Simply creating a GeneralizedIterativeClosestPoint6D (gicp) object causes segmentation fault

[jasjuang]

Your Environment

• Operating System and version: Ubuntu 16.04
• Compiler: GCC 5.4
• PCL Version: Latest

Minimal code to Reproduce

CMakeLists

cmake_minimum_required(VERSION 3.7)
project(Example)

set(PROJECT_SRCS ${PROJECT_SOURCE_DIR}/main.cpp )

find_package( PCL REQUIRED )

add_executable(${PROJECT_NAME} ${PROJECT_SRCS})

target_include_directories(${PROJECT_NAME} SYSTEM PUBLIC                          
 ${PCL_INCLUDE_DIRS})

target_link_libraries(${PROJECT_NAME} ${PCL_LIBRARIES})

main.cpp

#include "pcl/registration/gicp6d.h"

int main(){
  pcl::GeneralizedIterativeClosestPoint6D gicp;

  return 0;
}

Current Behavior

ubuntu@XXX.XXX.XX.XX:~/test/build$ ./Example 
Segmentation fault (core dumped)

Expected Behavior

ubuntu@XXX.XXX.XX.XX:~/test/build$ ./Example 
ubuntu@XXX.XXX.XX.XX:~/test/build$

Context

This problem is preventing me from using the GICP function, which I would like to improve my result by replacing the traditional ICP with GICP.

@MichaelKorn Thank you for adding GICP into PCL, could you help me solve this problem?

[taketwo]

FWIW, I get the following output (my environment is the same):

*** Error in `./Example': double free or corruption (out): 0x00007fffbd48d330 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f84e301e7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f84e302737a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f84e302b53c]
./Example(_ZN9__gnu_cxx13new_allocatorIfE10deallocateEPfm+0x20)[0x4e7310]
./Example(_ZNSt16allocator_traitsISaIfEE10deallocateERS0_Pfm+0x30)[0x4e72e0]
./Example(_ZNSt12_Vector_baseIfSaIfEE13_M_deallocateEPfm+0x3b)[0x4e727b]
./Example(_ZNSt12_Vector_baseIfSaIfEED2Ev+0x29)[0x4e71c9]
./Example(_ZNSt6vectorIfSaIfEED2Ev+0x48)[0x4e6f58]
./Example(_ZN3pcl19PointRepresentationINS_11PointXYZLABEED2Ev+0x27)[0x4e6fa7]
./Example(_ZN3pcl34GeneralizedIterativeClosestPoint6D21MyPointRepresentationD2Ev+0x15)[0x4e6e25]
./Example(_ZN3pcl34GeneralizedIterativeClosestPoint6DD2Ev+0x33)[0x4e6a03]
./Example(main+0x51)[0x4e6891]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f84e2fc7830]
./Example(_start+0x29)[0x4e6769]

[SergioRAgostinho]

Valgrind is a big help for memory related problems. I used it sometimes in the past for mem leaks, but I assume its functionalities should also be prepared for double free scenarios.

[SergioRAgostinho]

