[Insight-developers] FEM debian test failures

[Bradley Lowekamp]

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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