca_property.cc:(.text._ZNK5boost15program_options11typed_valueISscE6xparseERNS_3anyERKSt6vectorISsSaISsEE[boost::program_options::typed_value<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >, char>::xparse(boost::any&,
std::vector<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&) const]+0x19):
undefined reference to `boost::program_options::validate(boost::any&,
std::vector<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&,
std::basic_string<char, std::char_traits<char>, std::allocator<char> >*, int)'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function
`boost::program_options::typed_value<int, char>::name() const':
votca_property.cc:(.text._ZNK5boost15program_options11typed_valueIicE4nameEv[boost::program_options::typed_value<int,
char>::name() const]+0x31): undefined reference to
`boost::program_options::arg'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function
`boost::program_options::typed_value<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >, char>::name() const':
votca_property.cc:(.text._ZNK5boost15program_options11typed_valueISscE4nameEv[boost::program_options::typed_value<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >, char>::name() const]+0x31):
undefined reference to `boost::program_options::arg'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function
`VotcaProperty::Run()':
votca_property.cc:(.text._ZN13VotcaProperty3RunEv[VotcaProperty::Run()]+0x41):
undefined reference to
`boost::program_options::abstract_variables_map::operator[](std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const'
votca_property.cc:(.text._ZN13VotcaProperty3RunEv[VotcaProperty::Run()]+0x216):
undefined reference to
`boost::program_options::abstract_variables_map::operator[](std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const'
votca_property.cc:(.text._ZN13VotcaProperty3RunEv[VotcaProperty::Run()]+0x8b6):
undefined reference to
`boost::program_options::abstract_variables_map::operator[](std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const'
CMakeFiles/votca_property.dir/votca_property.cc.o: In function
`std::basic_string<char, std::char_traits<char>, std::allocator<char> > const&
boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> > > > const&, bool)':
votca_property.cc:(.text._ZN5boost15program_options10validators17get_single_stringIcEERKSbIT_St11char_traitsIS3_ESaIS3_EERKSt6vectorIS7_SaIS7_EEb[std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&
boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> > > > const&, bool)]+0xa0): undefined reference to
`boost::program_options::validation_error::get_template(boost::program_options::validation_error::kind_t)'
votca_property.cc:(.text._ZN5boost15program_options10validators17get_single_stringIcEERKSbIT_St11char_traitsIS3_ESaIS3_EERKSt6vectorIS7_SaIS7_EEb[std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&
boost::program_options::validators::get_single_string<char>(std::vector<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> > > > const&, bool)]+0xb4): 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/votca_property.dir/votca_property.cc.o: In function `void
boost::program_options::validate<int, char>(boost::any&,
std::vector<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&, int*, long)':
votca_property.cc:(.text._ZN5boost15program_options8validateIicEEvRNS_3anyERKSt6vectorISbIT0_St11char_traitsIS5_ESaIS5_EESaIS9_EEPT_l[void
boost::program_options::validate<int, char>(boost::any&,
std::vector<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&, int*, long)]+0xe1):
undefined reference to
`boost::program_options::invalid_option_value::invalid_option_value(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost15program_options11typed_valueIicEE[vtable
for boost::program_options::typed_value<int, char>]+0x38): undefined reference
to
`boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
std::vector<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
CMakeFiles/votca_property.dir/votca_property.cc.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/votca_property.dir/votca_property.cc.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/votca_property.dir/votca_property.cc.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/votca_property.dir/votca_property.cc.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/votca_property.dir/votca_property.cc.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/votca_property.dir/votca_property.cc.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): more undefined references to
`boost::program_options::error_with_option_name::substitute_placeholders(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&) const' follow
CMakeFiles/votca_property.dir/votca_property.cc.o:(.rodata._ZTVN5boost15program_options11typed_valueISscEE[vtable
for boost::program_options::typed_value<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >, char>]+0x38): undefined
reference to
`boost::program_options::value_semantic_codecvt_helper<char>::parse(boost::any&,
std::vector<std::basic_string<char, std::char_traits<char>,
std::allocator<char> >, std::allocator<std::basic_string<char,
std::char_traits<char>, std::allocator<char> > > > const&, bool) const'
/usr/local/lib/libboost_program_options.so: undefined reference to `VTT for
std::__cxx11::basic_stringstream<char, std::char_traits<char>,
std::allocator<char> >@GLIBCXX_3.4.21'
../libtools/libvotca_tools.so.5: undefined reference to
`boost::program_options::to_internal(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)'
/usr/local/lib/libboost_program_options.so: 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&)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::reserve(unsigned long)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>,
std::allocator<wchar_t> >::_M_mutate(unsigned long, unsigned long, wchar_t
const*, unsigned long)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::find_last_of(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::find_last_not_of(char const*, unsigned long, unsigned long)
