Eigen allocation segmentation fault (Open3D)

Question

I'm trying to make some operations on Pointcloud but when calling VoxelDownSample function i'm getting Segmentation fault signal. I see that the problem is that program want to allocate some astronomic amount of data but i don't know where it come from as actuall PointCloud object size is 120.

Code:

open3d::geometry::PointCloud open3d_source_original; 
open3d::geometry::PointCloud open3d_source_down; 
createPointCloud(open3d_source_original);
open3d_source_down = *open3d_source_original.VoxelDownSample(0.01);

createPointCloud is my function which creates PointCloud from csv file and it works fine.

gdb output:


#0 __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:51

#1 0x00007ffff6eb4921 in __GI_abort () at abort.c:79

#2 0x00007ffff7ad6957 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#3 0x00007ffff7adcae6 in ?? () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#4 0x00007ffff7adcb21 in std::terminate() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#5 0x00007ffff7adcd54 in __cxa_throw () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#6 0x00007ffff7b05012 in std::__throw_bad_alloc() () from /usr/lib/x86_64-linux-gnu/libstdc++.so.6

#7 0x0000555555563476 in __gnu_cxx::new_allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> >::allocate(unsigned long, void const*) ()

#8 0x0000555555562bec in std::allocator_traits<std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > >::allocate(std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> >&, unsigned long) ()

#9 0x0000555555562088 in std::_Vector_base<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > >::_M_allocate(unsigned long) ()

#10 0x00005555555613ac in Eigen::Matrix<double, 3, 1, 0, 3, 1>* std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > >::_M_allocate_and_copy<__gnu_cxx::__normal_iterator<Eigen::Matrix<double, 3, 1, 0, 3, 1> const*, std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > > > >(unsigned long, __gnu_cxx::__normal_iterator<Eigen::Matrix<double, 3, 1, 0, 3, 1> const*, std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > > >, __gnu_cxx::__normal_iterator<Eigen::Matrix<double, 3, 1, 0, 3, 1> const*, std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > > >) ()

#11 0x00005555555606e2 in std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > >::operator=(std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > > const&) ()
#12 0x000055555555fcfa in open3d::geometry::PointCloud::operator=(open3d::geometry::PointCloud const&) ()

#13 0x000055555555f400 in main ()

Valgrind output:


==14534== Invalid read of size 8

==14534== at 0x114D59: std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > >::begin() const (in /home/rufus/CLionProjects/isolatedSegFault/build/isolatedSegFault)

==14534== by 0x1147EA: std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > >::operator=(std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > > const&) (in /home/rufus/CLionProjects/isolatedSegFault/build/isolatedSegFault)

==14534== by 0x113CF9: open3d::geometry::PointCloud::operator=(open3d::geometry::PointCloud const&) (in /home/rufus/CLionProjects/isolatedSegFault/build/isolatedSegFault)
==14534== by 0x1133FF: main (in /home/rufus/CLionProjects/isolatedSegFault/build/isolatedSegFault)

==14534== Address 0x61da940 is 0 bytes after a block of size 112 alloc'd

==14534== at 0x4C3217F: operator new(unsigned long) (in /usr/lib/valgrind/vgpreload_memcheck-amd64-linux.so)

==14534== by 0x12C358: allocate (new_allocator.h:111)

==14534== by 0x12C358: allocate (alloc_traits.h:436)

==14534== by 0x12C358: __allocate_guarded<std::allocator<std::_Sp_counted_ptr_inplace<open3d::geometry::PointCloud, std::allocatoropen3d::geometry::PointCloud, (__gnu_cxx::_Lock_policy)2> > > (allocated_ptr.h:104)

==14534== by 0x12C358: __shared_count<open3d::geometry::PointCloud, std::allocatoropen3d::geometry::PointCloud > (shared_ptr_base.h:635)

==14534== by 0x12C358: __shared_ptr<std::allocatoropen3d::geometry::PointCloud > (shared_ptr_base.h:1295)

