Troubleshooting
This page compiles a list of common errors that can appear when using Scipion.
If you see an error like 'Cannot mix incompatible Qt library (version 0x40806) with this library (version 0x40804)'. This means the Qt installed on your computer is conflicting with the Qt distributed with EMAN2. In most cases it gets solved by removing the Qt that comes with EMAN2 from EMAN2DIR/extlib/lib.
If you have problems compiling Scipion with OpenCV support (CUDA version >=6.5), e.g. opencv-2.4.9 compilation fails with an error:
Error: target 'software/lib/libopencv_core.so' not built (after running 'make install > /home/user/soft/scipion/software/log/opencv_make_install.log 2>&1')
And log file (software/log/opencv_make.log) shows something like:
[ 9%] Building NVCC (Device) object modules/core/CMakeFiles/cuda_compile.dir/src/cuda/cuda_compile_generated_gpu_mat.cu.o
/usr/include/string.h: In function ‘void* __mempcpy_inline(void, const void, size_t)’:
/usr/include/string.h:652:42: error: ‘memcpy’ was not declared in this scope
return (char *) memcpy (__dest, __src, __n) + __n;
^
CMake Error at cuda_compile_generated_gpu_mat.cu.o.cmake:264 (message):
Error generating file
/home/mag/opencv/build_opencv_master/modules/core/CMakeFiles/cuda_compile.dir/src/cuda/./cuda_compile_generated_gpu_mat.cu.o
Then:
- Find the micro-architecture name for your GPU card, e.g. Kepler for K40 or Fermi for M2070 card
cd $SCIPION_HOME/software/tmp/opencv-2.4.9- Run
cmake -DCUDA_GENERATION=Kepler -DWITH_CUDA:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/path/to/scipion/software . > /path/to/scipion/software/log/opencv_cmake.log 2>&1substituting correct path and micro-architecture - Modify source files in opencv-2.4.9 folder according to this and this fix
- Re-run
scipion install, opencv now should compile cleanly
This likely happens because your machine doesn't have a default program to open bibtex. Type this in your terminal to set gedit as your default program for bibtex files:
xdg-mime default gedit.desktop text/x-bibtex