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R crashes using CSF on some clouds #12

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EvanZarrella opened this issue May 28, 2024 · 3 comments
Open

R crashes using CSF on some clouds #12

EvanZarrella opened this issue May 28, 2024 · 3 comments

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@EvanZarrella
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Running the classify_ground function with the CSF algorithm on some point clouds leads to R crashing.
The CSF parameters : lidR::csf(sloop_smooth = FALSE, iterations = 1000L, class_threshold = 0.5, cloth_resolution = 0.2)
Tested on both R v4.3.2 and v4.4.0 running on an AMD Ryzen 9 7850X3D, 64Gb of RAM and a RTX 4080.
Using CloudCompare's implementation of the CSF gives satisfactory results.

I've put on my personnal drive a file that's crashing.
https://drive.google.com/file/d/1s3eehS0lKVO-wFlreCCP6UNWJchPm1cg/view?usp=sharing

Let me know if I can be of further help investigating this issue or if I need to post this on the RCSF github issue tracker.
@Jean-Romain
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Jean-Romain commented May 28, 2024 •
edited
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The following works for me. Please provide more details. OS, reproducible example and so on. Ideally try to reproduce without lidR, only using RCSF

library(lidR)
las = readLAS("~/Téléchargements/plot_1000351_6769761.las")
plot(las, color = "Classification")
mycsf = lidR::csf(sloop_smooth = FALSE, iterations = 1000L, class_threshold = 0.5, cloth_resolution = 0.2)
las = classify_ground(las, mycsf)
plot(las, color = "Classification")

@EvanZarrella
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EvanZarrella commented May 28, 2024 •
edited by Jean-Romain
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Thank you for your response.

Regarding the OS, I'm on Windows 11, latest version.
Regarding more information, the cloth_resolution argument seems to be issue as plugin in 0.3 doesn't lead to any crashes
Tried with your code, crashed on the classify_ground so it is a reproductible example for me.
Tried the following code successfully :

las <- lidR::readLAS("plot_1000351_6769761.las")
data <- las@data
ground <- RCSF::CSF(data, sloop_smooth = FALSE, iterations = 1000L, class_threshold = 0.5, cloth_resolution = 0.2)

Leads me to believe that it comes from lidR and not the RCSF package.

@Jean-Romain
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I confirm it crashes on Windows and I can identify the issue on Linux even if it does not crash. It comes from the code of the CSF. The code is not mine. I'm not sure I can fix it. Maybe I should check if the original CSF has been updated.

==73165== Invalid read of size 8
==73165==    at 0x1C2FB974: c2cdist::calCloud2CloudDist(Cloth&, csf::PointCloud&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&) (c2cdist.cpp:50)
==73165==    by 0x1C2EADE0: CSF::do_filtering(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, bool) (CSF.cpp:180)
==73165==    by 0x1C2F1588: R_CSF(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>, bool, double, double, int, int, double) (R_CSF.cpp:57)
==73165==    by 0x1C2F7BDE: _RCSF_R_CSF (RcppExports.cpp:21)
==73165==    by 0x495A237: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x495A88C: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49961FF: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B119C: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B150A: Rf_eval (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B36DE: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B44C6: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B4EEC: ??? (in /usr/lib/R/lib/libR.so)
==73165==  Address 0x1f423ae8 is 24 bytes after a block of size 32 in arena "client"
==73165== 
==73165== Invalid read of size 8
==73165==    at 0x1C2FB98B: c2cdist::calCloud2CloudDist(Cloth&, csf::PointCloud&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&) (c2cdist.cpp:51)
==73165==    by 0x1C2EADE0: CSF::do_filtering(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, bool) (CSF.cpp:180)
==73165==    by 0x1C2F1588: R_CSF(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>, bool, double, double, int, int, double) (R_CSF.cpp:57)
==73165==    by 0x1C2F7BDE: _RCSF_R_CSF (RcppExports.cpp:21)
==73165==    by 0x495A237: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x495A88C: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49961FF: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B119C: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B150A: Rf_eval (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B36DE: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B44C6: ??? (in /usr/lib/R/lib/libR.so)
==73165==    by 0x49B4EEC: ??? (in /usr/lib/R/lib/libR.so)
==73165==  Address 0x1f423bc0 is 32 bytes before a block of size 16 in arena "client"
==73165==

