Hi,
Please don't remove CC to CCPEM.
This is strange.
> -- Found TIFF: /localhome/bssfh/libtiff/usr/local/lib64/libtiff.so.5 (found version "4.4.0")
This indicates that libtiff was found properly, but
> cd /localhome/bssfh/relion4/relion/build/src/apps && /usr/lib64/openmpi/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DHAVE_PNG -DHAVE_SINCOS -DHAVE_TIFF
> -DINSTALL_LIBRARY_DIR=/usr/local/lib/ -DSOURCE_DIR=/localhome/bssfh/relion4/relion/src/ -D_CUDA_ENABLED -fopenmp -std=c++11 -O3 -DNDEBUG
> -I/usr/include/openmpi-x86_64 -I/localhome/bssfh/relion4/relion -I/localhome/bssfh/relion4/relion/external/fltk/include -I/usr/local/cuda/include
> -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /localhome/bssfh/relion4/relion/src/autopicker.cpp
the path is not passed to the compiler via -I option.
What happens if you also add -DTIFF_FOUND=1 to cmake? Please delete the build directory
before trying.
Best regards,
Takanori Nakane
On 2022/06/10 18:20, Samuel Haysom [RPG] wrote:
> Hi Takanori,
>
> Yes I’ve tried deleting the build/ directory and also completely deleting the RELION directory and re downloading it, neither of which change the error.
>
> I just re-tried the compilation process using the command you recommended.
>
> $ cmake .. -DTIFF_INCLUDE_DIR="/localhome/bssfh/libtiff/usr/local/include/" -DTIFF_LIBRARY="/localhome/bssfh/libtiff/usr/local/lib64/libtiff.so.5”
>
> Gives 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: /usr/local/cuda (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
> -- 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
> -- Could NOT find FLTK (missing: FLTK_LIBRARIES FLTK_INCLUDE_DIR)
> -- No FLTK installation was found
> -- Found previously built non-system FLTK libraries that will be used.
> -- FLTK_INCLUDE_DIR: /localhome/bssfh/relion4/relion/external/fltk/include
> -- FLTK_LIBRARIES: /localhome/bssfh/relion4/relion/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: /localhome/bssfh/libtiff/usr/local/lib64/libtiff.so.5 (found version "4.4.0")
> -- 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:/localhome/bssfh/relion4/relion/build
> -- Git commit ID: 9b23e50e5d8f51b16e6f315e3b59777b5c44cc35
> PNG FOUND
> -- Could NOT find JPEG (missing: JPEG_LIBRARY JPEG_INCLUDE_DIR)
> JPEG NOT 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: /localhome/bssfh/relion4/relion/build
>
> $ VERBOSE=1 make -j1
>
> /usr/bin/cmake -H/localhome/bssfh/relion4/relion -B/localhome/bssfh/relion4/relion/build --check-build-system CMakeFiles/Makefile.cmake 0
> /usr/bin/cmake -E cmake_progress_start /localhome/bssfh/relion4/relion/build/CMakeFiles /localhome/bssfh/relion4/relion/build/CMakeFiles/progress.marks
> make -f CMakeFiles/Makefile2 all
> make[1]: Entering directory `/localhome/bssfh/relion4/relion/build'
> make -f CMakeFiles/class_ranker_model_file.dir/build.make CMakeFiles/class_ranker_model_file.dir/depend
> make[2]: Entering directory `/localhome/bssfh/relion4/relion/build'
> cd /localhome/bssfh/relion4/relion/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /localhome/bssfh/relion4/relion
> /localhome/bssfh/relion4/relion /localhome/bssfh/relion4/relion/build /localhome/bssfh/relion4/relion/build
> /localhome/bssfh/relion4/relion/build/CMakeFiles/class_ranker_model_file.dir/DependInfo.cmake --color=
> Dependee "/localhome/bssfh/relion4/relion/build/CMakeFiles/class_ranker_model_file.dir/DependInfo.cmake" is newer than depender
> "/localhome/bssfh/relion4/relion/build/CMakeFiles/class_ranker_model_file.dir/depend.internal".
> Dependee "/localhome/bssfh/relion4/relion/build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender
> "/localhome/bssfh/relion4/relion/build/CMakeFiles/class_ranker_model_file.dir/depend.internal".
