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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
440 stars 194 forks source link

build issues #852

Closed alisterburt closed 2 years ago

alisterburt commented 2 years ago

This is a template for reporting bugs. Please fill in as much information as you can.

Describe your problem

I am unable to build RELION successfully on the LMB cluster. I have previously built RELION successfully here but am now running into issues, any help would be much appreciated.

Environment:

Dataset: n/a

Job options: n/a

Error message:

cmake ..
cmake output
``` -- The C compiler identification is GNU 4.8.5 -- The CXX compiler identification is GNU 4.8.5 -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- BUILD TYPE set to the default type: 'Release' -- Setting fallback CUDA_ARCH=50 -- CUDA enabled - Building CUDA-accelerated version of RELION -- Setting cpu precision to double -- Setting accelerated code precision to single -- Found CUDA: /net/nfs1/public/EM/CUDA/cuda-10.2 (found version "10.2") -- Using cuda wrapper to compile.... -- Cuda version is >= 7.5 and single-precision build, enable double usage warning. -- Found MPI_C: /public/EM/OpenMPI/openmpi-4.1.1/build/lib/libmpi.so -- Found MPI_CXX: /public/EM/OpenMPI/openmpi-4.1.1/build/lib/libmpi.so -- MPI_INCLUDE_PATH : /public/EM/OpenMPI/openmpi-4.1.1/build/include -- MPI_LIBRARIES : /public/EM/OpenMPI/openmpi-4.1.1/build/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /public/EM/OpenMPI/openmpi-4.1.1/build/include -- MPI_CXX_LIBRARIES : /public/EM/OpenMPI/openmpi-4.1.1/build/lib/libmpi.so -- CMAKE_C_COMPILER : /usr/bin/cc -- CMAKE_CXX_COMPILER : /usr/bin/c++ -- MPI_C_COMPILER : /net/nfs1/public/EM/OpenMPI/openmpi-4.1.1/build/bin/mpicc -- MPI_CXX_COMPILER : /net/nfs1/public/EM/OpenMPI/openmpi-4.1.1/build/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so -- Looking for XOpenDisplay in /usr/lib64/libX11.so;/usr/lib64/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found X11: /usr/lib64/libX11.so -- Found FLTK: /lmb/home/aburt/relion4/external/fltk/lib/libfltk_images.so;/lmb/home/aburt/relion4/external/fltk/lib/libfltk_forms.so;/lmb/home/aburt/relion4/external/fltk/lib/libfltk.so -- X11 and FLTK were found -- FLTK_LIBRARIES: /lmb/home/aburt/relion4/external/fltk/lib/libfltk_images.so;/lmb/home/aburt/relion4/external/fltk/lib/libfltk_forms.so;/lmb/home/aburt/relion4/external/fltk/lib/libfltk.so;/usr/lib64/libSM.so;/usr/lib64/libICE.so;/usr/lib64/libX11.so;/usr/lib64/libXext.so;/usr/lib64/libm.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/lib64/libfftw3f.so;/usr/lib64/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for __sincos -- Looking for __sincos - not found -- Found TIFF: /usr/lib64/libtiff.so (found version "4.0.3") -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.7") -- Found PNG: /usr/lib64/libpng.so (found version "1.5.13") -- Checking class ranker model file... -- Found local copy of class ranker model BUILD_SHARED_LIBS = OFF -- Building static libs (larger build size and binaries) Running apps/CMakeLists.txt... -- CMAKE_BINARY_DIR:/lmb/home/aburt/relion4_2/build -- Git commit ID: e3537c82cf7a816df805f4e54c0bc12475803524 PNG FOUND -- Found JPEG: /usr/lib64/libjpeg.so JPEG FOUND -- Try OpenMP C flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Try OpenMP CXX flag = [-fopenmp] -- Performing Test OpenMP_FLAG_DETECTED -- Performing Test OpenMP_FLAG_DETECTED - Success -- Found OpenMP: -fopenmp -- Configuring done -- Generating done -- Build files have been written to: /lmb/home/aburt/relion4_2/build ``` 
make -j 24
make output
``` [ 0%] Built target class_ranker_model_file [ 0%] Built target relion_jaz_gpu_util [ 0%] Built target copy_scripts [ 1%] [ 1%] [ 2%] [ 2%] [ 2%] [ 2%] [ 2%] [ 2%] [ 2%] [ 2%] [ 3%] [ 3%] [ 3%] [ 4%] [ 4%] [ 4%] [ 4%] [ 4%] [ 4%] [ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o [ 5%] [ 5%] [ 5%] [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/renderEER.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/fftw.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeliner.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/postprocessing.cpp.o [ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o [ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/reconstructor_mpi.cpp.o [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/image.cpp.o [ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o [ 7%] Building 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src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/motion/three_hyperparameter_fit.cpp.o [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/motion/motion_refiner_mpi.cpp.o [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/motion/motion_helper.cpp.o [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/motion/motion_refiner.cpp.o [ 39%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/motion/motion_param_estimator.cpp.o [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/motion/gp_motion_fit.cpp.o [ 40%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/img_proc/filter_helper.cpp.o [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/tomo/backprojection_helper.cpp.o [ 41%] [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/io/star_converter.cpp.o Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/tomo/tomo_stack.cpp.o [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/programs/backproject_2d.cpp.o [ 41%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/programs/delete_blobs_2d.cpp.o [ 42%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/jaz/single_particle/programs/spa_backproject.cpp.o Linking CXX static library ../../lib/librelion_lib.a [ 61%] Built target relion_lib [ 61%] [ 61%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_projector_plan.cu.o [ 61%] [ 62%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_helper_functions.cu.o Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/./relion_gpu_util_generated_cuda_autopicker.cu.o Linking CXX static library ../../lib/librelion_gpu_util.a [ 62%] Built target relion_gpu_util Scanning dependencies of target add_tomogram_name Scanning dependencies of target catalogue_tomos Scanning dependencies of target Wiener_divide Scanning dependencies of target Zernike_test Scanning dependencies of target BP_test Scanning dependencies of target CTFPQ_test Scanning dependencies of target add_subset Scanning dependencies of target align_2d_classes Scanning dependencies of target align Scanning dependencies of target add_spheres Scanning dependencies of target blobs_from_points Scanning dependencies of target bin_stack Scanning dependencies of target analyse_dual_contrast Scanning dependencies of target autopick Scanning dependencies of target align_symmetry Scanning dependencies of target backproject_2d Scanning dependencies of target conversion_test Scanning dependencies of target convert_star Scanning dependencies of target align_mpi Scanning dependencies of target class_ranker Scanning dependencies of target compute_FCC Scanning dependencies of target autopick_mpi Linking CXX executable ../../bin/relion_tomo_convert_projections [ 62%] [ 62%] [ 62%] [ 62%] Building CXX object src/apps/CMakeFiles/Zernike_test.dir/Zernike_test.cpp.o [ 62%] [ 62%] [ 62%] Building CXX object src/apps/CMakeFiles/add_subset.dir/__/jaz/scripts/add_subset.cpp.o [ 62%] [ 63%] [ 63%] [ 63%] Building CXX object src/apps/CMakeFiles/add_tomogram_name.dir/__/jaz/scripts/add_tomogram_name.cpp.o [ 63%] [ 63%] Building CXX object src/apps/CMakeFiles/conversion_test.dir/__/jaz/scripts/conversion_test.cpp.o [ 63%] Building CXX object src/apps/CMakeFiles/convert_star.dir/convert_star.cpp.o Building CXX object src/apps/CMakeFiles/catalogue_tomos.dir/__/jaz/tomography/apps/catalogue_tomos.cpp.o [ 64%] [ 64%] [ 64%] [ 64%] Building CXX object src/apps/CMakeFiles/align_symmetry.dir/align_symmetry.cpp.o Building CXX object src/apps/CMakeFiles/bin_stack.dir/__/jaz/tomography/apps/bin_stack.cpp.o Building CXX object src/apps/CMakeFiles/CTFPQ_test.dir/__/jaz/scripts/CTFPQ_test.cpp.o Building CXX object src/apps/CMakeFiles/Wiener_divide.dir/__/jaz/tomography/apps/Wiener_divide.cpp.o Building CXX object src/apps/CMakeFiles/align.dir/__/jaz/tomography/apps/align.cpp.o Building CXX object src/apps/CMakeFiles/class_ranker.dir/class_ranker.cpp.o Building CXX object src/apps/CMakeFiles/align_2d_classes.dir/__/jaz/scripts/align_2d_classes.cpp.o [ 65%] [ 65%] [ 65%] Building CXX object src/apps/CMakeFiles/blobs_from_points.dir/__/jaz/scripts/blobs_from_points.cpp.o [ 65%] Building CXX object src/apps/CMakeFiles/align_mpi.dir/__/jaz/tomography/apps/align_mpi.cpp.o Building CXX object src/apps/CMakeFiles/autopick_mpi.dir/autopick_mpi.cpp.o Building CXX object src/apps/CMakeFiles/BP_test.dir/__/jaz/scripts/BP_test.cpp.o Building CXX object src/apps/CMakeFiles/analyse_dual_contrast.dir/__/jaz/scripts/analyse_dual_contrast.cpp.o Building CXX object src/apps/CMakeFiles/compute_FCC.dir/__/jaz/tomography/apps/compute_FCC.cpp.o Building CXX object src/apps/CMakeFiles/add_spheres.dir/__/jaz/tomography/apps/add_spheres.cpp.o Building CXX object src/apps/CMakeFiles/autopick.dir/autopick.cpp.o Building CXX object src/apps/CMakeFiles/backproject_2d.dir/__/jaz/single_particle/apps/backproject_2d.cpp.o Scanning dependencies of target box_PCA [ 66%] Building CXX object src/apps/CMakeFiles/box_PCA.dir/__/jaz/scripts/box_PCA.cpp.o [ 67%] Built target convert_projections Scanning dependencies of target convert_to_tiff [ 67%] Building CXX object src/apps/CMakeFiles/convert_to_tiff.dir/convert_to_tiff.cpp.o Linking CXX executable ../../bin/relion_Zernike_test Linking CXX executable ../../bin/relion_backproject_2d Linking CXX executable ../../bin/relion_exp_conversion_test Linking CXX executable ../../bin/relion_convert_star Linking CXX executable ../../bin/relion_exp_add_subset Linking CXX executable ../../bin/relion_convert_to_tiff [ 67%] [ 67%] Built target Zernike_test Built target conversion_test Linking CXX executable ../../bin/relion_tomo_compute_FCC Scanning dependencies of target ctf_mask_test Scanning dependencies of target convert_to_tiff_mpi [ 67%] [ 67%] Built target backproject_2d Linking CXX executable ../../bin/relion_tomo_align [ 68%] Building CXX object src/apps/CMakeFiles/convert_to_tiff_mpi.dir/convert_to_tiff_mpi.cpp.o Building CXX object