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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
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FLTK error in relion3.0 installation #874

Closed eariascib closed 2 years ago

eariascib commented 2 years ago

Good evening,

I am trying to install relion3.0 to access and re-process some jobs of a couple of years old dataset. However, I obtain an error while downloading the FTLK libraries (see below). Is the link to download this files still valid?

I would be very grateful if you could give me some assistance to solve this issue.

Kind regards, Ernesto.

Environment:

OS: Linux Mint 18.1. Linux kernel 4.4.0-53-generic MPI runtime: mpich-3.1.4 RELION version Relion4.0 Memory: 128 GB GPU: 2x GTX 1080Ti CUDA 11.1

Error message:

osaka build # cmake -DCUDA_ARCH=61 .. -- The C compiler identification is GNU 9.4.0 -- The CXX compiler identification is GNU 9.4.0 -- 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' -- Using provided CUDA_ARCH=61 -- CUDA enabled - Building CUDA-accelerated version of RELION -- Setting cpu precision to double -- Setting accelerated code precision to single -- Looking for pthread.h -- Looking for 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 (found version "11.1") -- Using cuda wrapper to compile.... -- Cuda version is >= 7.5 and single-precision build, enable double usage warning. -- Found MPI_C: /usr/local/mpich-3.1.4/lib/libmpi.so
-- Found MPI_CXX: /usr/local/mpich-3.1.4/lib/libmpicxx.so;/usr/local/mpich-3.1.4/lib/libmpi.so
-- MPI_INCLUDE_PATH : /usr/local/mpich-3.1.4/include -- MPI_LIBRARIES : /usr/local/mpich-3.1.4/lib/libmpicxx.so;/usr/local/mpich-3.1.4/lib/libmpi.so -- MPI_CXX_INCLUDE_PATH : /usr/local/mpich-3.1.4/include -- MPI_CXX_LIBRARIES : /usr/local/mpich-3.1.4/lib/libmpicxx.so;/usr/local/mpich-3.1.4/lib/libmpi.so -- CMAKE_C_COMPILER : /usr/bin/cc -- CMAKE_CXX_COMPILER : /usr/bin/c++ -- MPI_C_COMPILER : /usr/local/mpich-3.1.4/bin/mpicc -- MPI_CXX_COMPILER : /usr/local/mpich-3.1.4/bin/mpicxx -- CMAKE_CXX_COMPILER_ID : GNU -- CMAKE_C_COMPILER : /usr/local/mpich-3.1.4/bin/mpicc -- CMAKE_CXX_COMPILER : /usr/local/mpich-3.1.4/bin/mpicxx -- MPI_C_COMPILER : /usr/local/mpich-3.1.4/bin/mpicc -- MPI_CXX_COMPILER : /usr/local/mpich-3.1.4/bin/mpicxx -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/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/lib/x86_64-linux-gnu/libX11.so -- Could NOT find FLTK (missing: FLTK_INCLUDE_DIR FLTK_FLUID_EXECUTABLE) -- No FLTK installation was found

-- -------- NO EXISTING FLTK LIBRARIES WHERE FOUND. ------- -- -------------- FLTK WILL BE DOWNLOADED AND ------------- -- --------------- BUILT DURING COMPILE-TIME. -------------