> Scanning dependencies of target class_ranker_model_file
> make[2]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> make -f CMakeFiles/class_ranker_model_file.dir/build.make CMakeFiles/class_ranker_model_file.dir/build
> make[2]: Entering directory `/localhome/bssfh/relion4/relion/build'
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/external/torch_models/class_ranker/class_ranker_0.1.3_torch_1.0.1.pt
> /localhome/bssfh/relion4/relion/build/bin/relion_class_ranker_default_model.pt <http://relion_class_ranker_default_model.pt>
> make[2]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> /usr/bin/cmake -E cmake_progress_report /localhome/bssfh/relion4/relion/build/CMakeFiles
> [ 0%] Built target class_ranker_model_file
> make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/depend
> make[2]: Entering directory `/localhome/bssfh/relion4/relion/build'
> cd /localhome/bssfh/relion4/relion/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /localhome/bssfh/relion4/relion
> /localhome/bssfh/relion4/relion /localhome/bssfh/relion4/relion/build /localhome/bssfh/relion4/relion/build
> /localhome/bssfh/relion4/relion/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake --color=
> Dependee "/localhome/bssfh/relion4/relion/build/CMakeFiles/copy_scripts.dir/DependInfo.cmake" is newer than depender
> "/localhome/bssfh/relion4/relion/build/CMakeFiles/copy_scripts.dir/depend.internal".
> Dependee "/localhome/bssfh/relion4/relion/build/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender
> "/localhome/bssfh/relion4/relion/build/CMakeFiles/copy_scripts.dir/depend.internal".
> Scanning dependencies of target copy_scripts
> make[2]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> make -f CMakeFiles/copy_scripts.dir/build.make CMakeFiles/copy_scripts.dir/build
> make[2]: Entering directory `/localhome/bssfh/relion4/relion/build'
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/star_printtable /localhome/bssfh/relion4/relion/build/bin/relion_star_printtable
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/star_plottable /localhome/bssfh/relion4/relion/build/bin/relion_star_plottable
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/star_loopheader /localhome/bssfh/relion4/relion/build/bin/relion_star_loopheader
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/star_datablock_stack /localhome/bssfh/relion4/relion/build/bin/relion_star_datablock_stack
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/star_datablock_singlefiles
> /localhome/bssfh/relion4/relion/build/bin/relion_star_datablock_singlefiles
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/star_datablock_ctfdat
> /localhome/bssfh/relion4/relion/build/bin/relion_star_datablock_ctfdat
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/qsub.csh /localhome/bssfh/relion4/relion/build/bin/relion_qsub.csh
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/it.py /localhome/bssfh/relion4/relion/build/bin/relion_it.py
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/schemegui.py /localhome/bssfh/relion4/relion/build/bin/relion_schemegui.py
> /usr/bin/cmake -E copy /localhome/bssfh/relion4/relion/scripts/class_ranker.py /localhome/bssfh/relion4/relion/build/bin/relion_class_ranker.py
> make[2]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> /usr/bin/cmake -E cmake_progress_report /localhome/bssfh/relion4/relion/build/CMakeFiles
> [ 0%] Built target copy_scripts
> make -f src/apps/CMakeFiles/relion_jaz_gpu_util.dir/build.make src/apps/CMakeFiles/relion_jaz_gpu_util.dir/depend
> make[2]: Entering directory `/localhome/bssfh/relion4/relion/build'
> /usr/bin/cmake -E cmake_progress_report /localhome/bssfh/relion4/relion/build/CMakeFiles 32
> [ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o
> cd /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels && /usr/bin/cmake -E make_directory
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/.
> cd /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels && /usr/bin/cmake -D verbose:BOOL=1 -D
> build_configuration:STRING=Release -D
> generated_file:STRING=/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o
> -D
> generated_cubin_file:STRING=/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o.cubin.txt
> -P /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.cmake
> -- Removing /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o
> /usr/bin/cmake -E remove
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o
> -- Generating dependency file:
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.NVCC-depend
> /usr/local/cuda/bin/nvcc -M -D__CUDACC__ /localhome/bssfh/relion4/relion/src/jaz/cuda/kernels/add.cu -o
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.NVCC-depend
> -ccbin /usr/bin/cc -m64 -DINSTALL_LIBRARY_DIR=/usr/local/lib/ -DSOURCE_DIR=/localhome/bssfh/relion4/relion/src/ -DACC_CUDA=2 -DACC_CPU=1
> -D_CUDA_ENABLED -DHAVE_SINCOS -DHAVE_TIFF -DHAVE_PNG -Xcompiler ,\"-O3\",\"-DNDEBUG\" -arch=sm_50 -D__INTEL_COMPILER --default-stream per-thread
> --std=c++11 --disable-warnings -DNVCC -I/usr/local/cuda/include -I/usr/include/openmpi-x86_64 -I/localhome/bssfh/relion4/relion -I/usr/include
> -I/localhome/bssfh/relion4/relion/external/fltk/include -I/usr/local/cuda/include
> -- Generating temporary cmake readable file:
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.depend.tmp
> /usr/bin/cmake -D
> input_file:FILEPATH=/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.NVCC-depend
> -D
> output_file:FILEPATH=/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.depend.tmp
> -P /usr/share/cmake/Modules/FindCUDA/make2cmake.cmake
> -- Copy if different
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.depend.tmp to
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.depend
> /usr/bin/cmake -E copy_if_different
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.depend.tmp /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.depend
> -- Removing
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.depend.tmp and
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.NVCC-depend
> /usr/bin/cmake -E remove
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.depend.tmp /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/relion_jaz_gpu_util_generated_add.cu.o.NVCC-depend
> -- Generating
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o
> /usr/local/cuda/bin/nvcc /localhome/bssfh/relion4/relion/src/jaz/cuda/kernels/add.cu -c -o
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o -ccbin
> /usr/bin/cc -m64 -DINSTALL_LIBRARY_DIR=/usr/local/lib/ -DSOURCE_DIR=/localhome/bssfh/relion4/relion/src/ -DACC_CUDA=2 -DACC_CPU=1 -D_CUDA_ENABLED
> -DHAVE_SINCOS -DHAVE_TIFF -DHAVE_PNG -Xcompiler ,\"-O3\",\"-DNDEBUG\" -arch=sm_50 -D__INTEL_COMPILER --default-stream per-thread --std=c++11
> --disable-warnings -DNVCC -I/usr/local/cuda/include -I/usr/include/openmpi-x86_64 -I/localhome/bssfh/relion4/relion -I/usr/include
> -I/localhome/bssfh/relion4/relion/external/fltk/include -I/usr/local/cuda/include
> Generated
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o
> successfully.
> /usr/bin/cmake -E cmake_progress_report /localhome/bssfh/relion4/relion/build/CMakeFiles
> [ 1%] Building NVCC (Device) object src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o
> cd /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda && /usr/bin/cmake -E make_directory
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/.
> cd /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda && /usr/bin/cmake -D verbose:BOOL=1 -D
> build_configuration:STRING=Release -D
> generated_file:STRING=/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o
> -D
> generated_cubin_file:STRING=/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o.cubin.txt
> -P /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.cmake
> -- Removing /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o
> /usr/bin/cmake -E remove
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o
> -- Generating dependency file:
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.NVCC-depend
> /usr/local/cuda/bin/nvcc -M -D__CUDACC__ /localhome/bssfh/relion4/relion/src/jaz/cuda/test00.cu -o
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.NVCC-depend
> -ccbin /usr/bin/cc -m64 -DINSTALL_LIBRARY_DIR=/usr/local/lib/ -DSOURCE_DIR=/localhome/bssfh/relion4/relion/src/ -DACC_CUDA=2 -DACC_CPU=1
> -D_CUDA_ENABLED -DHAVE_SINCOS -DHAVE_TIFF -DHAVE_PNG -Xcompiler ,\"-O3\",\"-DNDEBUG\" -arch=sm_50 -D__INTEL_COMPILER --default-stream per-thread
> --std=c++11 --disable-warnings -DNVCC -I/usr/local/cuda/include -I/usr/include/openmpi-x86_64 -I/localhome/bssfh/relion4/relion -I/usr/include
> -I/localhome/bssfh/relion4/relion/external/fltk/include -I/usr/local/cuda/include
> -- Generating temporary cmake readable file:
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.depend.tmp
> /usr/bin/cmake -D
> input_file:FILEPATH=/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.NVCC-depend
> -D
> output_file:FILEPATH=/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.depend.tmp
> -P /usr/share/cmake/Modules/FindCUDA/make2cmake.cmake
> -- Copy if different
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.depend.tmp to
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.depend
> /usr/bin/cmake -E copy_if_different
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.depend.tmp
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.depend
> -- Removing
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.depend.tmp and
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.NVCC-depend
> /usr/bin/cmake -E remove
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.depend.tmp
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/relion_jaz_gpu_util_generated_test00.cu.o.NVCC-depend
> -- Generating /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o
> /usr/local/cuda/bin/nvcc /localhome/bssfh/relion4/relion/src/jaz/cuda/test00.cu -c -o
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o -ccbin
> /usr/bin/cc -m64 -DINSTALL_LIBRARY_DIR=/usr/local/lib/ -DSOURCE_DIR=/localhome/bssfh/relion4/relion/src/ -DACC_CUDA=2 -DACC_CPU=1 -D_CUDA_ENABLED
> -DHAVE_SINCOS -DHAVE_TIFF -DHAVE_PNG -Xcompiler ,\"-O3\",\"-DNDEBUG\" -arch=sm_50 -D__INTEL_COMPILER --default-stream per-thread --std=c++11
> --disable-warnings -DNVCC -I/usr/local/cuda/include -I/usr/include/openmpi-x86_64 -I/localhome/bssfh/relion4/relion -I/usr/include
> -I/localhome/bssfh/relion4/relion/external/fltk/include -I/usr/local/cuda/include
> Generated /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o
> successfully.