==14534== by 0x12C358: shared_ptr<std::allocatoropen3d::geometry::PointCloud > (shared_ptr.h:344)

==14534== by 0x12C358: allocate_shared<open3d::geometry::PointCloud, std::allocatoropen3d::geometry::PointCloud > (shared_ptr.h:691)

==14534== by 0x12C358: make_sharedopen3d::geometry::PointCloud (shared_ptr.h:707)

==14534== by 0x12C358: open3d::geometry::PointCloud::VoxelDownSample(double) const (PointCloud.cpp:306)

==14534== by 0x1133DB: main (in /home/rufus/CLionProjects/isolatedSegFault/build/isolatedSegFault)

==14534==

==14534==

==14534== HEAP SUMMARY:

==14534== in use at exit: 8 bytes in 1 blocks

==14534== total heap usage: 19 allocs, 18 frees, 107,576 bytes allocated

==14534==

==14534== LEAK SUMMARY:

==14534== definitely lost: 0 bytes in 0 blocks

==14534== indirectly lost: 0 bytes in 0 blocks

==14534== possibly lost: 0 bytes in 0 blocks

==14534== still reachable: 8 bytes in 1 blocks

==14534== suppressed: 0 bytes in 0 blocks

==14534== Rerun with --leak-check=full to see details of leaked memory

==14534==

==14534== For counts of detected and suppressed errors, rerun with: -v

==14534== Use --track-origins=yes to see where uninitialised values come from

==14534== ERROR SUMMARY: 6 errors from 6 contexts (suppressed: 0 from 0)

Operating system: Ubuntu 18.04
Open3D build from source
Compiler version: gcc 7.5

I tried to change macros from Eigen and change compilers but nothing worked.

First: You should post the content of the createPointCloud function as well. Otherwises it is hard to determine the error. Second: You are dereferencing a pointcloud object that is not a pointer . In `open3d_source_down = *open3d_source_original.VoxelDownSample(0.01);` you should get rid of the asterisk. — Bjoern Urban, Jan 20 '21 at 16:16
Third: VoxelDownSample returns a shared_pointer and you are trying to copy it into a pointcloud object. — Bjoern Urban, Jan 20 '21 at 16:24

Potatoswatter · Answer 1 · 2020-11-12T12:03:09.153

This part shows a SIGABRT due to too much memory, not a SIGSEGV:

#0 __GI_raise (sig=sig@entry=6) at ../sysdeps/unix/sysv/linux/raise.c:51
#1 0x00007ffff6eb4921 in __GI_abort () at abort.c:79

Valgrind is indicating that uninitialized data was used, not unmapped memory:

==14534== Invalid read of size 8

It appears to be pointing at the internal pointer to the start of the array which underlies the vector:

==14534== at 0x114D59: std::vector<Eigen::Matrix<double, 3, 1, 0, 3, 1>, std::allocator<Eigen::Matrix<double, 3, 1, 0, 3, 1> > >::begin() const (in /home/rufus/CLionProjects/isolatedSegFault/build/isolatedSegFault)

Then it says that the vector was created by make_shared inside voxelDownSample:

==14534== by 0x12C358: make_sharedopen3d::geometry::PointCloud (shared_ptr.h:707)
==14534== by 0x12C358: open3d::geometry::PointCloud::VoxelDownSample(double) const (PointCloud.cpp:306)

My intuition says,

If a weak_ptr is involved, then perhaps the vector was destroyed by losing all its shared_ptr references. Valgrind can't see this because it wouldn't be deallocated until the weak_ptr references are gone, too.
Otherwise, there's some other kind of memory error, such as
- trying to use the vector before it has actually been constructed
- using a raw pointer after the shared_ptr is destroyed
- a buffer overflow, or other randomly spraying memory (rather less likely to hit a shared_ptr object, but you never know)
In any case, it looks like a library bug, if this object was created after the last time any of your code ran, and your parameters were numerically valid.

Eigen allocation segmentation fault (Open3D)

1 Answers1