const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::runtime_error::runtime_error(char const*)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::basic_istream<wchar_t, std::char_traits<wchar_t> >& std::getline<wchar_t,
std::char_traits<wchar_t>, std::allocator<wchar_t>
>(std::basic_istream<wchar_t, std::char_traits<wchar_t> >&,
std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>,
std::allocator<wchar_t> >&, wchar_t)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::resize(unsigned long, char)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::_M_erase(unsigned long, unsigned long)@GLIBCXX_3.4.21'
../libtools/libvotca_tools.so.5: undefined reference to
`boost::program_options::options_description::options_description(std::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&, unsigned int, unsigned
int)'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::logic_error::logic_error(char const*)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::runtime_error::runtime_error(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::find_first_not_of(char const*, unsigned long, unsigned long)
const@GLIBCXX_3.4.21'
../libtools/libvotca_tools.so.5: undefined reference to
`boost::program_options::option_description::format_name() const'
../libtools/libvotca_tools.so.5: undefined reference to
`boost::program_options::detail::cmdline::set_additional_parser(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&>)'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20'
../libtools/libvotca_tools.so.5: undefined reference to
`boost::program_options::option_description::format_parameter() const'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::_M_append(char const*, unsigned long)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::compare(std::__cxx11::basic_string<char, std::char_traits<char>,
std::allocator<char> > const&) const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::find(char, unsigned long) const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>,
std::allocator<wchar_t> >::_M_create(unsigned long&, unsigned
long)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_stringstream<char, std::char_traits<char>,
std::allocator<char> >::~basic_stringstream()@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::logic_error::logic_error(std::logic_error const&)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_filesystem.so: undefined reference to
`__cxa_throw_bad_array_new_length@CXXABI_1.3.8'
/usr/local/lib/libboost_program_options.so: undefined reference to `vtable for
std::__cxx11::basic_stringstream<char, std::char_traits<char>,
std::allocator<char> >@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to `vtable for
std::__cxx11::basic_stringbuf<char, std::char_traits<char>,
std::allocator<char> >@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::_M_create(unsigned long&, unsigned long)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::runtime_error::runtime_error(std::runtime_error const&)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::_M_replace_aux(unsigned long, unsigned long, unsigned long,
char)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::basic_istream<char, std::char_traits<char> >& std::getline<char,
std::char_traits<char>, std::allocator<char> >(std::basic_istream<char,
std::char_traits<char> >&, std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> >&, char)@GLIBCXX_3.4.21'
../libtools/libvotca_tools.so.5: undefined reference to
`boost::program_options::detail::cmdline::cmdline(std::vector<std::basic_string<char,
std::char_traits<char>, std::allocator<char> >,
std::allocator<std::basic_string<char, std::char_traits<char>,
std::allocator<char> > > > const&)'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>,
std::allocator<wchar_t> >::compare(wchar_t const*) const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>,
std::allocator<wchar_t> >::_M_replace(unsigned long, unsigned long, wchar_t
const*, unsigned long)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>,
std::allocator<wchar_t> >::_M_assign(std::__cxx11::basic_string<wchar_t,
std::char_traits<wchar_t>, std::allocator<wchar_t> > const&)@GLIBCXX_3.4.21'
../libtools/libvotca_tools.so.5: undefined reference to
`boost::program_options::option_description::description() const'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::compare(char const*) const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_filesystem.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::find_first_of(char const*, unsigned long, unsigned long)
const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::_M_mutate(unsigned long, unsigned long, char const*, unsigned
long)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::~basic_string()@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::logic_error::logic_error(std::__cxx11::basic_string<char,
std::char_traits<char>, std::allocator<char> > const&)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<wchar_t, std::char_traits<wchar_t>,
std::allocator<wchar_t> >::~basic_string()@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to `operator
delete(void*, unsigned long)@CXXABI_1.3.9'
/usr/local/lib/libboost_program_options.so: 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)@GLIBCXX_3.4.21'
/usr/local/lib/libboost_program_options.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::find(char const*, unsigned long, unsigned long) const@GLIBCXX_3.4.21'
/usr/local/lib/libboost_filesystem.so: undefined reference to
`std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char>
>::rfind(char, unsigned long) const@GLIBCXX_3.4.21'
collect2: ld returned 1 exit status
make[2]: *** [src/tools/votca_property] Error 1
make[1]: *** [src/tools/CMakeFiles/votca_property.dir/all] Error 2
make: *** [all] Error 2
[32;01mThis is VOTCA build.sh, version 2.1.3[0m
Install prefix is '/usr/local/votca/'
[34;01mUsing 29 jobs for make/ninja[0m
[32;01mWorking on tools[0m