-- ---- A WORKING INTERNET CONNECTION WILL BE REQUIRED. ---

-- no previous fltk found, the following paths are set for libs/headers TO BE built -- FLTK_INCLUDE_DIR: /usr/local/relion-3.0/external/fltk/include -- FLTK_LIBRARIES: /usr/local/relion-3.0/external/fltk/lib/libfltk.so -- Found FFTW -- FFTW_PATH: /usr/include -- FFTW_INCLUDES: /usr/include -- FFTW_LIBRARIES: /usr/local/lib/libfftw3f.so;/usr/local/lib/libfftw3.so -- Looking for sincos -- Looking for sincos - found -- Looking for sincos -- Looking for sincos - not found -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.0.6") BUILD_SHARED_LIBS = OFF -- Building static libs (larger build size and binaries) Running apps/CMakeLists.txt... -- CMAKE_BINARY_DIR:/usr/local/relion-3.0/build TIFF 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: /usr/local/relion-3.0/build osaka build # make -j 6 Scanning dependencies of target copy_scripts [ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/relion_gpu_util_generated_cuda_projector.cu.o Scanning dependencies of target OWN_FLTK [ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/relion_gpu_util_generated_cuda_helper_functions.cu.o [ 2%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/cuda_kernels/relion_gpu_util_generated_helper.cu.o [ 3%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_ml_optimiser.cu.o [ 4%] Creating directories for 'OWN_FLTK' [ 4%] Built target copy_scripts [ 4%] Performing download step (download, verify and extract) for 'OWN_FLTK' [ 4%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/relion_gpu_util_generated_cuda_projector_plan.cu.o -- downloading... src='https://drive.google.com/uc?export=download&id=0B942d76zVnSeazZWcExRaXIyVDg' dst='/usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz' timeout='none' -- downloading... done -- verifying file... file='/usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz' -- MD5 hash of /usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz does not match expected value expected: 9ccdb0d19dc104b87179bd9fd10822e3 actual: 0fffe091602069287593150ca8122a31 Retrying download.

-- downloading... src='https://drive.google.com/uc?export=download&id=0B942d76zVnSeazZWcExRaXIyVDg' dst='/usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz' timeout='none' -- downloading... done -- MD5 hash of /usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz does not match expected value expected: 9ccdb0d19dc104b87179bd9fd10822e3 actual: 6a6902fe2f56ae1945f66e57644f216c Retrying download.

-- downloading... src='https://drive.google.com/uc?export=download&id=0B942d76zVnSeazZWcExRaXIyVDg' dst='/usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz' timeout='none' -- downloading... done -- MD5 hash of /usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz does not match expected value expected: 9ccdb0d19dc104b87179bd9fd10822e3 actual: 2a3fc51d758aae9caab15f902f8bbea8 Retrying download.

-- downloading... src='https://drive.google.com/uc?export=download&id=0B942d76zVnSeazZWcExRaXIyVDg' dst='/usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz' timeout='none' [ 4%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir/__/acc/cuda/relion_gpu_util_generated_cuda_backprojector.cu.o -- downloading... done CMake Error at /usr/local/relion-3.0/build/OWN_FLTK-prefix/src/OWN_FLTK-stamp/verify-OWN_FLTK.cmake:27 (message): error: MD5 hash of

/usr/local/relion-3.0/external/fltk/fltk-1.3.3-source.tar.gz

does not match expected value

expected: 9ccdb0d19dc104b87179bd9fd10822e3
  actual: 296c200839c014e0332196168537ddba

CMakeFiles/OWN_FLTK.dir/build.make:89: recipe for target 'OWN_FLTK-prefix/src/OWN_FLTK-stamp/OWN_FLTK-download' failed make[2]: [OWN_FLTK-prefix/src/OWN_FLTK-stamp/OWN_FLTK-download] Error 1 CMakeFiles/Makefile2:104: recipe for target 'CMakeFiles/OWN_FLTK.dir/all' failed make[1]: [CMakeFiles/OWN_FLTK.dir/all] Error 2 make[1]: Waiting for unfinished jobs.... [ 5%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/relion_gpu_util_generated_cuda_benchmark_utils.cu.o [ 5%] Building NVCC (Device) object src/apps/CMakeFiles/relion_gpu_util.dir//acc/cuda/relion_gpu_util_generated_cuda_autopicker.cu.o Scanning dependencies of target relion_gpu_util [ 5%] Linking CXX static library ../../lib/librelion_gpu_util.a [ 5%] Built target relion_gpu_util Makefile:138: recipe for target 'all' failed make: [all] Error 2 osaka build #

biochem-fan commented 2 years ago

Download https://www.fltk.org/pub/fltk/1.3.3/fltk-1.3.3-source.tar.gz and put it in the external/fltk directory.

eariascib commented 2 years ago

We were able to compile the program following your suggestions. Thank you very much for your help! Best, Ernesto.