We have pretty much the same without lidR

las <- rlas::read.las("~/Téléchargements/plot_1000351_6769761.las")
ground <- RCSF::CSF(data, sloop_smooth = FALSE, iterations = 1000L, class_threshold = 0.5, cloth_resolution = 0.2)
==73621== Invalid read of size 8
==73621==    at 0x1C2FB974: c2cdist::calCloud2CloudDist(Cloth&, csf::PointCloud&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&) (c2cdist.cpp:50)
==73621==    by 0x1C2EADE0: CSF::do_filtering(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, bool) (CSF.cpp:180)
==73621==    by 0x1C2F1588: R_CSF(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>, bool, double, double, int, int, double) (R_CSF.cpp:57)
==73621==    by 0x1C2F7BDE: _RCSF_R_CSF (RcppExports.cpp:21)
==73621==    by 0x495A237: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x495A88C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49961FF: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B119C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B150A: Rf_eval (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B36DE: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B44C6: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B163B: Rf_eval (in /usr/lib/R/lib/libR.so)
==73621==  Address 0x1d01fae8 is 8 bytes before a block of size 32 free'd
==73621==    at 0x484C91D: operator delete(void*, unsigned long) (vg_replace_malloc.c:1101)
==73621==    by 0x1C2EF658: deallocate (new_allocator.h:145)
==73621==    by 0x1C2EF658: deallocate (alloc_traits.h:496)
==73621==    by 0x1C2EF658: _M_deallocate (stl_vector.h:354)
==73621==    by 0x1C2EF658: void std::vector<Particle*, std::allocator<Particle*> >::_M_realloc_insert<Particle* const&>(__gnu_cxx::__normal_iterator<Particle**, std::vector<Particle*, std::allocator<Particle*> > >, Particle* const&) (vector.tcc:500)
==73621==    by 0x1C2ECEA8: push_back (stl_vector.h:1198)
==73621==    by 0x1C2ECEA8: makeConstraint (Cloth.h:101)
==73621==    by 0x1C2ECEA8: Cloth::Cloth(Vec3 const&, int, int, double, double, double, double, int, double) (Cloth.cpp:75)
==73621==    by 0x1C2EAC44: CSF::do_filtering(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, bool) (CSF.cpp:141)
==73621==    by 0x1C2F1588: R_CSF(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>, bool, double, double, int, int, double) (R_CSF.cpp:57)
==73621==    by 0x1C2F7BDE: _RCSF_R_CSF (RcppExports.cpp:21)
==73621==    by 0x495A237: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x495A88C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49961FF: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B119C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B150A: Rf_eval (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B36DE: ??? (in /usr/lib/R/lib/libR.so)
==73621==  Block was alloc'd at
==73621==    at 0x4848F75: operator new(unsigned long) (vg_replace_malloc.c:483)
==73621==    by 0x1C2EF692: allocate (new_allocator.h:127)
==73621==    by 0x1C2EF692: allocate (alloc_traits.h:464)
==73621==    by 0x1C2EF692: _M_allocate (stl_vector.h:346)
==73621==    by 0x1C2EF692: void std::vector<Particle*, std::allocator<Particle*> >::_M_realloc_insert<Particle* const&>(__gnu_cxx::__normal_iterator<Particle**, std::vector<Particle*, std::allocator<Particle*> > >, Particle* const&) (vector.tcc:440)
==73621==    by 0x1C2ECEC1: push_back (stl_vector.h:1198)
==73621==    by 0x1C2ECEC1: makeConstraint (Cloth.h:100)
==73621==    by 0x1C2ECEC1: Cloth::Cloth(Vec3 const&, int, int, double, double, double, double, int, double) (Cloth.cpp:75)
==73621==    by 0x1C2EAC44: CSF::do_filtering(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, bool) (CSF.cpp:141)
==73621==    by 0x1C2F1588: R_CSF(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>, bool, double, double, int, int, double) (R_CSF.cpp:57)
==73621==    by 0x1C2F7BDE: _RCSF_R_CSF (RcppExports.cpp:21)
==73621==    by 0x495A237: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x495A88C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49961FF: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B119C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B150A: Rf_eval (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B36DE: ??? (in /usr/lib/R/lib/libR.so)