[34;01mSource dir (tools) is already there - skipping checkout[0m
[34;01mcmake -DCMAKE_INSTALL_PREFIX='/usr/local/votca/'
-DBoost_INCLUDE_DIR=/usr/local/include/boost/
-DBoost_PROGRAM_OPTIONS_LIBRARY=/usr/local/lib/libboost_program_options.so
-DBoost_FILESYSTEM_LIBRARY=/usr/local/lib/libboost_filesystem.so
-DFFTW3_INCLUDE_DIR=/usr/local/fftw_shared/include/
-DFFTW3_LIBRARY=/usr/local/fftw_shared/lib/libfftw3.so
-DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON .[0m
-- Found Git: /usr/local/bin/bin/git (found version "2.3.0")
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found PkgConfig: /usr/local/bin/pkg-config (found version "0.29.2")
-- Checking for module 'gsl'
-- Found gsl, version 2.3
-- Found GSL: /usr/local/lib/libgsl.so
-- Looking for gsl_linalg_QR_decomp in /usr/local/lib/libgsl.so;
-- Looking for gsl_linalg_QR_decomp in /usr/local/lib/libgsl.so; - not found
-- Found GSLCBLAS: /usr/local/lib/libgslcblas.so
-- Looking for cblas_dsyrk in /usr/local/lib/libgslcblas.so;
-- Looking for cblas_dsyrk in /usr/local/lib/libgslcblas.so; - found
-- Looking for gsl_linalg_QR_lssolve in
/usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so;
-- Looking for gsl_linalg_QR_lssolve in
/usr/local/lib/libgsl.so;/usr/local/lib/libgslcblas.so; - found
-- Intel(R) MKL was found:
MKL_INCLUDE_DIRS:
/public/software/compiler/intel/composer_xe_2015.2.164/mkl/include
MKL_LIBRARY_DIRS:
/public/software/compiler/intel/composer_xe_2015.2.164/mkl/lib/intel64;/public/software/compiler/intel/composer_xe_2015.2.164/compiler/lib/intel64
MKL_LIBRARIES:
/public/software/compiler/intel/composer_xe_2015.2.164/mkl/lib/intel64/libmkl_rt.so;/public/software/compiler/intel/composer_xe_2015.2.164/compiler/lib/intel64/libiomp5.so;/public/software/compiler/intel/composer_xe_2015.2.164/compiler/lib/intel64/libimf.so
-- Checking for module 'fftw3'
-- No package 'fftw3' found
-- Found FFTW3: /usr/local/fftw_shared/lib/libfftw3.so
-- Looking for fftw_plan_r2r_1d in /usr/local/fftw_shared/lib/libfftw3.so;
-- Looking for fftw_plan_r2r_1d in /usr/local/fftw_shared/lib/libfftw3.so; -
found
-- Looking for assert.h
-- Looking for assert.h - found
-- Looking for math.h
-- Looking for math.h - found
-- Looking for stdio.h
-- Looking for stdio.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for C++ include cmath
-- Looking for C++ include cmath - found
-- Looking for C++ include fstream
-- Looking for C++ include fstream - found
-- Looking for C++ include functional
-- Looking for C++ include functional - found
-- Looking for C++ include iostream
-- Looking for C++ include iostream - found
-- Looking for C++ include limits
-- Looking for C++ include limits - found
-- Looking for C++ include list
-- Looking for C++ include list - found
-- Looking for C++ include map
-- Looking for C++ include map - found
-- Looking for C++ include ostream
-- Looking for C++ include ostream - found
-- Looking for C++ include sstream
-- Looking for C++ include sstream - found
-- Looking for C++ include stack
-- Looking for C++ include stack - found
-- Looking for C++ include stdexcept
-- Looking for C++ include stdexcept - found
-- Looking for C++ include string
-- Looking for C++ include string - found
-- Looking for C++ include vector
-- Looking for C++ include vector - found
-- Looking for sqrt in m
-- Looking for sqrt in m - found
-- Checking for module 'expat'
-- Found expat, version 2.2.0
-- Found EXPAT: /usr/lib64/libexpat.so
-- Checking for module 'sqlite3'
-- No package 'sqlite3' found
-- Found SQLITE3: /usr/lib64/libsqlite3.so
-- Performing Test HAVE_AIX
-- Performing Test HAVE_AIX - Failed
-- Found Doxygen: /usr/bin/doxygen (found version "1.6.1")
--
-- The following OPTIONAL packages have been found:
* Git
* GSL
* MKL
* FFTW3
* EXPAT
* PkgConfig
* SQLITE3
* Doxygen
-- The following REQUIRED packages have been found:
* Threads
-- The following REQUIRED packages have not been found:
* Boost (required version >= 1.39.0)
-- Configuring incomplete, errors occurred!
See also "/home/xiong/votca/src/tools/CMakeFiles/CMakeOutput.log".
See also "/home/xiong/votca/src/tools/CMakeFiles/CMakeError.log".
Determining if the pthread_create exist failed with the following output:
Change Dir: /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_e198f/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_e198f.dir/build.make CMakeFiles/cmTC_e198f.dir/build
gmake[1]: Entering directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_e198f.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTC_e198f.dir/CheckSymbolExists.c.o -c /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTC_e198f
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_e198f.dir/link.txt --verbose=1
/usr/bin/cc CMakeFiles/cmTC_e198f.dir/CheckSymbolExists.c.o -o cmTC_e198f -rdynamic
CMakeFiles/cmTC_e198f.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c:(.text+0xc): undefined reference to `pthread_create'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_e198f] Error 1
gmake[1]: Leaving directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_e198f/fast] Error 2
File /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include <pthread.h>
int main(int argc, char** argv)
{
(void)argv;
#ifndef pthread_create
return ((int*)(&pthread_create))[argc];
#else
(void)argc;
return 0;
#endif
}
Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_1cb5a/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_1cb5a.dir/build.make CMakeFiles/cmTC_1cb5a.dir/build
gmake[1]: Entering directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_1cb5a.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_1cb5a.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-3.7/Modules/CheckFunctionExists.c
Linking C executable cmTC_1cb5a
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_1cb5a.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTC_1cb5a.dir/CheckFunctionExists.c.o -o cmTC_1cb5a -rdynamic -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_1cb5a] Error 1
gmake[1]: Leaving directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_1cb5a/fast] Error 2
Determining if the function gsl_linalg_QR_decomp exists in the /usr/local/lib/libgsl.so; failed with the following output:
Change Dir: /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_1fb23/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_1fb23.dir/build.make CMakeFiles/cmTC_1fb23.dir/build
gmake[1]: Entering directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_1fb23.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=gsl_linalg_QR_decomp -o CMakeFiles/cmTC_1fb23.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-3.7/Modules/CheckFunctionExists.c
Linking C executable cmTC_1fb23
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_1fb23.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=gsl_linalg_QR_decomp CMakeFiles/cmTC_1fb23.dir/CheckFunctionExists.c.o -o cmTC_1fb23 -Wl,-rpath,/usr/local/lib -rdynamic /usr/local/lib/libgsl.so
/usr/local/lib/libgsl.so: undefined reference to `cblas_ctrmv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zswap'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zsymm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cgeru'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sgemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ctrsv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sgemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_srotg'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zgemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cdotu_sub'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dznrm2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ddot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_csymm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cher2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zdotu_sub'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sdot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sdsdot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cgerc'
/usr/local/lib/libgsl.so: undefined reference to `cblas_scnrm2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ctrmm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_strmm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zcopy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsyrk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cherk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zherk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zher'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ztrmv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_drotmg'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dswap'
/usr/local/lib/libgsl.so: undefined reference to `cblas_scopy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_scasum'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_drotg'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zdotc_sub'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_caxpy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zsyr2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssyr2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_csyr2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ztrsm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ctrsm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssymm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cdotc_sub'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zher2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_saxpy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_idamax'
/usr/local/lib/libgsl.so: undefined reference to `cblas_snrm2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsdot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cher'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dger'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cher2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dzasum'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsyr2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssyrk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_strmv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dgemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cgemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dasum'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsymv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_srotm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sswap'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dtrmv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_isamax'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zhemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zaxpy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dcopy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sasum'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsyr'
/usr/local/lib/libgsl.so: undefined reference to `cblas_strsm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_drot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ztrsv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_izamax'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssymv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_chemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zgeru'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dtrsv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sger'
/usr/local/lib/libgsl.so: undefined reference to `cblas_srot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsymm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ztrmm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zdscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zher2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssyr'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dtrmm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zgerc'
