'xmipp.conf' detected. Checking configuration ------------------------------  'xmipp.conf' is already checked. Set VERIFIED=False to re-checked Getting Dependencies -------------------------------------  Checkouting CTPL ...  git checkout master Already on 'master' Your branch is up to date with 'origin/master'. Already up to date. Getting sources -------------------------------------  Checkouting xmippCore ... Already up to date.  Checkouting xmippViz ... Already up to date.  Checkouting scipion-em-xmipp ... Already up to date.  Checkouting xmipp ... Already up to date. Building Dependencies ------------------------------------- Compiling -------------------------------------------  scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: `lib/libXmippCore.so' is up to date. scons: `lib/xmippCore.so' is up to date. scons: done building targets.  scons -j8 scons: Reading SConscript files ... scons: done reading SConscript files. scons: Building targets ... scons: `lib/libXmipp.so' is up to date. scons: `lib/_swig_frm.so' is up to date. mpiCC -o libraries/parallel/mpi_angular_accuracy_pca.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_angular_accuracy_pca.cpp mpiCC -o libraries/parallel/mpi_angular_class_average.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_angular_class_average.cpp mpiCC -o libraries/parallel/mpi_angular_continuous_assign.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_angular_continuous_assign.cpp mpiCC -o libraries/parallel/mpi_angular_projection_matching.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_angular_projection_matching.cpp mpiCC -o libraries/parallel/mpi_angular_sph_alignment.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_angular_sph_alignment.cpp mpiCC -o libraries/parallel/mpi_classify_CL2D.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_classify_CL2D.cpp mpiCC -o libraries/parallel/mpi_classify_CL2D_core_analysis.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_classify_CL2D_core_analysis.cpp mpiCC -o libraries/parallel/mpi_classify_CLTomo_prog.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_classify_CLTomo_prog.cpp mpiCC -o libraries/parallel/mpi_classify_FTTRI.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_classify_FTTRI.cpp mpiCC -o libraries/parallel/mpi_image_rotational_pca.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_image_rotational_pca.cpp mpiCC -o libraries/parallel/mpi_image_sort.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_image_sort.cpp mpiCC -o libraries/parallel/mpi_ml_align2d.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_ml_align2d.cpp mpiCC -o libraries/parallel/mpi_multireference_aligneability.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_multireference_aligneability.cpp mpiCC -o libraries/parallel/mpi_nma_alignment.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_nma_alignment.cpp mpiCC -o libraries/parallel/mpi_nma_alignment_vol.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_nma_alignment_vol.cpp mpiCC -o libraries/parallel/mpi_performance_test.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_performance_test.cpp mpiCC -o libraries/parallel/mpi_project_XR.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_project_XR.cpp mpiCC -o libraries/parallel/mpi_reconstruct_admm.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_reconstruct_admm.cpp mpiCC -o libraries/parallel/mpi_reconstruct_art.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_reconstruct_art.cpp mpiCC -o libraries/parallel/mpi_reconstruct_fourier.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_reconstruct_fourier.cpp mpiCC -o libraries/parallel/mpi_reconstruct_fourier_accel.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_reconstruct_fourier_accel.cpp mpiCC -o libraries/parallel/mpi_reconstruct_significant.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_reconstruct_significant.cpp mpiCC -o libraries/parallel/mpi_reconstruct_wbp.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_reconstruct_wbp.cpp mpiCC -o libraries/parallel/mpi_run.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_run.cpp mpiCC -o libraries/parallel/mpi_transform_adjust_image_grey_levels.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_transform_adjust_image_grey_levels.cpp mpiCC -o libraries/parallel/mpi_validation_nontilt.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_validation_nontilt.cpp mpiCC -o libraries/parallel/mpi_volumeset_align.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/mpi_volumeset_align.cpp mpiCC -o libraries/parallel/xmipp_mpi.os -c -mtune=native -march=native -std=c++11 -O3 -I../ -I/home/guest/miniconda3/include -fPIC -I/home/guest/miniconda3/include/python3.8 -I/home/guest/miniconda3/lib/python3.8/site-packages/numpy/core/include -Iexternal -Ilibraries -I/home/guest/xmipp-bundle/xmipp/src/xmippCore libraries/parallel/xmipp_mpi.cpp g++ -o bin/xmipp_angular_accuracy_pca applications/programs/angular_accuracy_pca/angular_accuracy_pca_main.o -L/home/guest/xmipp-bundle/xmipp/src/xmippCore/lib -Llib -Llib -L/home/guest/miniconda3/lib -L/usr/lib -L/usr/lib64/openmpi3/lib -L/usr/lib -L/usr/lib64/openmpi3/lib -L/usr/local/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore g++ -o bin/xmipp_angular_break_symmetry applications/programs/angular_break_symmetry/angular_break_symmetry_main.o -L/home/guest/xmipp-bundle/xmipp/src/xmippCore/lib -Llib -Llib -L/home/guest/miniconda3/lib -L/usr/lib -L/usr/lib64/openmpi3/lib -L/usr/lib -L/usr/lib64/openmpi3/lib -L/usr/local/IMOD/lib -lXmipp -lhdf5 -lhdf5_cpp -lfftw3 -lfftw3_threads -ljpeg -ltiff -lfftw3f -lfftw3f_threads -lpthread -lpython3.8 -lXmippCore lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' /home/guest/xmipp-bundle/xmipp/src/xmippCore/lib/libXmippCore.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' /home/guest/xmipp-bundle/xmipp/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' /home/guest/xmipp-bundle/xmipp/src/xmippCore/lib/libXmippCore.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_accuracy_pca] Error 1 lib/libXmipp.so: undefined reference to `non-virtual thunk to H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `H5::H5File::throwException(std::string const&, std::string const&) const' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' /home/guest/xmipp-bundle/xmipp/src/xmippCore/lib/libXmippCore.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' /home/guest/xmipp-bundle/xmipp/src/xmippCore/lib/libXmippCore.so: undefined reference to `H5::H5Location::getFileName() const' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' lib/libXmipp.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' /home/guest/xmipp-bundle/xmipp/src/xmippCore/lib/libXmippCore.so: undefined reference to `void produceSplineCoefficients(int, MultidimArray&, MultidimArray const&)' collect2: error: ld returned 1 exit status scons: *** [bin/xmipp_angular_break_symmetry] Error 1 scons: building terminated because of errors.  Some error occurred during the compilation of 'xmipp' ('bin/xmipp_angular_break_symmetry').