compile opencv 3 on ubuntu 16.04 linking error: /usr/lib/x86_64-linux-gnu/libsoxr.so.0: undefined reference to `GOMP_parallel@GOMP_4.0'

Question

Trying to install openCV 3.1, CUDA 8.0.44 on Ubuntu 16.04 by building from the source.

The following are the errors I met during the compilation.

Scanning dependencies of target opencv_test_video
[ 37%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/test_optflowpyrlk.cpp.o
[ 37%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/test_accum.cpp.o
[ 37%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/test_kalman.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/test_ecc.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/test_tvl1optflow.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/test_main.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/test_camshift.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/ocl/test_optflowpyrlk.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/ocl/test_optflow_farneback.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/ocl/test_bgfg_mog2.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/ocl/test_optflow_tvl1flow.cpp.o
[ 38%] Building CXX object modules/video/CMakeFiles/opencv_test_video.dir/test/test_estimaterigid.cpp.o
[ 38%] Linking CXX executable ../../bin/opencv_test_video
//usr/lib/x86_64-linux-gnu/libsoxr.so.0: undefined reference to `GOMP_parallel@GOMP_4.0'
collect2: error: ld returned 1 exit status
modules/video/CMakeFiles/opencv_test_video.dir/build.make:391: recipe for target 'bin/opencv_test_video' failed
make[2]: *** [bin/opencv_test_video] Error 1
CMakeFiles/Makefile2:3336: recipe for target 'modules/video/CMakeFiles/opencv_test_video.dir/all' failed
make[1]: *** [modules/video/CMakeFiles/opencv_test_video.dir/all] Error 2
Makefile:160: recipe for target 'all' failed
make: *** [all] Error 2

I consider the issue is related to the openMP or the ld configuration.

The following are the detailed configuration:

1. LD_LIBRARY_PATH:

/usr/lib/nvidia-current:/usr/local/cuda/lib64:/usr/local/cuda/lib

2. GCC version: 5.4.0

3. CMake configuration command:

cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=/usr/local -D WITH_TBB=ON -D WITH_V4L=ON -D WITH_QT=ON -D WITH_OPENGL=ON -D WITH_CUBLAS=ON -DCUDA_NVCC_FLAGS="-D_FORCE_INLINES" ..

Answer 1

Firstly, I thought this problem was caused because I installed Anaconda and put it into my PATH.

Different GCC version are used between Anaconda and System default. For Ubuntu 16.04, the GCC version is 5.4.0 however Anaconda only provides GCC 4 (I can't remember it's 4.4 or 4.8). Although I used the system default gcc to compile opencv, it somehow will find the lib located in Anaconda, which caused the problem.

I think there are two ways to solve this issue.

1. Method 1: Pass the option -D WITH_OPENMP=ON, or, when using cmake-gui, check the choice WITH-OPENMP.
2. Method 2: Delete Anaconda from your $PATH and LD_LIBRARY_PATH.