[Insight-users] crashes N-D Linear Time Exact Signed Euclidean Distance Transform
Bill Lorensen
bill.lorensen at gmail.com
Fri May 30 10:27:36 EDT 2008
You are not getting a line # in itkAnalyzeImageIO.cxx. Looks like you
are building against an installed ITK. Can you try to build your own
version of ITK? The installed versionj does not have debug symbols.
Also, where did you get SquareBinary201.hdr? We distribute a
SquareBinary201.png.
Bill
On Fri, May 30, 2008 at 10:01 AM, Oleksandr Dzyubak <adzyubak at gmail.com> wrote:
> Hi Bill,
>
> I also was thinking of rebuilding ITK in the debug mode.
> So last night I found a box and did that.
> After running the valgrind on an executable, I got the lines causing failure
> (from up to bottom).
>
> Actually, the program that causes failure is
> "SignedMaurerDistanceMapImageFilterTest.cxx"
> and in particular line 23 ( reader->Update(); actually generated by
> (itkImageFileReader.txx:153) )
> and line 38 ( writer->Update(); generated by (itkImageFileWriter.txx:232)
> ). See log below.
>
> What could cause such a failure?
>
> Alex
>
> ********* Debug error log *******
>
> dzyubak at debian: /Images$ valgrind ./SignedMaurerDistanceMapImageFilterTest
> SquareBinary201.hdr test.hdr
>
> ==5109== Invalid write of size 8
> ==5109== at 0x40AE720: itk::AnalyzeImageIO::ReadImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
> (itkImageFileReader.txx:153)
> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
> (itkImageBase.txx:177)
> ==5109== by 0x44A9991: itk::DataObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x808C088: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
> ==5109== Address 0x4f4f340 is 0 bytes after a block of size 16 alloc'd
> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
> ==5109== by 0x40AE5BE: itk::AnalyzeImageIO::ReadImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
> (itkImageFileReader.txx:153)
> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
> (itkImageBase.txx:177)
> ==5109== by 0x44A9991: itk::DataObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x808C088: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
> ==5109==
> ==5109== Invalid write of size 8
> ==5109== at 0x40AE740: itk::AnalyzeImageIO::ReadImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
> (itkImageFileReader.txx:153)
> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
> (itkImageBase.txx:177)
> ==5109== by 0x44A9991: itk::DataObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x808C088: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
> ==5109== Address 0x4f4f380 is 0 bytes after a block of size 16 alloc'd
> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
> ==5109== by 0x40AE638: itk::AnalyzeImageIO::ReadImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
> (itkImageFileReader.txx:153)
> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
> (itkImageBase.txx:177)
> ==5109== by 0x44A9991: itk::DataObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x808C088: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
> ==5109==
> ==5109== Invalid write of size 8
> ==5109== at 0x40AE75A: itk::AnalyzeImageIO::ReadImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
> (itkImageFileReader.txx:153)
> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
> (itkImageBase.txx:177)
> ==5109== by 0x44A9991: itk::DataObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x808C088: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
> ==5109== Address 0x4f4f3c0 is 0 bytes after a block of size 16 alloc'd
> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
> ==5109== by 0x40AE6B2: itk::AnalyzeImageIO::ReadImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80C0D14: itk::ImageFileReader<itk::Image<int, 2>,
> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation()
> (itkImageFileReader.txx:153)
> ==5109== by 0x44E9A05: itk::ProcessObject::UpdateOutputInformation() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x80C132B: itk::ImageBase<2>::UpdateOutputInformation()
> (itkImageBase.txx:177)
> ==5109== by 0x44A9991: itk::DataObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x44E9AB5: itk::ProcessObject::Update() (in
> /usr/lib/libITKCommon.so.3.4.0)
> ==5109== by 0x808C088: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:23)
> ==5109==
> ==5109== Invalid read of size 8
> ==5109== at 0x409D27E:
> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>::GenerateData() (itkImageFileWriter.txx:279)
> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>::Write() (itkImageFileWriter.txx:232)
> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>::Update() (itkImageFileWriter.h:148)
> ==5109== by 0x808C1D2: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
> ==5109== Address 0x5241e50 is 0 bytes after a block of size 16 alloc'd
> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
> ==5109== by 0x409D150:
> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>::GenerateData() (itkImageFileWriter.txx:279)
> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>::Write() (itkImageFileWriter.txx:232)
> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>::Update() (itkImageFileWriter.h:148)
> ==5109== by 0x808C1D2: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
> ==5109==
> ==5109== Invalid read of size 8
> ==5109== at 0x409D292:
> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>::GenerateData() (itkImageFileWriter.txx:279)
> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>::Write() (itkImageFileWriter.txx:232)
> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>::Update() (itkImageFileWriter.h:148)
> ==5109== by 0x808C1D2: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
> ==5109== Address 0x5241cd0 is 0 bytes after a block of size 16 alloc'd
> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
> ==5109== by 0x409D03D:
> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>::GenerateData() (itkImageFileWriter.txx:279)
> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>::Write() (itkImageFileWriter.txx:232)
> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>::Update() (itkImageFileWriter.h:148)
> ==5109== by 0x808C1D2: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
> ==5109==
> ==5109== Invalid read of size 8
> ==5109== at 0x409D2A6:
> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>::GenerateData() (itkImageFileWriter.txx:279)
> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>::Write() (itkImageFileWriter.txx:232)
> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>::Update() (itkImageFileWriter.h:148)
> ==5109== by 0x808C1D2: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
> ==5109== Address 0x5241b50 is 0 bytes after a block of size 16 alloc'd
> ==5109== at 0x4023294: operator new(unsigned) (vg_replace_malloc.c:224)
> ==5109== by 0x409CF30:
> itk::NiftiImageIO::SetNIfTIOrientationFromImageIO(int, int) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409E65E: itk::NiftiImageIO::WriteImageInformation() (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x409C1C1: itk::NiftiImageIO::Write(void const*) (in
> /usr/lib/libITKIO.so.3.4.0)
> ==5109== by 0x80CBB00: itk::ImageFileWriter<itk::Image<double, 2>
>>::GenerateData() (itkImageFileWriter.txx:279)
> ==5109== by 0x80D0F99: itk::ImageFileWriter<itk::Image<double, 2>
>>::Write() (itkImageFileWriter.txx:232)
> ==5109== by 0x808C79D: itk::ImageFileWriter<itk::Image<double, 2>
>>::Update() (itkImageFileWriter.h:148)
> ==5109== by 0x808C1D2: main
> (SignedMaurerDistanceMapImageFilterTest.cxx:38)
> ==5109==
> ==5109== ERROR SUMMARY: 6 errors from 6 contexts (suppressed: 71 from 1)
> ==5109== malloc/free: in use at exit: 0 bytes in 0 blocks.
> ==5109== malloc/free: 16,858 allocs, 16,858 frees, 3,500,876 bytes
> allocated.
> ==5109== For counts of detected errors, rerun with: -v
> ==5109== All heap blocks were freed -- no leaks are possible.
>
> ************ End of log ******
>
> Bill Lorensen wrote:
>>
>> Oleksandr,
>>
>> That's not a good error and may explain your problem. An invalid write
>> means that it is trying to write to memory that is not allocated.
>>
>> You must be building release. If you build debug, valgrind will give
>> the exact offending line.
>>
>> Bill
>>
>> On Thu, May 29, 2008 at 5:42 PM, Oleksandr Dzyubak <adzyubak at gmail.com>
>> wrote:
>>
>>>
>>> Hi Bill,
>>>
>>> I ran valgrind on my box.
>>>
>>> dzyubak at debian: /Images$ valgrind --tool=memcheck
>>> ./SignedMaurerDistanceMapImageFilterTest SquareBinary201.hdr test.hdr
>>>
>>> I got several interesting results.
>>>
>>> 1) Running valgrind on an executable results in producing output image
>>> which
>>> matches that
>>> in the archive. This never happens if I just run an executable since a
>>> program aborts right away.
>>>
>>> 2) Valgrind produces a huge log with errors. In the end it says:
>>>
>>> ==15656== ERROR SUMMARY: 29 errors from 7 contexts (suppressed: 69 from
>>> 1).
>>>
>>> 3) And it starts its log with as below.
>>>
>>> ==15656== Invalid write of size 8
>>> ==15656== at 0x40DF148: itk::AnalyzeImageIO::ReadImageInformation()
>>> (in
>>> /usr/local/lib/InsightToolkit/libITKIO.so.3.7.0)
>>> ==15656== by 0x80C66A6: itk::ImageFileReader<itk::Image<int, 2>,
>>> itk::DefaultConvertPixelTraits<int> >::GenerateOutputInformation() (in
>>>
>>> /home/dzyubak/Test/N-D_Linear_Time_Exact_Signed_Euclidean_Distance_Transform/Images/SignedMaurerDistanceMapImageFilterTest)
>>>
>>>
>>> Is this memory block size mismatch coming from type traits or what?
>>> Any ideas how to treat that?
>>>
>>> Thanks,
>>> Alex
>>>
>>>
>>> Bill Lorensen wrote:
>>>
>>>>
>>>> Oleksandr,
>>>>
>>>> If you have valgrind on your linux box, try running it. It can find
>>>> some tricky memory problems.
>>>>
>>>> Bill
>>>>
>>>
>>>
>
>
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