[Insight-developers] FEM debian test failures

Tue Jun 12 14:44:11 EDT 2012

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 <paul at paulnovo.us> 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
>> <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
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>> >
>> > ========================================================
>> >
>> > Bradley Lowekamp
>> >
>> > Medical Science and Computing for
>> >
>> > Office of High Performance Computing and Communications
>> >
>> > National Library of Medicine
>> >
>> > blowekamp at mail.nih.gov
>> >
>> >
>> >
>> >
>>
>>
>>
>

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