Undefined symbol in Boost.Python module

Question

I'm trying to build a small Python extension for a certain instantiation of a templated library, using Boost.Python. This library uses extensively the CGAL library, which integrates fairly well with CMake, that I'm therefore using for my project.

Here's the code for my module (python_export.cpp):

#include <boost/python.hpp>
#include <CGAL/Exact_spherical_kernel_3.h>
#include "Sphere_intersecter.h" // header-only

typedef CGAL::Exact_spherical_kernel_3 SK;
template class Sphere_intersecter<SK>; // explicit for "-fno-implicit-templates"
typedef Sphere_intersecter<SK> SI;

BOOST_PYTHON_MODULE(thickness_diag)
{
    using namespace boost::python;
    class_<SI>("SphereIntersecter", no_init)
        .def("add_sphere", &SI::add_sphere)
    ;
}

And the CMakeLists.txt:

cmake_minimum_required(VERSION 2.6.2)
project(ThicknessDiag-Python)

# CGAL
find_package(CGAL REQUIRED)
include(${CGAL_USE_FILE})

# Boost
find_package(Boost REQUIRED COMPONENTS python)
find_package(PythonLibs 2.7 REQUIRED)
include_directories(${Boost_INCLUDE_DIRS})
include_directories(${PYTHON_INCLUDE_DIRS})

# Shared library
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fno-implicit-templates")
set(ThicknessDiag-Python "thickness_diag")
add_library(${ThicknessDiag-Python} SHARED python_export.cpp)
set_target_properties(${ThicknessDiag-Python} PROPERTIES PREFIX "")
target_link_libraries(${ThicknessDiag-Python}
    ${PYTHON_LIBRARIES} ${Boost_LIBRARIES}
    ${CGAL_LIBRARIES} ${CGAL_3RD_PARTY_LIBRARIES})

Detailed output of the compile command:

[100%] Building CXX object CMakeFiles/thickness_diag.dir/python_export.cpp.o
/usr/bin/c++ -Dthickness_diag_EXPORTS -DCGAL_USE_MPFR -DCGAL_USE_GMP -frounding-math -fno-implicit-templates -O3 -DNDEBUG -fPIC -isystem /usr/local/include -I/usr/include/python2.7 -o CMakeFiles/thickness_diag.dir/python_export.cpp.o -c /home/jmcomets/ThicknessDiag/tests/python_export.cpp
Linking CXX shared library thickness_diag.so
/usr/bin/c++ -fPIC -frounding-math -fno-implicit-templates -O3 -DNDEBUG -shared -Wl,-soname,thickness_diag.so -o thickness_diag.so CMakeFiles/thickness_diag.dir/python_export.cpp.o -L/usr/local/lib -lmpfr -lgmp /usr/local/lib/libCGAL.so /usr/local/lib/libboost_thread.so -lpthread /usr/local/lib/libboost_system.so -lpython2.7 /usr/local/lib/libboost_python.so /usr/local/lib/libCGAL.so /usr/local/lib/libboost_thread.so -lpthread /usr/local/lib/libboost_system.so -lpython2.7 /usr/local/lib/libboost_python.so -Wl,-rpath,/usr/local/lib

Output of importing the shared library:

$ python -c 'import thickness_diag'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
ImportError: ./thickness_diag.so: undefined symbol: _ZN5boost6python9converter6detail15registered_baseIRVK18Sphere_intersecterIN4CGAL18Spherical_kernel_3INS5_9CartesianINS5_4GmpqEEENS5_32Algebraic_kernel_for_spheres_2_3IS8_EEEEEE10convertersE
$ nm thickness_diag.so | grep _ZN5boost6python9converter6detail15registered_baseIRVK18Sphere_intersecterIN4CGAL18Spherical_kernel_3INS5_9CartesianINS5_4GmpqEEENS5_32Algebraic_kernel_for_spheres_2_3IS8_EEEEEE10convertersE
                 U _ZN5boost6python9converter6detail15registered_baseIRVK18Sphere_intersecterIN4CGAL18Spherical_kernel_3INS5_9CartesianINS5_4GmpqEEENS5_32Algebraic_kernel_for_spheres_2_3IS8_EEEEEE10convertersE