src/apps/CMakeFiles/ctf_mask_test.dir/ctf_mask_test.cpp.o [ 68%] Built target convert_star [ 68%] Built target convert_to_tiff Scanning dependencies of target ctf_nyquist_test Scanning dependencies of target ctf_refine_mpi Scanning dependencies of target ctf_refine [ 68%] Built target add_subset Linking CXX executable ../../bin/relion_tomo_align_mpi [ 68%] [ 68%] Scanning dependencies of target ctf_toolbox Building CXX object src/apps/CMakeFiles/ctf_refine_mpi.dir/ctf_refine_mpi.cpp.o Building CXX object src/apps/CMakeFiles/ctf_nyquist_test.dir/ctf_nyquist_test.cpp.o [ 68%] Building CXX object src/apps/CMakeFiles/ctf_refine.dir/ctf_refine.cpp.o [ 68%] Building CXX object src/apps/CMakeFiles/ctf_toolbox.dir/ctf_toolbox.cpp.o Linking CXX executable ../../bin/relion_exp_add_tomogram_name [ 68%] Built target compute_FCC [ 68%] Built target align Linking CXX executable ../../bin/relion_tomo_add_spheres Linking CXX executable ../../bin/relion_autopick Linking CXX executable ../../bin/relion_exp_cuda_test Linking CXX executable ../../bin/relion_autopick_mpi [ 68%] Built target align_mpi Linking CXX executable ../../bin/relion_tomo_dark_erase [ 68%] Built target add_tomogram_name Scanning dependencies of target defilament Scanning dependencies of target defocus_stats [ 68%] [ 68%] Building CXX object src/apps/CMakeFiles/defocus_stats.dir/defocus_stats.cpp.o Building CXX object src/apps/CMakeFiles/defilament.dir/__/jaz/scripts/defilament.cpp.o [ 69%] Built target cuda_test Scanning dependencies of target delete_blobs [ 69%] Built target add_spheres [ 69%] Built target dark_erase Scanning dependencies of target delete_blobs_2d Scanning dependencies of target demodulate [ 70%] ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `HandleError(cudaError, char const*, int)': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x9f): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `LaunchHandleError(cudaError, char const*, int)': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x1c7): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `bool MetaDataTable::setValue(EMDLabel, int const&, long) [clone .constprop.188]': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x3b2): undefined reference to `MetaDataTable::addLabel(EMDLabel, std::string)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `bool MetaDataTable::setValue(EMDLabel, double const&, long) [clone .constprop.189]': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x47f): undefined reference to `MetaDataTable::addLabel(EMDLabel, std::string)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x505): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `LaunchHandleError(cudaError, char const*, int) [clone .constprop.193]': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x63d): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `HandleError(cudaError, char const*, int) [clone .constprop.194]': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x755): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `void runCenterFFT(AccPtr&, int, int, bool, int) [clone .constprop.183]': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x8f9): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `AutoPickerCuda::AutoPickerCuda(AutoPickerMpi*, int, char const*)': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x114e): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o):tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x19ca): more undefined references to `RelionError::RelionError(std::string const&, std::string const&, long)' follow ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `MultidimArray::resize(long, long, long, long) [clone .constprop.184]': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x28f1): undefined reference to `FileName::addExtension(std::string const&) const' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x2a1a): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x2d4c): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x2e2d): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x2ffc): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `AutoPickerCuda::autoPickOneMicrograph(FileName&, long)': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x3bb5): undefined reference to `MetaDataContainer::getValue(long, std::string&) const' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x652e): undefined reference to `FileName::compose(std::string const&, long, std::string const&, int)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x6700): undefined reference to `FileName::compose(std::string const&, long, std::string const&, int)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x6a4f): undefined reference to `FileName::compose(std::string const&, long, std::string const&, int)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x6c14): undefined reference to `FileName::compose(std::string const&, long, std::string const&, int)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x9684): undefined reference to `MetaDataTable::addLabel(EMDLabel, std::string)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0x9d07): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0xa5d8): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `AutoPickerCuda::run()': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text+0xa9be): undefined