/usr/local/lib/libgsl.so: undefined reference to `cblas_csscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsyr2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_chemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dnrm2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_drotm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_icamax'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zgemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zhemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cgemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssyr2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_strsv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dgemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_srotmg'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dtrsm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ccopy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zsyrk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cswap'
/usr/local/lib/libgsl.so: undefined reference to `cblas_daxpy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_csyrk'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_1fb23] Error 1
gmake[1]: Leaving directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_1fb23/fast] Error 2
Performing C SOURCE FILE Test HAVE_AIX failed with the following output:
Change Dir: /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_b1b7c/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_b1b7c.dir/build.make CMakeFiles/cmTC_b1b7c.dir/build
gmake[1]: Entering directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_b1b7c.dir/src.c.o
/usr/bin/cc -DHAVE_AIX -o CMakeFiles/cmTC_b1b7c.dir/src.c.o -c /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp/src.c
/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp/src.c:3:8: error: #error
gmake[1]: *** [CMakeFiles/cmTC_b1b7c.dir/src.c.o] Error 1
gmake[1]: Leaving directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_b1b7c/fast] Error 2
Source file was:
int main(void) {
#ifndef _AIX
#error
#endif
return 0;
}
Determining if the pthread_create exist failed with the following output:
Change Dir: /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_6740d/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_6740d.dir/build.make CMakeFiles/cmTC_6740d.dir/build
gmake[1]: Entering directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_6740d.dir/CheckSymbolExists.c.o
/usr/bin/cc -o CMakeFiles/cmTC_6740d.dir/CheckSymbolExists.c.o -c /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp/CheckSymbolExists.c
Linking C executable cmTC_6740d
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_6740d.dir/link.txt --verbose=1
/usr/bin/cc CMakeFiles/cmTC_6740d.dir/CheckSymbolExists.c.o -o cmTC_6740d -rdynamic
CMakeFiles/cmTC_6740d.dir/CheckSymbolExists.c.o: In function `main':
CheckSymbolExists.c:(.text+0xc): undefined reference to `pthread_create'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_6740d] Error 1
gmake[1]: Leaving directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_6740d/fast] Error 2
File /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp/CheckSymbolExists.c:
/* */
#include <pthread.h>
int main(int argc, char** argv)
{
(void)argv;
#ifndef pthread_create
return ((int*)(&pthread_create))[argc];
#else
(void)argc;
return 0;
#endif
}
Determining if the function pthread_create exists in the pthreads failed with the following output:
Change Dir: /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_6663b/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_6663b.dir/build.make CMakeFiles/cmTC_6663b.dir/build
gmake[1]: Entering directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_6663b.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTC_6663b.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-3.7/Modules/CheckFunctionExists.c
Linking C executable cmTC_6663b
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_6663b.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTC_6663b.dir/CheckFunctionExists.c.o -o cmTC_6663b -rdynamic -lpthreads
/usr/bin/ld: cannot find -lpthreads
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_6663b] Error 1
gmake[1]: Leaving directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_6663b/fast] Error 2
Determining if the function gsl_linalg_QR_decomp exists in the /usr/local/lib/libgsl.so; failed with the following output:
Change Dir: /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_34c89/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_34c89.dir/build.make CMakeFiles/cmTC_34c89.dir/build
gmake[1]: Entering directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_34c89.dir/CheckFunctionExists.c.o
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=gsl_linalg_QR_decomp -o CMakeFiles/cmTC_34c89.dir/CheckFunctionExists.c.o -c /usr/local/share/cmake-3.7/Modules/CheckFunctionExists.c
Linking C executable cmTC_34c89
/usr/local/bin/cmake -E cmake_link_script CMakeFiles/cmTC_34c89.dir/link.txt --verbose=1
/usr/bin/cc -DCHECK_FUNCTION_EXISTS=gsl_linalg_QR_decomp CMakeFiles/cmTC_34c89.dir/CheckFunctionExists.c.o -o cmTC_34c89 -Wl,-rpath,/usr/local/lib -rdynamic /usr/local/lib/libgsl.so
/usr/local/lib/libgsl.so: undefined reference to `cblas_ctrmv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zswap'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zsymm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cgeru'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sgemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ctrsv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sgemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_srotg'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zgemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cdotu_sub'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dznrm2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ddot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_csymm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cher2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zdotu_sub'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sdot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sdsdot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cgerc'