I've been struggling with this for the past two days, any help would be awesome ! :)

EDIT: output of ldd

$ ldd thickness_diag.so
    linux-vdso.so.1 =>  (0x00007fffdfdff000)
    libgmp.so.10 => /usr/lib/x86_64-linux-gnu/libgmp.so.10 (0x00007fd91eadf000)
    libCGAL.so.10 => /usr/local/lib/libCGAL.so.10 (0x00007fd91e8b4000)
    libboost_thread.so.1.55.0 => /usr/local/lib/libboost_thread.so.1.55.0 (0x00007fd91e699000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fd91e47c000)
    libboost_system.so.1.55.0 => /usr/local/lib/libboost_system.so.1.55.0 (0x00007fd91e278000)
    libpython2.7.so.1.0 => /usr/lib/libpython2.7.so.1.0 (0x00007fd91dd79000)
    libboost_python.so.1.55.0 => /usr/local/lib/libboost_python.so.1.55.0 (0x00007fd91db2c000)
    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fd91d829000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fd91d612000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fd91d253000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fd91cf57000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007fd91cd4e000)
    /lib64/ld-linux-x86-64.so.2 (0x00007fd91ef85000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fd91cb37000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fd91c933000)
libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x00007fd91c72f000)

score 3 · Answer 1 · answered Jul 23 '13 at 13:01

Okay I figured it out. Turns out that the option -fno-implicit-templates was preventing boost from doing its normal template instanciation (which is actually pretty obvious).

I then fell back on an error that I thought was fixed: undefined symbol: _ZN18Sphere_intersecterIN4CGAL18Spherical_kernel_3INS0_9CartesianINS0_4GmpqEEENS0_32Algebraic_kernel_for_spheres_2_3IS3_EEEEEC1ERKS8_ (./thickness_diag.so)

Which, when translated via c++filt, gives: Sphere_intersecter<...> >::Sphere_intersecter(Sphere_intersecter<...> const&)

The copy-constructor, which wasn't implemented (non-copyable class)...

The solution was to remove the add the boost::noncopyable parameter to boost::python::class_:

#include <boost/python.hpp>
#include <CGAL/Exact_spherical_kernel_3.h>
#include "Sphere_intersecter.h"

typedef CGAL::Exact_spherical_kernel_3 SK;
template class Sphere_intersecter<SK>;
typedef Sphere_intersecter<SK> SI;

BOOST_PYTHON_MODULE(thickness_diag)
{
    using namespace boost::python;
    class_<SI, boost::noncopyable>("SphereIntersecter")
        .def("add_sphere", &SI::add_sphere)
    ;
}

score 1 · Answer 2 · edited May 23 '17 at 12:13

1

$man nm
...
"U" The symbol is undefined.

What does that mean? It's not there.

Try ldd on your so . This will tell you all the libraries it uses. You then need to make sure all the libraries are on LD_LIBRARY_PATH

edited May 23 '17 at 12:13

Community

1
1

answered Jul 23 '13 at 09:29

doctorlove

18,872
2
46
62

I edited the question and added the output of ldd, I'm checking to see if all the libraries are there, but everything seems normal. – Jean-Marie Comets Jul 23 '13 at 09:36
How do you set the path to pick these up? – doctorlove Jul 23 '13 at 09:38
I don't. That is `LD_LIBRARY_PATH` is at its default (empty). CMake adds `-L/usr/local/lib` and `-Wl,-rpath,/usr/local/lib`, and all the libraries are in standard directories if I'm not mistaken. – Jean-Marie Comets Jul 23 '13 at 09:44

Undefined symbol in Boost.Python module

2 Answers2

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