reference to `FileName::beforeLastOf(std::string const&) const' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `CudaCustomAllocator::alloc(unsigned long)': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN19CudaCustomAllocator5allocEm[_ZN19CudaCustomAllocator5allocEm]+0x2f9): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `CudaFFT::forward()': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN7CudaFFT7forwardEv[_ZN7CudaFFT7forwardEv]+0x9e): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `CudaFFT::backward()': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN7CudaFFT8backwardEv[_ZN7CudaFFT8backwardEv]+0x9e): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `AccPtr::hostAlloc()': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN6AccPtrIfE9hostAllocEv[_ZN6AccPtrIfE9hostAllocEv]+0x7b): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `AccPtr::AccPtr(unsigned long, CudaCustomAllocator*)': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN6AccPtrIfEC2EmP19CudaCustomAllocator[_ZN6AccPtrIfEC5EmP19CudaCustomAllocator]+0xa2): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o):tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN6AccPtrI6float2EC2EmP19CudaCustomAllocator[_ZN6AccPtrI6float2EC5EmP19CudaCustomAllocator]+0xa2): more undefined references to `RelionError::RelionError(std::string const&, std::string const&, long)' follow ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `MultidimArray::operator=(MultidimArray const&)': tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN13MultidimArrayIdEaSERKS0_[_ZN13MultidimArrayIdEaSERKS0_]+0x315): undefined reference to `FileName::addExtension(std::string const&) const' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN13MultidimArrayIdEaSERKS0_[_ZN13MultidimArrayIdEaSERKS0_]+0x6cd): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN13MultidimArrayIdEaSERKS0_[_ZN13MultidimArrayIdEaSERKS0_]+0x765): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN13MultidimArrayIdEaSERKS0_[_ZN13MultidimArrayIdEaSERKS0_]+0x862): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' tmpxft_0010c22f_00000000-5_cuda_autopicker.cudafe1.cpp:(.text._ZN13MultidimArrayIdEaSERKS0_[_ZN13MultidimArrayIdEaSERKS0_]+0xa83): undefined reference to `RelionError::RelionError(std::string const&, std::string const&, long)' ../../lib/librelion_gpu_util.a(relion_gpu_util_generated_cuda_autopicker.cu.o): In function `Image::writeIMAGIC(long, int, DataType)': ... more undefined references to `RelionError::RelionError(std::string const&, std::string const&, long)' follow collect2: error: ld returned 1 exit status make[2]: *** [bin/relion_autopick_mpi] Error 1 make[1]: *** [src/apps/CMakeFiles/autopick_mpi.dir/all] Error 2 make[1]: *** Waiting for unfinished jobs.... collect2: error: ld returned 1 exit status make[2]: *** [bin/relion_autopick] Error 1 make[1]: *** [src/apps/CMakeFiles/autopick.dir/all] Error 2 [ 70%] [ 70%] Building CXX object src/apps/CMakeFiles/delete_blobs_2d.dir/__/jaz/single_particle/apps/delete_blobs_2d.cpp.o Building CXX object src/apps/CMakeFiles/demodulate.dir/demodulate.cpp.o Linking CXX executable ../../bin/relion_class_ranker Linking CXX executable ../../bin/relion_convert_to_tiff_mpi [ 70%] Built target convert_to_tiff_mpi [ 70%] Built target class_ranker Linking CXX executable ../../bin/relion_ctf_refine_mpi Linking CXX executable ../../bin/relion_ctf_refine Linking CXX executable ../../bin/relion_defocus_stats [ 70%] [ 70%] Built target ctf_refine Built target ctf_refine_mpi Linking CXX executable ../../bin/relion_tomo_delete_blobs [ 70%] Built target defocus_stats Linking CXX executable ../../bin/relion_delete_blobs_2d Linking CXX executable ../../bin/relion_ctf_nyquist_test [ 70%] Built target delete_blobs [ 70%] Built target delete_blobs_2d [ 70%] Built target ctf_nyquist_test Linking CXX executable ../../bin/relion_tomo_catalogue_tomos Linking CXX executable ../../bin/relion_align_symmetry Linking CXX executable ../../bin/relion_exp_CTFPQ_test [ 70%] Built target align_symmetry [ 70%] Built target catalogue_tomos Linking CXX executable ../../bin/relion_ctf_mask_test [ 70%] Built target CTFPQ_test Linking CXX executable ../../bin/relion_tomo_bin_stack [ 70%] Built target ctf_mask_test Linking CXX executable ../../bin/relion_exp_align_2d_classes [ 70%] Built target bin_stack [ 70%] Built target align_2d_classes Linking CXX executable ../../bin/relion_ctf_toolbox Linking CXX executable ../../bin/relion_exp_BP_test [ 70%] Built target ctf_toolbox [ 70%] Built target BP_test Linking CXX executable ../../bin/relion_tomo_Wiener_divide Linking CXX executable ../../bin/relion_demodulate [ 70%] Built target Wiener_divide [ 70%] Built target demodulate Linking CXX executable ../../bin/relion_exp_blobs_from_points [ 70%] Built target blobs_from_points Linking CXX executable ../../bin/relion_exp_analyse_dual_contrast [ 70%] Built target analyse_dual_contrast Linking CXX executable ../../bin/relion_exp_defilament [ 70%] Built target defilament Linking CXX executable ../../bin/relion_exp_box_PCA [ 70%] Built target box_PCA make: *** [all] Error 2 ```

