[ndt/filter] call pcl::NormalDistributionsTransform::setInputTarget twice got segfault

[marf-cn]

Describe the bug

A clear and concise description of what the bug is.
got segfault when calling pcl::NormalDistributionsTransform::setInputTarget second time.

Context

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Expected behavior

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Current Behavior

What happens instead of the expected behavior?

To Reproduce

chang the map and call
pcl::NormalDistributionsTransform::setInputTarget
again
static pcl::NormalDistributionsTransform<pcl::PointXYZI, pcl::PointXYZI> ndt;
.......
ndt.setTransformationEpsilon(trans_eps);
ndt.setStepSize(step_size);
ndt.setResolution(ndt_res);
ndt.setMaximumIterations(max_iter);
ndt.setInputSource(filtered_scan_ptr);
ndt.setInputTarget(map_ptr1);
ndt.align(*output_cloud, init_guess);
....
ndt.setTransformationEpsilon(trans_eps);
ndt.setStepSize(step_size);
ndt.setResolution(ndt_res);
ndt.setMaximumIterations(max_iter);
ndt.setInputSource(filtered_scan_ptr);
ndt.setInputTarget(map_ptr2); //got segfault

Provide a link to a live example, or an unambiguous set of steps to reproduce this bug. A reproducible example helps to provide faster answers.

Screenshots/Code snippets
#0 0x00007fffe8e2ea6d in free () from /lib/x86_64-linux-gnu/libc.so.6
#1 0x00005555555ca47f in Eigen::internal::handmade_aligned_free(void*) ()
#2 0x00005555555ca4db in Eigen::internal::aligned_free(void*) ()
#3 0x00005555555ccd7d in void Eigen::internal::conditional_aligned_free(void*) ()
#4 0x00005555555d2420 in void Eigen::internal::conditional_aligned_delete_auto<float, true>(float*, unsigned long) ()
#5 0x00005555555cd19d in Eigen::DenseStorage<float, -1, -1, 1, 0>::~DenseStorage() ()
#6 0x00005555555cb578 in Eigen::PlainObjectBase<Eigen::Matrix<float, -1, 1, 0, -1, 1> >::~PlainObjectBase() ()
#7 0x00005555555cb594 in Eigen::Matrix<float, -1, 1, 0, -1, 1>::~Matrix() ()
#8 0x00005555555f145c in pcl::VoxelGridCovariancepcl::PointXYZ::Leaf::~Leaf() ()
#9 0x00005555555f147c in std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>::~pair() ()
#10 0x00005555555f149c in void __gnu_cxx::new_allocator<std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::destroy<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >(std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>) ()
#11 0x00005555555ecc6f in void std::allocator_traits<std::allocator<std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > > >::destroy<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >(std::allocator<std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >&, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>) ()
#12 0x00005555555e882d in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_destroy_node(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#13 0x00005555555e355d in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_drop_node(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#14 0x00005555555dafea in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_erase(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#15 0x00005555555dafc7 in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_erase(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#16 0x00005555555dafc7 in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_erase(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#17 0x00005555555dafc7 in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_erase(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#18 0x00005555555dafc7 in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_erase(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#19 0x00005555555dafc7 in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_erase(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#20 0x00005555555dafc7 in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_erase(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
#21 0x00005555555dafc7 in std::_Rb_tree<unsigned long, std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf>, std::_Select1st<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >, std::less, std::allocator<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> > >::_M_erase(std::_Rb_tree_node<std::pair<unsigned long const, pcl::VoxelGridCovariancepcl::PointXYZ::Leaf> >) ()
In order to help explain your problem, please consider adding

• screenshots of the GUI issues
• code snippets: syntax for code with correct language highlights

Your Environment (please complete the following information):

• OS: [e.g. Ubuntu 18.04]
• Compiler: [:eg GCC 8.1]
• PCL Version [e.g. 1.10, HEAD]

Possible Solution
try putting PCL_MAKE_ALIGNED_OPERATOR_NEW in VoxelGridCovariance

class VoxelGridCovariance : public VoxelGrid
{
// public:
// PCL_MAKE_ALIGNED_OPERATOR_NEW
...
Not obligatory, but suggest a fix/reason for the bug. Feel free to create a PR if you feel comfortable.

Additional context

Add any other context about the problem here.

