[ITK] [ITK-users] Possible memory leak in itk::IterativeTriangleCellSubdivisionQuadEdgeMeshFilter

Arnaud Gelas arnaudgelas at gmail.com
Fri Jun 5 02:27:28 EDT 2015 

Hi,

Thanks for pointing out this problem!

The real problem is not with itk::QuadEdgeMesh, but with itk::Mesh, if you just change the mesh type from itk::QuadEdgeMesh to itk::Mesh, you’ll also get memory leaks.
It just happens, that CellsContainer memory is not released for the current mesh when doing a Graft on another one.

I’ll submit a patch very soon to fix it, and add both of you as reviewer!

Thanks
Arnaud

> On 04 Jun 2015, at 18:55, wanlin zhu <wanlin.zhu at outlook.com> wrote:
> 
> I think the memory leak issue origined from QuadEdgeMesh,
> 
> #include "itkQuadEdgeMesh.h"
> #include "itkRegularSphereMeshSource.h"
> 
> 
> typedef itk::QuadEdgeMesh< double, 3 > TMesh;
> typedef itk::RegularSphereMeshSource< TMesh > TSource;
> 
> int main(int argc, char ** argv)
> {
>   TSource::Pointer source = TSource::New();
>   source->Update();
>   TSource::Pointer source1 = TSource::New();
>   source1->SetResolution(5);
>   source1->Update();
>   TMesh::Pointer mesh = source->GetOutput();
>   mesh->Graft( source1->GetOutput());
> 
>   return EXIT_SUCCESS;
> 
> }
> 
> It gives memory leak errors as well. 
> 
> 
> 
> wanlin
> 
> > Date: Wed, 3 Jun 2015 09:49:33 -0700
> > From: davis.vigneault at gmail.com <mailto:davis.vigneault at gmail.com>
> > To: insight-users at itk.org <mailto:insight-users at itk.org>
> > Subject: [ITK-users] Possible memory leak in itk::IterativeTriangleCellSubdivisionQuadEdgeMeshFilter
> > 
> > All--
> > 
> > I've been observing some erratic behavior in my program, which after some
> > investigation I believe may be due to a memory leak in
> > itk::IterativeTriangleCellSubdivisionQuadEdgeMeshFilter. I've copied below
> > a minimal example which exhibits the problem, along with the output from
> > valgrind showing 15,360 bytes lost in 128 blocks. Is anyone able to
> > reproduce this issue? (Note that the 72,704 bytes still reachable is 
> > valgrind's fault
> > <http://stackoverflow.com/questions/30376601/valgrind-memory-still-reachable-with-trivial-program-using-iostream> 
> > , not ITK's).
> > 
> > ///////////////////////////////////////
> > // MINIMAL EXAMPLE //
> > ///////////////////////////////////////
> > 
> > #include "itkQuadEdgeMesh.h"
> > #include "itkRegularSphereMeshSource.h"
> > #include "itkLoopTriangleCellSubdivisionQuadEdgeMeshFilter.h"
> > #include "itkIterativeTriangleCellSubdivisionQuadEdgeMeshFilter.h"
> > 
> > typedef itk::QuadEdgeMesh< double, 3 > TMesh;
> > typedef itk::RegularSphereMeshSource< TMesh > TSource;
> > typedef itk::LoopTriangleCellSubdivisionQuadEdgeMeshFilter< TMesh, TMesh >
> > TLoop;
> > typedef itk::IterativeTriangleCellSubdivisionQuadEdgeMeshFilter< TMesh,
> > TLoop > TSubdivide;
> > 
> > int main(int argc, char ** argv)
> > {
> > 
> > TSource::Pointer source = TSource::New();
> > TSubdivide::Pointer sub = TSubdivide::New();
> > sub->SetInput( source->GetOutput() );
> > sub->SetResolutionLevels( 1 );
> > sub->Update();
> > 
> > return EXIT_SUCCESS;
> > 
> > }
> > 
> > ////////////////////////////////////////
> > // VALGRIND OUTPUT //
> > ////////////////////////////////////////
> > 
> > $ valgrind --leak-check=full ./dv-registration
> > ==20328== Memcheck, a memory error detector
> > ==20328== Copyright (C) 2002-2013, and GNU GPL'd, by Julian Seward et al.
> > ==20328== Using Valgrind-3.10.1 and LibVEX; rerun with -h for copyright info
> > ==20328== Command: ./dv-registration
> > ==20328== 
> > ==20328== 
> > ==20328== HEAP SUMMARY:
> > ==20328== in use at exit: 92,160 bytes in 257 blocks
> > ==20328== total heap usage: 13,030 allocs, 12,773 frees, 879,010 bytes
> > allocated
> > ==20328== 
> > ==20328== 19,456 (15,360 direct, 4,096 indirect) bytes in 128 blocks are
