[Build Error] [CentOS 7] undefined reference to pthread_*

Support
1

Hi,

VTK builds independently in my CentOS 7 machine but appears not to as part of Slicer:

Console log:

[ 50%] Building CXX object Interaction/Widgets/CMakeFiles/vtkInteractionWidgetsObjects.dir/vtkContourLineInterpolator.cxx.o
[ 50%] Linking CXX executable ../../bin/vtkProbeOpenGLVersion
../../lib/libvtkexodusII-8.2.so.1: error: undefined reference to 'pthread_setspecific'
../../lib/libvtkexodusII-8.2.so.1: error: undefined reference to 'pthread_getspecific'
../../lib/libvtkexodusII-8.2.so.1: error: undefined reference to 'pthread_key_create'
../../lib/libvtkexodusII-8.2.so.1: error: undefined reference to 'pthread_mutexattr_settype'
../../lib/libvtkexodusII-8.2.so.1: error: undefined reference to 'pthread_mutexattr_init'
../../lib/libvtkexodusII-8.2.so.1: error: undefined reference to 'pthread_once'
../../lib/libvtkhdf5-8.2.so.1: error: undefined reference to 'dlerror'
../../lib/libvtkhdf5-8.2.so.1: error: undefined reference to 'dlopen'
../../lib/libvtkhdf5-8.2.so.1: error: undefined reference to 'dlsym'
../../lib/libvtkhdf5-8.2.so.1: error: undefined reference to 'dlclose'
collect2: error: ld returned 1 exit status
make[5]: *** [bin/vtkProbeOpenGLVersion] Error 1
make[4]: *** [Rendering/OpenGL2/CMakeFiles/vtkProbeOpenGLVersion.dir/all] Error 2
make[4]: *** Waiting for unfinished jobs....
[ 50%] Building CXX object Interaction/Widgets/CMakeFiles/vtkInteractionWidgetsObjects.dir/vtkContourWidget.cxx.o
...
...
[ 57%] Building CXX object Wrapping/Python/CMakeFiles/vtkCommonKitPythonD.dir/vtkCommonKitPythonInitImpl.cxx.o
[ 57%] Linking CXX shared library ../../lib/libvtkCommonKitPython36D-8.2.so
[ 57%] Built target vtkCommonKitPythonD
make[3]: *** [all] Error 2
make[2]: *** [VTK-prefix/src/VTK-stamp/VTK-build] Error 2
make[1]: *** [CMakeFiles/VTK.dir/all] Error 2
make: *** [all] Error 2

CMakeError.log:

Run Build Command(s):/usr/bin/gmake cmTC_f23cb/fast
gmake[3]: Entering directory `/data/pnl/soft/pnlpipe3/Slicer-4.11/build/VTK-build/ThirdParty/libxml2/vtklibxml2/CMakeFiles/CMakeTmp'
/usr/bin/gmake -f CMakeFiles/cmTC_f23cb.dir/build.make CMakeFiles/cmTC_f23cb.dir/build
gmake[4]: Entering directory `/data/pnl/soft/pnlpipe3/Slicer-4.11/build/VTK-build/ThirdParty/libxml2/vtklibxml2/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_f23cb.dir/platformTestsC.c.o
/apps/software-compiled/GCCcore/7.3.0/bin/cc -DTEST_HAVE_SYS_NDIR_H  -w -w    -o CMakeFiles/cmTC_f23cb.dir/platformTestsC.c.o   -c /data/pnl/soft/pnlpipe3/Slicer-4.11/build/VTK/ThirdParty/libxml2/vtklibxml2/platformTestsC.c
/data/pnl/soft/pnlpipe3/Slicer-4.11/build/VTK/ThirdParty/libxml2/vtklibxml2/platformTestsC.c:82:10: fatal error: sys/ndir.h: No such file or directory
 #include <sys/ndir.h>
          ^~~~~~~~~~~~
compilation terminated.
gmake[4]: *** [CMakeFiles/cmTC_f23cb.dir/platformTestsC.c.o] Error 1
gmake[4]: Leaving directory `/data/pnl/soft/pnlpipe3/Slicer-4.11/build/VTK-build/ThirdParty/libxml2/vtklibxml2/CMakeFiles/CMakeTmp'
gmake[3]: *** [cmTC_f23cb/fast] Error 2
gmake[3]: Leaving directory `/data/pnl/soft/pnlpipe3/Slicer-4.11/build/VTK-build/ThirdParty/libxml2/vtklibxml2/CMakeFiles/CMakeTmp'

I have cmake 3.14.2, gcc 7.3.0, and Mesa/18.1.1-foss-2018b. I am trying to build the default configuration with my own Qt5_DIR. Do the above errors look familiar? Any tip is appreciated.

2

Probably the default vtk build doesn’t enable features that lead to the build issue. You can try enabling the same features that the superbuild does and isolate what leads to the error. If you can reproduce it at the VTK level you can try reporting on their discourse.

3

I have same errors. And I tried to add pthread and dl in vtk-cmakelists, but the errors still exists.Have you solve them?really appreciate for your help.

4

I’ve fixed the bugs by modify the CmakeLists in /build/VTK.

5

Could you describe the changes that solved the issue for you? Just in case someone else runs into the same problem.

6

I have ran the same issues when preparin the docker image for Gate.I solved in the moment with

RUN if [ "$Centos_Version" = "centos:7" ]; then \
     yum install -y devtoolset-7-gcc-c++ \
  fi

But Centos7 proves to be very non friendly with modern packages.So I must move to Centos8 and that’s the current base for dockerized Gate

1 Like
7

Add
set(CMAKE_CXX_FLAGS “${CMAKE_CXX_FLAGS} -pthread”)
set(CMAKE_CXX_FLAGS “${CMAKE_CXX_FLAGS} -ldl”)
after project(VTK) in build/VTK/CmakeLists.txt could solve the issues in my ubuntu20 machine.