[tin1254]

This is weird because in the call stack it tries to destroy Leaf, but by just calling setInputTarget it shouldn't happen.

We may need more context, can you provide us some runnable code to reproduce the error?

[mvieth]

You suggest to add PCL_MAKE_ALIGNED_OPERATOR_NEW. Have you done that and it fixed the problem for you or is that just an idea?
Please fill out the rest of the issue template, or delete the lines that don't apply.

[marf-cn]

Yes, it fixed my problem.
Calling setInputTarget again may release target point cloud last time I set. Due to "TargetGrid target_cells_" in NormalDistributionsTransform is not aliged, it may happen.

You can reproduce the bug as fellowed:

pcl::NormalDistributionsTransform<pcl::PointXYZI, pcl::PointXYZI> ndt;
pcl::PointCloudpcl::PointXYZI map;
pcl::PointCloudpcl::PointXYZI::Ptr cloud(new pcl::PointCloudpcl::PointXYZI);
Eigen::Matrix4f loc(Eigen::Matrix4f::Identity()) = Eigen::Matrix4f::Identity();

const std::vectorstd::string pcd_paths = {std::string(1.pcd),std::string(2.pcd),std::string(3.pcd),std::string(4.pcd)};

bool is_map_init = false;
bool is_reload_map = false;
for (int i=0; i<pcd_paths.size(); i++){
pcl::PointCloudpcl::PointXYZI::Ptr transformed_cloud(new pcl::PointCloudpcl::PointXYZI());
pcl::io::loadPCDFilepcl::PointXYZI(pcd_paths[i], *cloud);

if(!is_map_init ){
pcl::transformPointCloud(*cloud, *transformed_cloud, loc);
map += *transformed_cloud;
is_map_init = true;
continue;
}

pcl::VoxelGridpcl::PointXYZI voxel_grid_filter;
voxel_grid_filter.setLeafSize(1.0,1.0,1.0);
voxel_grid_filter.setInputCloud(cloud);
voxel_grid_filter.filter(*filtered_scan_ptr);

pcl::PointCloudpcl::PointXYZI::Ptr map_ptr(new pcl::PointCloudpcl::PointXYZI(map));

ndt.setTransformationEpsilon(0.01);
ndt.setStepSize(0.1);
ndt.setResolution(0.1);
ndt.setMaximumIterations(10);
ndt.setInputSource(filtered_scan_ptr);
if(is_reload_map)
ndt.setInputTarget(map_ptr);

double fitness_score = ndt.getFitnessScore();
loc= ndt.getFinalTransformation();

if(fitness_score < 0.5){
pcl::transformPointCloud(*cloud, *transformed_cloud, loc);
map += *transformed_cloud;
is_reload_map = true;
}
}

[tin1254]

@mvieth Overall it makes sense to me to add PCL_MAKE_ALIGNED_OPERATOR_NEW even without reproducing it, what do you think? @mvieth

[mvieth]

But the trace suggests that the segfault happens while destroying a leaf, so why would adding PCL_MAKE_ALIGNED_OPERATOR_NEW to VoxelGridCovariance prevent that?
Also: Adding that macro is necessary for fixed-size Eigen types, but not dynamic-size types. However, the type in the trace is a dynamic-size type (recognizable by the -1 in the template list).
Plus I can't reproduce the error with the given code. If I had to guess what made the code first not work, then work, I would guess luck/bad luck or a case of not enabling SIMD extensions (e.g. -mavx)

[marf-cn]

There are some fixed-size Eigen types in struct Leaf which is included in class VoxelGridCovariance . Is it the cause?

[marf-cn]

" not enabling SIMD extensions" may be the cause, I'll try later。

[tin1254]

There are some fixed-size Eigen types in struct Leaf which is included in class VoxelGridCovariance . Is it the cause?

I also doubted that but as @mvieth said, the trace indicating it was caused by dynamic size matrix, which adding PCL_MAKE_ALIGNED_OPERATOR_NEW only solves issues with fixed size matrix

@marf-cn Since you close the issue, have you fixed your issue already?

[marf-cn]

@mvieth Yes，I fixed my issue by adding PCL_MAKE_ALIGNED_OPERATOR_NEW temporarily! I haven't dig into the issue if SIMD worked, due to I have quited from the project.