[Insight-developers] FEM debian test failures

[Paul Novotny]

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
> <blowekamp at mail.nih.gov> 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
> >
> > blowekamp at mail.nih.gov
> >
> >
> >
> >
> 
> 
> 

-------------- next part --------------
A non-text attachment was scrubbed...
Name: SpatialObject-Test-Segfaults.patch
Type: text/x-patch
Size: 1259 bytes
Desc: not available
URL: <http://www.itk.org/pipermail/insight-developers/attachments/20120612/e06ea09a/attachment.bin>