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Hi All,
IM compiling freesurfer, after many bumps reached a point i havent figured out how to proceed.
My setup:
Centos7 GCC 4.8.5 Freesurfer 6.0.0
Dependencies as in /usr/pubsw/packages/ - KWWWidgets : CVS-vtk560 - petsc : 2.3.3-p13 - mni 1.5 - tcltktixblt : 8.4.6 - wxWidgets wxGTK-2.8.9 - xawplus: 3.1.0
Dependencies I built and installed in /usr/pubsw/packages/ - dcmtk: 3.6.4 - itk: 4.9.1 - vxl: v1.17.0
The rest of dependencies installed through RPM packages (yum) system-wise.. including VTK, etc ...
then I do:
FS_PACKAGES_DIR=/usr/pubsw/packages VTK_DIR=/usr VTK_LIBRARIES=/usr/lib64 PREFIX=/share/apps/NYUAD3/freesurfer/6.0.0 CMAKE_BUILD_TYPE=Release PETSC_DIR=/usr/pubsw/packages/petsc/current ITK_DIR=/usr/pubsw/packages/itk/4.9.1/lib/cmake/ITK-4.9/ OpenGL_GL_PREFERENCE=GLVND DANN_LIBRARIES=/usr/lib64
export CPATH=$CPATH:/usr/pubsw/packages/itk/4.9.1/include/ITK-4.9/
cmake3 ../freesurfer -DFS_PACKAGES_DIR=${FS_PACKAGES_DIR} -DVTK_LIBRARIES=${VTK_LIBRARIES} -DVTK_DIR=${VTK_DIR} -DCMAKE_INSTALL_PREFIX=${PREFIX} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DPETSC_DIR=${PETSC_DIR} -DITK_DIR=${ITK_DIR} -DOpenGL_GL_PREFERENCE=${OpenGL_GL_PREFERENCE} -DANN_LIBRARIES=${DANN_LIBRARIES} -DUSE_PYTHON_INCLUDE_DIR=ON -DCMAKE_EXE_LINKER_FLAGS="-L/usr/lib64/ -lglut"
make
NOTE: the glut thing is because if I let the system use the libglut inside packages dir in the source code ... compilation breaks with : /bin/ld: ../packages/glut/libglut.a(glut_win.c.o): undefined reference to symbol 'glXCreateContextWithConfigSGIX'
Well, the thing is that will all the above, the compilation breaks with this message:
[ 57%] Built target trk_tools [ 57%] Built target streamlineFilter [ 57%] Built target testOrientationPlanesFromParcellation [ 57%] Building CXX object anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o /scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx: In function ‘int main(int, char**)’: /scratch/apps/singularity-sandboxes/braimcore-sandbox/SOFTWARE/FREESURFER/freesurfer/anatomicuts/AnatomiCuts_correspondences.cxx:648:62: error: expected primary-expression before ‘double’ vcl_vector<unsigned int> assign = vnl_hungarian_algorithm<double>( distances ); //.GetAssignmentVector(); ^ make[2]: *** [anatomicuts/CMakeFiles/dmri_match.dir/AnatomiCuts_correspondences.cxx.o] Error 1 make[1]: *** [anatomicuts/CMakeFiles/dmri_match.dir/all] Error 2 make: *** [all] Error 2
Any help !?? will be highly appreciated
thanks!
*Jorge A. Naranjo* HPC Computational Specialist NYU Abu Dhabi Office Tel (UAE): +971 2 628 4750 Mobile (UAE): +971 56 319 2814
New York University - Abu Dhabi (NYUAD) Saadiyat Campus - A2, Room-131 P.O. Box 129188 Abu Dhabi, United Arab Emirates
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