Paul, Can you send me the updated file (not a debian patch) so I can submit it as a gerrit patch?
Bill On Tue, Jun 12, 2012 at 2:28 PM, Paul Novotny <[email protected]> wrote: > 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] >> > >> > >> > >> > >> >> >> > -- Unpaid intern in BillsBasement at noware dot com -- To UNSUBSCRIBE, email to [email protected] with a subject of "unsubscribe". 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