==73621== 
==73621== Invalid read of size 8
==73621==    at 0x1C2FB98B: c2cdist::calCloud2CloudDist(Cloth&, csf::PointCloud&, std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&) (c2cdist.cpp:51)
==73621==    by 0x1C2EADE0: CSF::do_filtering(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, bool) (CSF.cpp:180)
==73621==    by 0x1C2F1588: R_CSF(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>, bool, double, double, int, int, double) (R_CSF.cpp:57)
==73621==    by 0x1C2F7BDE: _RCSF_R_CSF (RcppExports.cpp:21)
==73621==    by 0x495A237: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x495A88C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49961FF: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B119C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B150A: Rf_eval (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B36DE: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B44C6: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B163B: Rf_eval (in /usr/lib/R/lib/libR.so)
==73621==  Address 0x1d01fbc0 is 16 bytes before a block of size 16 free'd
==73621==    at 0x484C91D: operator delete(void*, unsigned long) (vg_replace_malloc.c:1101)
==73621==    by 0x1C2EF658: deallocate (new_allocator.h:145)
==73621==    by 0x1C2EF658: deallocate (alloc_traits.h:496)
==73621==    by 0x1C2EF658: _M_deallocate (stl_vector.h:354)
==73621==    by 0x1C2EF658: void std::vector<Particle*, std::allocator<Particle*> >::_M_realloc_insert<Particle* const&>(__gnu_cxx::__normal_iterator<Particle**, std::vector<Particle*, std::allocator<Particle*> > >, Particle* const&) (vector.tcc:500)
==73621==    by 0x1C2ECEC1: push_back (stl_vector.h:1198)
==73621==    by 0x1C2ECEC1: makeConstraint (Cloth.h:100)
==73621==    by 0x1C2ECEC1: Cloth::Cloth(Vec3 const&, int, int, double, double, double, double, int, double) (Cloth.cpp:75)
==73621==    by 0x1C2EAC44: CSF::do_filtering(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, bool) (CSF.cpp:141)
==73621==    by 0x1C2F1588: R_CSF(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>, bool, double, double, int, int, double) (R_CSF.cpp:57)
==73621==    by 0x1C2F7BDE: _RCSF_R_CSF (RcppExports.cpp:21)
==73621==    by 0x495A237: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x495A88C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49961FF: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B119C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B150A: Rf_eval (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B36DE: ??? (in /usr/lib/R/lib/libR.so)
==73621==  Block was alloc'd at
==73621==    at 0x4848F75: operator new(unsigned long) (vg_replace_malloc.c:483)
==73621==    by 0x1C2EF692: allocate (new_allocator.h:127)
==73621==    by 0x1C2EF692: allocate (alloc_traits.h:464)
==73621==    by 0x1C2EF692: _M_allocate (stl_vector.h:346)
==73621==    by 0x1C2EF692: void std::vector<Particle*, std::allocator<Particle*> >::_M_realloc_insert<Particle* const&>(__gnu_cxx::__normal_iterator<Particle**, std::vector<Particle*, std::allocator<Particle*> > >, Particle* const&) (vector.tcc:440)
==73621==    by 0x1C2ECDDF: push_back (stl_vector.h:1198)
==73621==    by 0x1C2ECDDF: makeConstraint (Cloth.h:101)
==73621==    by 0x1C2ECDDF: Cloth::Cloth(Vec3 const&, int, int, double, double, double, double, int, double) (Cloth.cpp:66)
==73621==    by 0x1C2EAC44: CSF::do_filtering(std::vector<int, std::allocator<int> >&, std::vector<int, std::allocator<int> >&, bool) (CSF.cpp:141)
==73621==    by 0x1C2F1588: R_CSF(Rcpp::DataFrame_Impl<Rcpp::PreserveStorage>, bool, double, double, int, int, double) (R_CSF.cpp:57)
==73621==    by 0x1C2F7BDE: _RCSF_R_CSF (RcppExports.cpp:21)
==73621==    by 0x495A237: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x495A88C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49961FF: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B119C: ??? (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B150A: Rf_eval (in /usr/lib/R/lib/libR.so)
==73621==    by 0x49B36DE: ??? (in /usr/lib/R/lib/libR.so)
==73621==

@Jean-Romain Jean-Romain transferred this issue from r-lidar/lidR May 28, 2024
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@Jean-Romain @EvanZarrella