Slicer build in linux freezes when building simpleitk

Development
1

Hi All,

I am trying to build Slicer in Ubuntu but it freezes when it’s building SimpleITK. It seems to be working all the time but it doesn’t show any progress.
I tried building it several times from the scratch but same thing happens every time.
BTW, I keep everything in the Cmake as default.
Any suggestions?

Thanks,

2

SimpleITK takes a while to build. If you don’t see any progress for 24 hours then upload the complete build log somewhere and copy-paste the link here.

3

SimpleITK can also be disabled if you don’t need it, with Slicer_USE_SimpleITK=OFF.

4

Thank you guys,

I am still struggling building the slicer on Linux. I started building it this morning again, I will wait till tomorrow and if it doesn’t build, I will upload the build log here.

5

OK, I decided to turn off the simpleITK for now and also build the slicer with QT5. Now I have some errors when building CTK.
I uploaded some output and error log files here:

https://drive.google.com/drive/folders/11r_wY-wDT9yrfKJQGITR731eMxFU6YIF?usp=sharing

Any help is appreciated. It’s my first time building slicer in Linux and it is really frustrating :frowning:

Thanks,
Samira

6

Sorry you are running into trouble. I’m not sure what’s up but this message from the error log indicates perhaps the compiler is not installed right:

/home/samira/slicer/debug/VTKv9/Utilities/KWIML/vtkkwiml/include/kwiml/int.h:1052:1: note: in expansion of macro ‘KWIML_INT_private_VERIFY_SIGN’
KWIML_INT_private_VERIFY_SIGN(KWIML_INT_uintptr_t, KWIML_INT_uintptr_t, >);
^
c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,

You might try building vtk independent of Slicer and see if you can narrow down what leads to this.

(FWIW I regularly build on unbuntu 16.04 with no problems)

7

Thanks Steve,

I have already built the CTK independent and it was successful. Now all the dependencies are built. Here is the error I am getting now:

c++: internal compiler error: Killed (program cc1plus)
Please submit a full bug report,
with preprocessed source if appropriate.
See <file:///usr/share/doc/gcc-5/README.Bugs> for instructions.
Libs/MRML/Widgets/Testing/CMakeFiles/qMRMLWidgetsCxxTests.dir/build.make:1229: recipe for target 'Libs/MRML/Widgets/Testing/CMakeFiles/qMRMLWidgetsCxxTests.dir/qMRMLScalarInvariantComboBoxEventTranslatorPlayerTest1.cxx.o' failed
make[5]: *** [Libs/MRML/Widgets/Testing/CMakeFiles/qMRMLWidgetsCxxTests.dir/qMRMLScalarInvariantComboBoxEventTranslatorPlayerTest1.cxx.o] Error 4
make[5]: *** Waiting for unfinished jobs....
[ 53%] Built target qMRMLWidgetsPlugins
In file included from /home/samira/slicer/Slicer/Libs/MRML/Widgets/Testing/qMRMLLayoutManagerWithCustomFactoryTest.cxx:23:0:
/home/samira/slicer/Slicer/Libs/MRML/Widgets/Testing/qMRMLLayoutManagerTestHelper.cxx:13:6: warning: ‘bool {anonymous}::checkViewArrangement(int, qMRMLLayoutManager*, vtkMRMLLayoutNode*, int)’ defined but not used [-Wunused-function]
 bool checkViewArrangement(int line, qMRMLLayoutManager* layoutManager,
      ^
[ 53%] Linking CXX shared library ../../bin/libqSlicerBaseQTGUI.so
In file included from /home/samira/slicer/Slicer/Libs/MRML/Widgets/Testing/qMRMLLayoutManagerVisibilityTest.cxx:23:0:
/home/samira/slicer/Slicer/Libs/MRML/Widgets/Testing/qMRMLLayoutManagerTestHelper.cxx:13:6: warning: ‘bool {anonymous}::checkViewArrangement(int, qMRMLLayoutManager*, vtkMRMLLayoutNode*, int)’ defined but not used [-Wunused-function]
 bool checkViewArrangement(int line, qMRMLLayoutManager* layoutManager,
      ^
In file included from /home/samira/slicer/Slicer/Libs/MRML/Widgets/Testing/qMRMLLayoutManagerTest1.cxx:23:0:
/home/samira/slicer/Slicer/Libs/MRML/Widgets/Testing/qMRMLLayoutManagerTestHelper.cxx:13:6: warning: ‘bool {anonymous}::checkViewArrangement(int, qMRMLLayoutManager*, vtkMRMLLayoutNode*, int)’ defined but not used [-Wunused-function]
 bool checkViewArrangement(int line, qMRMLLayoutManager* layoutManager,
      ^
CMakeFiles/Makefile2:2626: recipe for target 'Libs/MRML/Widgets/Testing/CMakeFiles/qMRMLWidgetsCxxTests.dir/all' failed
make[4]: *** [Libs/MRML/Widgets/Testing/CMakeFiles/qMRMLWidgetsCxxTests.dir/all] Error 2
make[4]: *** Waiting for unfinished jobs....
[ 53%] Built target qSlicerBaseQTGUI
Makefile:162: recipe for target 'all' failed
make[3]: *** [all] Error 2
CMakeFiles/Slicer.dir/build.make:141: recipe for target 'Slicer-prefix/src/Slicer-stamp/Slicer-build' failed
make[2]: *** [Slicer-prefix/src/Slicer-stamp/Slicer-build] Error 2
CMakeFiles/Makefile2:101: recipe for target 'CMakeFiles/Slicer.dir/all' failed
make[1]: *** [CMakeFiles/Slicer.dir/all] Error 2
Makefile:94: recipe for target 'all' failed
make: *** [all] Error 2

I have built the Slicer in windows million times, it’s my first time in linux and I might do something wrong that’s totally possible.
Do you still think it can be the compiler?

Samira

8

This may be due to running out of memory. Try to disable parallel build by running make -j1 or increase amount of physical RAM or swap size.

9

Yes! Thanks Andras, I disabled the parallel build and it worked :slight_smile: