Hi all,
I'm trying to build Relion 3.1b (commit 6c49f845, fresh as of now) and get run into some problem with the tiff_converter.cpp (see cmake and make output for error below). Previously, I successfully built 3.1b from October this year on the same system. Any help would be appreciated.
Regards,
Daniel
> cmake -DCMAKE_INSTALL_PREFIX=${HOME}/software/relion3.1_20191213 -DFORCE_OWN_FLTK=ON -DBUILD_SHARED_LIBS=ON ..
-- The C compiler identification is GNU 4.4.7
-- The CXX compiler identification is GNU 4.4.7
-- 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
-- Detecting C compile features
-- Detecting C compile features - 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
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- BUILD TYPE set to the default type: 'Release'
-- Setting fallback CUDA_ARCH=35
-- CUDA enabled - Building CUDA-accelerated version of RELION
-- Setting cpu precision to double
-- Setting accelerated code precision to single
-- Looking for include file pthread.h
-- Looking for include file pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
-- Found CUDA: /usr/local/cuda-7.5 (found version "7.5")
-- Using cuda wrapper to compile....
-- Cuda version is >= 7.5 and single-precision build, enable double usage warning.
-- Found MPI_C: /usr/lib64/openmpi/lib/libmpi.so
-- Found MPI_CXX: /usr/lib64/openmpi/lib/libmpi_cxx.so;/usr/lib64/openmpi/lib/libmpi.so
-- MPI_INCLUDE_PATH : /usr/include/openmpi-x86_64
-- MPI_LIBRARIES : /usr/lib64/openmpi/lib/libmpi_cxx.so;/usr/lib64/openmpi/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH : /usr/include/openmpi-x86_64
-- MPI_CXX_LIBRARIES : /usr/lib64/openmpi/lib/libmpi_cxx.so;/usr/lib64/openmpi/lib/libmpi.so
-- CMAKE_C_COMPILER : /usr/bin/cc
-- CMAKE_CXX_COMPILER : /usr/bin/c++
-- MPI_C_COMPILER : /usr/lib64/openmpi/bin/mpicc
-- MPI_CXX_COMPILER : /usr/lib64/openmpi/bin/mpicxx
-- CMAKE_CXX_COMPILER_ID : GNU
-- CMAKE_C_COMPILER : /usr/lib64/openmpi/bin/mpicc
-- CMAKE_CXX_COMPILER : /usr/lib64/openmpi/bin/mpicxx
-- MPI_C_COMPILER : /usr/lib64/openmpi/bin/mpicc
-- MPI_CXX_COMPILER : /usr/lib64/openmpi/bin/mpicxx
-- 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 previously built non-system FLTK libraries that will be used.
-- FLTK_INCLUDE_DIR: /home/larsson/src/relion3/external/fltk/include
-- FLTK_LIBRARIES: /home/larsson/src/relion3/external/fltk/lib/libfltk.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 "3.9.4")
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.3")
-- Found PNG: /usr/lib64/libpng.so (found version "1.2.49")
BUILD_SHARED_LIBS = ON
-- Building shared libs (smaller build size and binaries)
Running apps/CMakeLists.txt...
-- CMAKE_BINARY_DIR:/home/larsson/src/relion3/build3.1_20191213
-- Git commit ID: 6c49f8450c3e9152df1c0cba593bb3c5a44bdb26
TIFF FOUND
PNG 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
OPENMP FOUND
-- Configuring done
-- Generating done
-- Build files have been written to: /home/larsson/src/relion3/build3.1_20191213
> make -j 20
Scanning dependencies of target copy_scripts
[ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/cuda_kernels/relion_gpu_util_generated_helper.cu.o
[ 2%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_ml_optimiser.cu.o
[ 2%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o
[ 2%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o
[ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_backprojector.cu.o
[ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o
[ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_benchmark_utils.cu.o
[ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o
[ 3%] Built target copy_scripts
Scanning dependencies of target relion_gpu_util
[ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o
[ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o
[ 3%] Linking CXX shared library ../../lib/librelion_gpu_util.so
[ 3%] Built target relion_gpu_util
Scanning dependencies of target relion_lib
[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_jobs.cpp.o
[ 3%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o
[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o
[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/matrix1d.cpp.o
[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o
[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/pipeline_control.cpp.o
[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o
[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_container.cpp.o
[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/mask.cpp.o
[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o
[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o
[ 7%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/tabfuncs.cpp.o
[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o
[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/transformations.cpp.o
[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o
[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/multidim_array.cpp.o
[ 9%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/CPlot2D.cpp.o
[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o
[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/metadata_table.cpp.o
[ 10%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o
[ 11%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/filename.cpp.o
[ 12%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o
/home/larsson/src/relion3/src/tiff_converter.cpp: In member function ‘void TIFFConverter::initialise(int, int)’:
/home/larsson/src/relion3/src/tiff_converter.cpp:286: error: ‘class FileName’ has no member named ‘back’
make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/tiff_converter.cpp.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[1]: *** [src/apps/CMakeFiles/relion_lib.dir/all] Error 2
make: *** [all] Error 2
När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/
E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy
########################################################################
To unsubscribe from the CCPEM list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
|