/usr/local/lib/libgsl.so: undefined reference to `cblas_scnrm2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ctrmm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_strmm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zcopy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsyrk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cherk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zherk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zher'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ztrmv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_drotmg'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dswap'
/usr/local/lib/libgsl.so: undefined reference to `cblas_scopy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_scasum'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_drotg'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zdotc_sub'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_caxpy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zsyr2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssyr2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_csyr2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ztrsm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ctrsm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssymm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cdotc_sub'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zher2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_saxpy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_idamax'
/usr/local/lib/libgsl.so: undefined reference to `cblas_snrm2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsdot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cher'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dger'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cher2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dzasum'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsyr2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssyrk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_strmv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dgemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cgemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dasum'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsymv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_srotm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sswap'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dtrmv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_isamax'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zhemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zaxpy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dcopy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sasum'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsyr'
/usr/local/lib/libgsl.so: undefined reference to `cblas_strsm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_drot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ztrsv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_izamax'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssymv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_chemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zgeru'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dtrsv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_sger'
/usr/local/lib/libgsl.so: undefined reference to `cblas_srot'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsymm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ztrmm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zdscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zher2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssyr'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dtrmm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zgerc'
/usr/local/lib/libgsl.so: undefined reference to `cblas_csscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dsyr2k'
/usr/local/lib/libgsl.so: undefined reference to `cblas_chemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dnrm2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_drotm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_icamax'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zgemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zhemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cgemv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ssyr2'
/usr/local/lib/libgsl.so: undefined reference to `cblas_strsv'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dscal'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dgemm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_srotmg'
/usr/local/lib/libgsl.so: undefined reference to `cblas_dtrsm'
/usr/local/lib/libgsl.so: undefined reference to `cblas_ccopy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_zsyrk'
/usr/local/lib/libgsl.so: undefined reference to `cblas_cswap'
/usr/local/lib/libgsl.so: undefined reference to `cblas_daxpy'
/usr/local/lib/libgsl.so: undefined reference to `cblas_csyrk'
collect2: ld returned 1 exit status
gmake[1]: *** [cmTC_34c89] Error 1
gmake[1]: Leaving directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_34c89/fast] Error 2
Performing C SOURCE FILE Test HAVE_AIX failed with the following output:
Change Dir: /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp
Run Build Command:"/usr/bin/gmake" "cmTC_dc8d6/fast"
/usr/bin/gmake -f CMakeFiles/cmTC_dc8d6.dir/build.make CMakeFiles/cmTC_dc8d6.dir/build
gmake[1]: Entering directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_dc8d6.dir/src.c.o
/usr/bin/cc -DHAVE_AIX -o CMakeFiles/cmTC_dc8d6.dir/src.c.o -c /home/xiong/votca/src/tools/CMakeFiles/CMakeTmp/src.c
/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp/src.c:3:8: error: #error
gmake[1]: *** [CMakeFiles/cmTC_dc8d6.dir/src.c.o] Error 1
gmake[1]: Leaving directory `/home/xiong/votca/src/tools/CMakeFiles/CMakeTmp'
gmake: *** [cmTC_dc8d6/fast] Error 2
Source file was:
int main(void) {
#ifndef _AIX
#error
#endif
return 0;
}
