I spent some time on this too, and again was about to submit a patch (man, I am just too slow). The code in ComputeMatrix looked a bit odd to me, ie using where the for counter stopped as a condition in the next if. I am thinking gcc does some for-loop branching optimization that does't like this. Anyway, if you compile with the attached patch, the Spatial Object segfaults go away.
-Paul On Tue, 2012-06-12 at 13:58 -0400, Bill Lorensen wrote: > First, I can't imagine how you figured this out. You are starting to > become a legend in your time... > > Why not #ifdef your solution. Something like: > > #if (__GNUC__ == 4.7) > InputVectorType m_MatrixScale __attribute__ ((aligned) ); > #else > InputVectorType m_MatrixScale; > #endif > > > On Tue, Jun 12, 2012 at 12:16 PM, Bradley Lowekamp > <[email protected]> wrote: > > Hello Steve, > > > > I spent some time looking into this. > > > > I downloaded the latest Debian 64-bit and then updated to the sid unstable > > with gcc 4.7. I think this is the same version you are using? > > > > These are the failing tests I had: > > > > The following tests FAILED: > > 508 - itkDiffusionTensor3DReconstructionImageFilterTest (SEGFAULT) > > 885 - itkReadWriteSpatialObjectTest (SEGFAULT) > > 886 - itkReadWriteSpatialObjectTest1 (SEGFAULT) > > 887 - itkReadWriteSpatialObjectTest2 (SEGFAULT) > > 1504 - itkMeshSpatialObjectIOTest (SEGFAULT) > > 1505 - itkMeshSpatialObjectIOTest1 (SEGFAULT) > > 1506 - itkMeshSpatialObjectIOTest2 (SEGFAULT) > > 1924 - itkImageSpatialObjectTest (SEGFAULT) > > 1925 - itkSpatialObjectToImageStatisticsCalculatorTest (SEGFAULT) > > 1926 - itkImageMaskSpatialObjectTest (SEGFAULT) > > 1927 - itkImageMaskSpatialObjectTest2 (SEGFAULT) > > 1928 - itkImageMaskSpatialObjectTest3 (SEGFAULT) > > 1931 - itkSceneSpatialObjectTest (SEGFAULT) > > 1933 - itkMetaArrowConverterTest (SEGFAULT) > > 1946 - itkArrowSpatialObjectTest (SEGFAULT) > > 2124 - itkTransformsSetParametersTest (SEGFAULT) > > Errors while running CTest > > > > > > I was able to repeat many of your test failures. I then hacked and debugged > > the code for a little bit. I don't see anything wrong with it. Based on you > > experiment of mixing optimization levels and what I observed, I would tend > > to agree that there is likely some kind of gcc bug, perhaps in intra-unit > > optimization or how the data get laid out in certain circumstances. > > > > The most interesting things I was able to do it the following change: > > > > diff --git a/Modules/Core/Transform/include/itkScalableAffineTransform.h > > b/Modules/Core/Transform/i > > index 6032127..8dbcdc4 100644 > > --- a/Modules/Core/Transform/include/itkScalableAffineTransform.h > > +++ b/Modules/Core/Transform/include/itkScalableAffineTransform.h > > @@ -166,7 +166,7 @@ private: > > const Self & operator=(const Self &); > > > > double m_Scale[NDimensions]; > > - InputVectorType m_MatrixScale; > > + InputVectorType m_MatrixScale __attribute__ ((aligned) ); > > }; //class ScalableAffineTransform > > } // namespace itk > > > > > > With this change all tests pass. Which is _really_ good to know! This mean > > that all these failing tests are related to this same bug. So I think I have > > taken this as far as it needs to... I guess I hope that a patch in gcc 4.7 > > will address this issue. > > > > > > On another note. Have you looking at the SimpleITK project? Have you > > considered also packaging that for Debian distributions? > > > > Thanks, > > Brad > > > > > > > > On Jun 10, 2012, at 1:41 AM, Steve M. Robbins wrote: > > > > On Sun, Jun 10, 2012 at 12:03:39AM -0500, Steve M. Robbins wrote: > > > > Well, I spent some time looking at itkReadWriteSpatialObjectTest and > > > > I've determined a few things. > > > > [...] > > > > 2. It works when built using gcc 4.7 in RelWithDebInfo mode (flags -O2 -g). > > > > [...] > > > > 4. It fails when built using gcc 4.7 with flags -O3 -g -DNDEBUG. > > > > > > One further item. Of the three files that make up > > ITKIOSpatialObjectsTestDriver, as long as this one > > is built with -O2: > > > > itkPolygonGroupSpatialObjectXMLFileTest.cxx.o > > > > I can build the other two with -O3: > > > > ITKIOSpatialObjectsTestDriver.cxx.o > > itkReadWriteSpatialObjectTest.cxx.o > > > > and the test completes successfully. This makes no sense to me > > because itkPolygonGroupSpatialObjectXMLFileTest code is not even > > executed when running the test in question ("ctest -R > > itkReadWriteSpatialObjectTest"). > > > > > > -Steve > > <signature.asc>_______________________________________________ > > Powered by www.kitware.com > > > > Visit other Kitware open-source projects at > > http://www.kitware.com/opensource/opensource.html > > > > Kitware offers ITK Training Courses, for more information visit: > > http://kitware.com/products/protraining.php > > > > Please keep messages on-topic and check the ITK FAQ at: > > http://www.itk.org/Wiki/ITK_FAQ > > > > Follow this link to subscribe/unsubscribe: > > http://www.itk.org/mailman/listinfo/insight-developers > > > > > > ======================================================== > > > > Bradley Lowekamp > > > > Medical Science and Computing for > > > > Office of High Performance Computing and Communications > > > > National Library of Medicine > > > > [email protected] > > > > > > > > > > >
Description: Fix Spatial Object Test Segfaults This bug fixes some segfaults that occur when compiling with O3 on gcc 4.7. I am not 100% sure why this works. ComputeMatrix looks fine, just that it is a bit unusual to use the final counter value of the for loop as a condition in the next if. I am thinking gcc does some for-loop branching optimization that does't like this. Author: Paul Novotny <[email protected]> --- debian-svn.orig/Modules/Core/Transform/include/itkScalableAffineTransform.hxx +++ debian-svn/Modules/Core/Transform/include/itkScalableAffineTransform.hxx @@ -180,20 +180,19 @@ ScalableAffineTransform< TScalarType, NDimensions > ::ComputeMatrix() { - unsigned int i; - - for ( i = 0; i < NDimensions; i++ ) + bool scaleChanged = false; + for ( unsigned int i = 0; i < NDimensions; i++ ) { if ( m_Scale[i] != m_MatrixScale[i] ) { - break; + scaleChanged = true; } } - if ( i < NDimensions ) + if ( scaleChanged ) { MatrixType mat; typename MatrixType::InternalMatrixType & imat = mat.GetVnlMatrix(); - for ( i = 0; i < NDimensions; i++ ) + for ( unsigned int i = 0; i < NDimensions; i++ ) { if ( m_MatrixScale[i] != 0 && m_Scale[i] != 0 ) {