> > definitely lost in loss record 2 of 3
> > ==20328== at 0x4C2B0A5: operator new(unsigned long)
> > (vg_replace_malloc.c:324)
> > ==20328== by 0x4984F8: itk::QuadEdgeMesh<double, 3u,
> > itk::QuadEdgeMeshTraits<double, 3u, bool, bool, float, float>
> > >::AddFace(itk::GeometricalQuadEdge<unsigned long, unsigned long, bool,
> > bool, true>*) (in
> > /home/davis/Developer/oxford/Stebbing_Method/SubTest/bin/dv-registration)
> > ==20328== by 0x49926F: itk::QuadEdgeMesh<double, 3u,
> > itk::QuadEdgeMeshTraits<double, 3u, bool, bool, float, float>
> > >::AddFaceWithSecurePointList(std::vector<unsigned long,
> > std::allocator<unsigned long> > const&, bool) (in
> > /home/davis/Developer/oxford/Stebbing_Method/SubTest/bin/dv-registration)
> > ==20328== by 0x49D0D5: void
> > itk::CopyMeshToMeshCells<itk::QuadEdgeMesh<double, 3u,
> > itk::QuadEdgeMeshTraits<double, 3u, bool, bool, float, float> >,
> > itk::QuadEdgeMesh<double, 3u, itk::QuadEdgeMeshTraits<double, 3u, bool,
> > bool, float, float> > >(itk::QuadEdgeMesh<double, 3u,
> > itk::QuadEdgeMeshTraits<double, 3u, bool, bool, float, float> > const*,
> > itk::QuadEdgeMesh<double, 3u, itk::QuadEdgeMeshTraits<double, 3u, bool,
> > bool, float, float> >*) (in
> > /home/davis/Developer/oxford/Stebbing_Method/SubTest/bin/dv-registration)
> > ==20328== by 0x491766:
> > itk::QuadEdgeMeshToQuadEdgeMeshFilter<itk::QuadEdgeMesh<double, 3u,
> > itk::QuadEdgeMeshTraits<double, 3u, bool, bool, float, float> >,
> > itk::QuadEdgeMesh<double, 3u, itk::QuadEdgeMeshTraits<double, 3u, bool,
> > bool, float, float> > >::CopyInputMeshToOutputMeshCells() (in
> > /home/davis/Developer/oxford/Stebbing_Method/SubTest/bin/dv-registration)
> > ==20328== by 0x4916E2:
> > itk::QuadEdgeMeshToQuadEdgeMeshFilter<itk::QuadEdgeMesh<double, 3u,
> > itk::QuadEdgeMeshTraits<double, 3u, bool, bool, float, float> >,
> > itk::QuadEdgeMesh<double, 3u, itk::QuadEdgeMeshTraits<double, 3u, bool,
> > bool, float, float> > >::CopyInputMeshToOutputMeshGeometry() (in
> > /home/davis/Developer/oxford/Stebbing_Method/SubTest/bin/dv-registration)
> > ==20328== by 0x491063:
> > itk::IterativeTriangleCellSubdivisionQuadEdgeMeshFilter<itk::QuadEdgeMesh<double,
> > 3u, itk::QuadEdgeMeshTraits<double, 3u, bool, bool, float, float> >,
> > itk::LoopTriangleCellSubdivisionQuadEdgeMeshFilter<itk::QuadEdgeMesh<double,
> > 3u, itk::QuadEdgeMeshTraits<double, 3u, bool, bool, float, float> >,
> > itk::QuadEdgeMesh<double, 3u, itk::QuadEdgeMeshTraits<double, 3u, bool,
> > bool, float, float> > > >::GenerateData() (in
> > /home/davis/Developer/oxford/Stebbing_Method/SubTest/bin/dv-registration)
> > ==20328== by 0x4C578C:
> > itk::ProcessObject::UpdateOutputData(itk::DataObject*) (in
> > /home/davis/Developer/oxford/Stebbing_Method/SubTest/bin/dv-registration)
> > ==20328== by 0x4866C6: main (in
> > /home/davis/Developer/oxford/Stebbing_Method/SubTest/bin/dv-registration)
> > ==20328== 
> > ==20328== LEAK SUMMARY:
> > ==20328== definitely lost: 15,360 bytes in 128 blocks
> > ==20328== indirectly lost: 4,096 bytes in 128 blocks
> > ==20328== possibly lost: 0 bytes in 0 blocks
> > ==20328== still reachable: 72,704 bytes in 1 blocks
> > ==20328== suppressed: 0 bytes in 0 blocks
> > ==20328== Reachable blocks (those to which a pointer was found) are not
> > shown.
> > ==20328== To see them, rerun with: --leak-check=full --show-leak-kinds=all
> > ==20328== 
> > ==20328== For counts of detected and suppressed errors, rerun with: -v
> > ==20328== ERROR SUMMARY: 1 errors from 1 contexts (suppressed: 0 from 0)
> > 
> > 
> > 
> > 
> > --
> > View this message in context: http://itk-insight-users.2283740.n2.nabble.com/Possible-memory-leak-in-itk-IterativeTriangleCellSubdivisionQuadEdgeMeshFilter-tp7587434.html
> > Sent from the ITK Insight Users mailing list archive at Nabble.com.
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