full error message was too long to paste so has been truncated in the middle of the sea of undefined references

biochem-fan commented 2 years ago

My guess is that your CUDA is calling a different version of g++ from the one used to compile non-CUDA objects (i.e. 4.8.5).

The build scripts for binaries in /public are as follows:

GPU version (built in csh):

setenv LD_LIBRARY_PATH /public/EM/OpenMPI/openmpi-2.0.1/build/lib:$LD_LIBRARY_PATH
setenv PATH /public/EM/OpenMPI/openmpi-2.0.1/build/bin:$PATH
setenv CC /public/gcc/6_2_0/bin/gcc
setenv CXX /public/gcc/6_2_0/bin/g++
setenv LD_LIBRARY_PATH /public/gcc/6_2_0/lib64:$LD_LIBRARY_PATH
setenv PATH /public/gcc/6_2_0/bin:/public/gnu/bin:$PATH
setenv PATH /public/EM/CUDA/cuda-10.1/bin:$PATH
setenv LD_LIBRARY_PATH /public/EM/CUDA/cuda-10.1/lib64:$LD_LIBRARY_PATH
setenv CUDA_HOME /public/EM/CUDA/cuda-10.1
/public/gnu/bin/cmake -DCMAKE_BUILD_TYPE=Release -DCUDA_ARCH=61 -DFORCE_OWN_FFTW=ON -DFORCE_OWN_FLTK=ON -DTORCH=ON ..

CPU accelerated version (built in bash, because ICC's script does not support csh):

source /public/gcc/gcc10_2_0.sh 
source /public/compilers/intel-2021.3/setvars.sh
export OMPI_CC=icc
export OMPI_CXX=icpc
export PATH=/public/EM/OpenMPI/openmpi-4.0.1/build/bin:$PATH
export LANG=en_US.utf8
export LC_ALL=en_US.utf8

/public/gnu/bin/cmake .. -DMKLFFT=ON -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DMPI_C_COMPILER=mpicc -DMPI_CXX_COMPILER=mpicxx -DALTCPU=ON -DGUI=OFF -DCMAKE_C_FLAGS="-O3 -ip -g -xCOMMON-AVX512 -restrict " -DCMAKE_CXX_FLAGS="-O3 -ip -g -xCOMMON-AVX512 -restrict "
alisterburt commented 2 years ago

@biochem-fan thank you for your response, this was extremely useful