Comments (6)
kaspermarstal
commented on July 18, 2024
Having just checked that it compiles successfully with GCC 5.3.1 on Ubuntu 16.04, I don't think it is a problem with Elastix source. However, you should probably double check that the process is not killed by the out of memory manager before submitting the bug report. Elastix uses about 4GB per core during compilation so if you compile with e.g. -j4 you need a machine with 16GB of RAM 😊
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L-Steiner
commented on July 18, 2024
@npyoung Did you find any solutions?
@kaspermarstal I am also compiling on Ubuntu 16.04 with GCC 5.4.0, 1 core and 8 GB and had internal errors in two runs. First one was segmentation fault. Here's the second one:
[ 79%] Building CXX object src/Components/MovingImagePyramids/MovingShrinkingPyramid/CMakeFiles/MovingShrinkingPyramid.dir/elxMovingShrinkingPyramid.cxx.o
In file included from /home/lukas/SimpleElastixGit/build/ITK-prefix/include/ITK-4.8/itkImageToImageFilter.h:372:0,
from /home/lukas/SimpleElastixGit/build/ITK-prefix/include/ITK-4.8/itkChangeInformationImageFilter.h:21,
from /home/lukas/SimpleElastixGit/build/elastix/src/Core/Kernel/elxElastixBase.h:40,
from /home/lukas/SimpleElastixGit/build/elastix/src/Core/Kernel/elxElastixTemplate.h:21,
from /home/lukas/SimpleElastixGit/build/elastix/src/Core/Install/elxIncludes.h:39,
from /home/lukas/SimpleElastixGit/build/elastix/src/Components/MovingImagePyramids/MovingShrinkingPyramid/elxMovingShrinkingPyramid.h:21,
from /home/lukas/SimpleElastixGit/build/elastix/src/Components/MovingImagePyramids/MovingShrinkingPyramid/elxMovingShrinkingPyramid.cxx:19:
/home/lukas/SimpleElastixGit/build/ITK-prefix/include/ITK-4.8/itkImageToImageFilter.hxx: In instantiation of ‘void itk::ImageToImageFilter<TInputImage, TOutputImage>::VerifyInputInformation() [with TInputImage = itk::Image<unsigned int, 2u>; TOutputImage = itk::Image<double, 2u>]’:
/home/lukas/SimpleElastixGit/build/elastix/src/Components/MovingImagePyramids/MovingShrinkingPyramid/elxMovingShrinkingPyramid.cxx:21:42: required from here
/home/lukas/SimpleElastixGit/build/ITK-prefix/include/ITK-4.8/itkImageToImageFilter.hxx:253:1: internal compiler error: in tree_node_structure_for_code, at tree.c:508
}
^
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.
src/Components/MovingImagePyramids/MovingShrinkingPyramid/CMakeFiles/MovingShrinkingPyramid.dir/build.make:62: recipe for target 'src/Components/MovingImagePyramids/MovingShrinkingPyramid/CMakeFiles/MovingShrinkingPyramid.dir/elxMovingShrinkingPyramid.cxx.o' failed
make[5]: *** [src/Components/MovingImagePyramids/MovingShrinkingPyramid/CMakeFiles/MovingShrinkingPyramid.dir/elxMovingShrinkingPyramid.cxx.o] Error 1
CMakeFiles/Makefile2:4236: recipe for target 'src/Components/MovingImagePyramids/MovingShrinkingPyramid/CMakeFiles/MovingShrinkingPyramid.dir/all' failed
make[4]: *** [src/Components/MovingImagePyramids/MovingShrinkingPyramid/CMakeFiles/MovingShrinkingPyramid.dir/all] Error 2
Makefile:127: recipe for target 'all' failed
make[3]: *** [all] Error 2
CMakeFiles/elastix.dir/build.make:113: recipe for target 'elastix-prefix/src/elastix-stamp/elastix-build' failed
make[2]: *** [elastix-prefix/src/elastix-stamp/elastix-build] Error 2
CMakeFiles/Makefile2:255: recipe for target 'CMakeFiles/elastix.dir/all' failed
make[1]: *** [CMakeFiles/elastix.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2Any ideas?
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npyoung
commented on July 18, 2024
I got further with -j1 but ultimately ran into more problems. For some reason several files require an enormous amount of memory to compile (even with 16GB of RAM).
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kaspermarstal
commented on July 18, 2024
To reduce memory consumption you can set USE_ALL_PIXELTYPES to OFF in the SuperBuild/External_Elastix.cmake file. You will then have support for 2D float images, 3D float and short images, and 4D short images. Images of other types can be cast using SimpleITK's Cast() method. Also can you double check you are compiling in Release mode?
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L-Steiner
commented on July 18, 2024
I tested these settings already yesterday, however, with another segmentation fault. Nonetheless, i double checked all and had another run just now with the following result:
[ 38%] Linking CXX executable ../bin/SimpleITKTclsh
CMakeFiles/SimpleITKTclsh.dir/SimpleITKTCL_wrap.cxx.o: In function `main':
SimpleITKTCL_wrap.cxx:(.text.startup+0x20): undefined reference to `Tcl_MainEx'
collect2: error: ld returned 1 exit status
Wrapping/CMakeFiles/SimpleITKTclsh.dir/build.make:549: recipe for target 'bin/SimpleITKTclsh' failed
make[5]: *** [bin/SimpleITKTclsh] Error 1
CMakeFiles/Makefile2:2642: recipe for target 'Wrapping/CMakeFiles/SimpleITKTclsh.dir/all' failed
make[4]: *** [Wrapping/CMakeFiles/SimpleITKTclsh.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make[3]: *** [all] Error 2
CMakeFiles/SimpleITK.dir/build.make:115: recipe for target 'SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build' failed
make[2]: *** [SimpleITK-prefix/src/SimpleITK-stamp/SimpleITK-build] Error 2
CMakeFiles/Makefile2:180: recipe for target 'CMakeFiles/SimpleITK.dir/all' failed
make[1]: *** [CMakeFiles/SimpleITK.dir/all] Error 2
Makefile:83: recipe for target 'all' failed
make: *** [all] Error 2
I should maybe note that my memory was maximally about 3/4 full.
Thank you very much for your help, btw.
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L-Steiner
commented on July 18, 2024
After disabling wrapping of C# and TCL I gave it another try and had no more problems. Thank you.
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