[Insight-developers] FEM debian test failures

Tue Jun 12 15:06:33 EDT 2012

Paul sent me his code and I'll submit a gerrit patch.

On Tue, Jun 12, 2012 at 2:56 PM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> That is great! It's a much more sane patch than my alignment hack. I have
> verified that is solved the problem on my system too.
>
> There are still a lot more failing tests on the 32-bit version dashboard
> build. It certainly appears to be an optimization bug with this version of
> GCC. I am not sure how worth wild it will be to pursue the remaining test
> failures that are occurring here:
>
> http://open.cdash.org/viewTest.php?onlyfailed&buildid=2355571
>
> If we have to just hack the structure of the loops, or move around how the
> data is laid out in memory.
>
> The version of this compiler is:
>
> $ gcc-4.7 --version
> gcc-4.7 (Debian 4.7.0-12) 4.7.0
> Copyright (C) 2012 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> So it's still very new. Is it likely that Debian is going to release with
> this version of the compiler? or are the bug is gcc going to get patched?
>
> Thanks,
> Brad
>
> On Jun 12, 2012, at 2:44 PM, Bill Lorensen wrote:
>
> 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
>
> <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
>
>
>
>
>
>
>
>
>
>
>
>
> --
> Unpaid intern in BillsBasement at noware dot com
>
>
> ========================================================
>
> Bradley Lowekamp
>
> Medical Science and Computing for
>
> Office of High Performance Computing and Communications
>
> National Library of Medicine
>
> blowekamp at mail.nih.gov
>
>
>
>

-- 
Unpaid intern in BillsBasement at noware dot com