$ valgrind ./gicp_double_free 
==20154== Memcheck, a memory error detector
==20154== Copyright (C) 2002-2015, and GNU GPL'd, by Julian Seward et al.
==20154== Using Valgrind-3.11.0 and LibVEX; rerun with -h for copyright info
==20154== Command: ./gicp_double_free
==20154== 
==20154== Conditional jump or move depends on uninitialised value(s)
==20154==    at 0x528DAB: std::_Vector_base<float, std::allocator<float> >::_M_deallocate(float*, unsigned long) (stl_vector.h:177)
==20154==    by 0x525BA7: std::_Vector_base<float, std::allocator<float> >::~_Vector_base() (stl_vector.h:160)
==20154==    by 0x523A93: std::vector<float, std::allocator<float> >::~vector() (stl_vector.h:425)
==20154==    by 0x523D99: pcl::PointRepresentation<pcl::PointXYZLAB>::~PointRepresentation() (in /home/sergio/Development/pcl_test_cases/gicp_double_free/build/gicp_double_free)
==20154==    by 0x521D7B: pcl::GeneralizedIterativeClosestPoint6D::MyPointRepresentation::~MyPointRepresentation() (gicp6d.h:183)
==20154==    by 0x534846: pcl::GeneralizedIterativeClosestPoint6D::~GeneralizedIterativeClosestPoint6D() (in /home/sergio/Development/pcl_test_cases/gicp_double_free/build/gicp_double_free)
==20154==    by 0x51F50B: main (gicp_double_free.cpp:4)
==20154== 
==20154== 
==20154== Process terminating with default action of signal 11 (SIGSEGV)
==20154==  Bad permissions for mapped region at address 0x5B51F8
==20154==    at 0x51F9B2: boost::detail::atomic_exchange_and_add(int*, int) (sp_counted_base_gcc_x86.hpp:50)
==20154==    by 0x51FAC6: boost::detail::sp_counted_base::release() (sp_counted_base_gcc_x86.hpp:144)
==20154==    by 0x51FB7A: boost::detail::shared_count::~shared_count() (shared_count.hpp:443)
==20154==    by 0x5357C9: boost::shared_ptr<std::vector<int, std::allocator<int> > const>::~shared_ptr() (shared_ptr.hpp:323)
==20154==    by 0x535BA0: boost::shared_ptr<std::vector<int, std::allocator<int> > const>::reset() (shared_ptr.hpp:614)
==20154==    by 0x5358F4: pcl::KdTreeFLANN<pcl::PointXYZLAB, flann::L2_Simple<float> >::cleanup() (kdtree_flann.hpp:220)
==20154==    by 0x5352A6: pcl::KdTreeFLANN<pcl::PointXYZLAB, flann::L2_Simple<float> >::~KdTreeFLANN() (kdtree_flann.h:138)
==20154==    by 0x534858: pcl::GeneralizedIterativeClosestPoint6D::~GeneralizedIterativeClosestPoint6D() (in /home/sergio/Development/pcl_test_cases/gicp_double_free/build/gicp_double_free)
==20154==    by 0x51F50B: main (gicp_double_free.cpp:4)
==20154== 
==20154== HEAP SUMMARY:
==20154==     in use at exit: 325,934 bytes in 2,341 blocks
==20154==   total heap usage: 3,026 allocs, 685 frees, 494,484 bytes allocated
==20154== 
==20154== LEAK SUMMARY:
==20154==    definitely lost: 0 bytes in 0 blocks
==20154==    indirectly lost: 0 bytes in 0 blocks
==20154==      possibly lost: 0 bytes in 0 blocks
==20154==    still reachable: 325,934 bytes in 2,341 blocks
==20154==         suppressed: 0 bytes in 0 blocks
==20154== Rerun with --leak-check=full to see details of leaked memory
==20154== 
==20154== For counts of detected and suppressed errors, rerun with: -v
==20154== Use --track-origins=yes to see where uninitialised values come from
==20154== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
Segmentation fault (core dumped)

[SergioRAgostinho]

The problem seems not to be in GeneralizedIterativeClosestPoint6D but in GeneralizedIterativeClosestPoint.

[SergioRAgostinho]

I just made a stripped the GICP6D class to the bare minimum so I can compile the snippet.

• If I define the constructor inline no segfault and no double free occurs;
• If not, then the segfault occurs.

I'm starting to think this is an issue with compilation flags.

#define PCL_NO_PRECOMPILE
#include <pcl/registration/gicp.h>

namespace pcl
{
  struct EIGEN_ALIGN16 _PointXYZLAB
  {
    PCL_ADD_POINT4D; // this adds the members x,y,z
    union
    {
      struct
      {
        float L;
        float a;
        float b;
      };
      float data_lab[4];
    };
    EIGEN_MAKE_ALIGNED_OPERATOR_NEW
  };

  /** \brief A custom point type for position and CIELAB color value */
  struct PointXYZLAB : public _PointXYZLAB
  {
    inline PointXYZLAB ()
    {
      x = y = z = 0.0f; data[3]     = 1.0f;  // important for homogeneous coordinates
      L = a = b = 0.0f; data_lab[3] = 0.0f;
    }
  };
}

// register the custom point type in PCL
POINT_CLOUD_REGISTER_POINT_STRUCT(pcl::_PointXYZLAB,
    (float, x, x)
    (float, y, y)
    (float, z, z)
    (float, L, L)
    (float, a, a)
    (float, b, b)
)
POINT_CLOUD_REGISTER_POINT_WRAPPER(pcl::PointXYZLAB, pcl::_PointXYZLAB)

namespace pcl
{
  
  class PCL_EXPORTS GeneralizedIterativeClosestPoint6D : public GeneralizedIterativeClosestPoint<PointXYZRGBA, PointXYZRGBA>
  {
    typedef PointXYZRGBA PointSource;
    typedef PointXYZRGBA PointTarget;

      /** \brief Holds the converted (LAB) data cloud. */
      pcl::PointCloud<PointXYZLAB>::Ptr cloud_lab_;

      /** \brief Holds the converted (LAB) model cloud. */
      pcl::PointCloud<PointXYZLAB>::Ptr target_lab_;

      /** \brief 6d-tree to search in model cloud. */
      KdTreeFLANN<PointXYZLAB> target_tree_lab_;

      /** \brief The color weight. */
      float lab_weight_;

    public:

      /** \brief constructor.
       *
       * \param[in] lab_weight the color weight
       */
      GeneralizedIterativeClosestPoint6D (float lab_weight = 0.032f)
        : cloud_lab_ (new pcl::PointCloud<PointXYZLAB>)
        , target_lab_ (new pcl::PointCloud<PointXYZLAB>)
        , lab_weight_ (lab_weight)
      {
        // set rescale mask (leave x,y,z unchanged, scale L,a,b by lab_weight)
        float alpha[6] = { 1.0, 1.0, 1.0, lab_weight_, lab_weight_, lab_weight_ };
        point_rep_.setRescaleValues (alpha);
      }


    protected:
      /**  \brief Custom point representation to perform kdtree searches in more than 3 (i.e. in all 6) dimensions. */
      class MyPointRepresentation : public PointRepresentation<PointXYZLAB>
      {
          using PointRepresentation<PointXYZLAB>::nr_dimensions_;
          using PointRepresentation<PointXYZLAB>::trivial_;

        public:
          typedef boost::shared_ptr<MyPointRepresentation> Ptr;
          typedef boost::shared_ptr<const MyPointRepresentation> ConstPtr;

          MyPointRepresentation ()
          {
            nr_dimensions_ = 6;
            trivial_ = false;
          }

          virtual
          ~MyPointRepresentation ()
          {
          }

          inline Ptr
          makeShared () const
          {
            return Ptr (new MyPointRepresentation (*this));
          }

          virtual void
          copyToFloatArray (const PointXYZLAB &p, float * out) const
          {
            // copy all of the six values
            out[0] = p.x;
            out[1] = p.y;
            out[2] = p.z;
            out[3] = p.L;
            out[4] = p.a;
            out[5] = p.b;
          }
      };

      /** \brief Enables 6d searches with kd-tree class using the color weight. */
      MyPointRepresentation point_rep_;
  };
}

[SergioRAgostinho]

tldr: SSE definitions are not being properly exported anymore.

cd /home/sergio/Development/3rdparty/pcl/build/registration && /usr/bin/c++   -DPCLAPI_EXPORTS -DQT_CORE_LIB -DQT_GUI_LIB -Dqh_QHpointer -isystem /usr/include/eigen3 -isystem /usr/include/ni -isystem /usr/include/openni2 -I/home/sergio/Development/3rdparty/pcl/recognition/include/pcl/recognition/3rdparty -isystem /usr/include/qt4 -isystem /usr/include/qt4/QtGui -isystem /usr/include/qt4/QtCore -I/home/sergio/Development/3rdparty/pcl/build/include -I/home/sergio/Development/3rdparty/pcl/common/include -I/home/sergio/Development/3rdparty/pcl/octree/include -I/home/sergio/Development/3rdparty/pcl/kdtree/include -I/home/sergio/Development/3rdparty/pcl/search/include -I/home/sergio/Development/3rdparty/pcl/sample_consensus/include -I/home/sergio/Development/3rdparty/pcl/features/include -I/home/sergio/Development/3rdparty/pcl/filters/include -I/home/sergio/Development/3rdparty/pcl/registration/include  -Wall -Wextra -Wno-unknown-pragmas -fno-strict-aliasing -Wno-format-extra-args -Wno-sign-compare -Wno-invalid-offsetof -Wno-conversion  -march=native -msse4.2 -mfpmath=sse -Wabi -pthread -fopenmp -g -fPIC   -o CMakeFiles/pcl_registration.dir/src/gicp6d.cpp.o -c /home/sergio/Development/3rdparty/pcl/registration/src/gicp6d.cpp

if I add target_compile_definitions(${PROJECT_NAME} PUBLIC ${PCL_DEFINITIONS}) this is the output

/usr/bin/c++   -D -march="native -msse4.2 -mfpmath=sse " -DDISABLE_DAVIDSDK -DDISABLE_DSSDK -DDISABLE_ENSENSO -DDISABLE_LIBUSB_1_0 -DDISABLE_PCAP -DDISABLE_PNG -DDISABLE_RSSDK -Dqh_QHpointer -I/usr/include/vtk-5.10 -I/home/sergio/Development/3rdparty/pcl/install/include/pcl-1.8 -I/usr/include/eigen3 -I/usr/include/ni -I/usr/include/openni2  -Wno-deprecated -g   -o CMakeFiles/gicp_double_free.dir/gicp_double_free.cpp.o -c /home/sergio/Development/pcl_test_cases/gicp_double_free/gicp_double_free.cpp
<command-line>:0:1: error: macro names must be identifiers
CMakeFiles/gicp_double_free.dir/build.make:62: recipe for target 'CMakeFiles/gicp_double_free.dir/gicp_double_free.cpp.o' failed

If I then compile with the same SSE definitions no more compiler error and not more segfaults

cmake .. -DPCL_DIR=~/Development/3rdparty/pcl/install/share/pcl-1.8/ -DCMAKE_BUILD_TYPE=Debug -DCMAKE_CXX_FLAGS="-march=native -msse4.2 -mfpmath=sse"