> cd /localhome/bssfh/relion4/relion/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /localhome/bssfh/relion4/relion
> /localhome/bssfh/relion4/relion/src/apps /localhome/bssfh/relion4/relion/build /localhome/bssfh/relion4/relion/build/src/apps
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/DependInfo.cmake --color=
> Dependee "/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/DependInfo.cmake" is newer than depender
> "/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/depend.internal".
> Dependee "/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender
> "/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_jaz_gpu_util.dir/depend.internal".
> Scanning dependencies of target relion_jaz_gpu_util
> make[2]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> make -f src/apps/CMakeFiles/relion_jaz_gpu_util.dir/build.make src/apps/CMakeFiles/relion_jaz_gpu_util.dir/build
> make[2]: Entering directory `/localhome/bssfh/relion4/relion/build'
> Linking CXX static library ../../lib/librelion_jaz_gpu_util.a
> cd /localhome/bssfh/relion4/relion/build/src/apps && /usr/bin/cmake -P CMakeFiles/relion_jaz_gpu_util.dir/cmake_clean_target.cmake
> cd /localhome/bssfh/relion4/relion/build/src/apps && /usr/bin/cmake -E cmake_link_script CMakeFiles/relion_jaz_gpu_util.dir/link.txt --verbose=1
> /usr/bin/ar cr ../../lib/librelion_jaz_gpu_util.a CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/./relion_jaz_gpu_util_generated_test00.cu.o
> CMakeFiles/relion_jaz_gpu_util.dir/__/jaz/cuda/kernels/./relion_jaz_gpu_util_generated_add.cu.o
> /usr/bin/ranlib ../../lib/librelion_jaz_gpu_util.a
> make[2]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> /usr/bin/cmake -E cmake_progress_report /localhome/bssfh/relion4/relion/build/CMakeFiles 32
> [ 1%] Built target relion_jaz_gpu_util
> make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/depend
> make[2]: Entering directory `/localhome/bssfh/relion4/relion/build'
> cd /localhome/bssfh/relion4/relion/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /localhome/bssfh/relion4/relion
> /localhome/bssfh/relion4/relion/src/apps /localhome/bssfh/relion4/relion/build /localhome/bssfh/relion4/relion/build/src/apps
> /localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake --color=
> Dependee "/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_lib.dir/DependInfo.cmake" is newer than depender
> "/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_lib.dir/depend.internal".
> Dependee "/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/CMakeDirectoryInformation.cmake" is newer than depender
> "/localhome/bssfh/relion4/relion/build/src/apps/CMakeFiles/relion_lib.dir/depend.internal".
> Scanning dependencies of target relion_lib
> make[2]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> make -f src/apps/CMakeFiles/relion_lib.dir/build.make src/apps/CMakeFiles/relion_lib.dir/build
> make[2]: Entering directory `/localhome/bssfh/relion4/relion/build'
> /usr/bin/cmake -E cmake_progress_report /localhome/bssfh/relion4/relion/build/CMakeFiles
> [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/batchrunner.cpp.o
> cd /localhome/bssfh/relion4/relion/build/src/apps && /usr/lib64/openmpi/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DHAVE_PNG -DHAVE_SINCOS -DHAVE_TIFF
> -DINSTALL_LIBRARY_DIR=/usr/local/lib/ -DSOURCE_DIR=/localhome/bssfh/relion4/relion/src/ -D_CUDA_ENABLED -fopenmp -std=c++11 -O3 -DNDEBUG
> -I/usr/include/openmpi-x86_64 -I/localhome/bssfh/relion4/relion -I/localhome/bssfh/relion4/relion/external/fltk/include -I/usr/local/cuda/include
> -o CMakeFiles/relion_lib.dir/__/batchrunner.cpp.o -c /localhome/bssfh/relion4/relion/src/batchrunner.cpp
> /usr/bin/cmake -E cmake_progress_report /localhome/bssfh/relion4/relion/build/CMakeFiles
> [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o
> cd /localhome/bssfh/relion4/relion/build/src/apps && /usr/lib64/openmpi/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DHAVE_PNG -DHAVE_SINCOS -DHAVE_TIFF
> -DINSTALL_LIBRARY_DIR=/usr/local/lib/ -DSOURCE_DIR=/localhome/bssfh/relion4/relion/src/ -D_CUDA_ENABLED -fopenmp -std=c++11 -O3 -DNDEBUG
> -I/usr/include/openmpi-x86_64 -I/localhome/bssfh/relion4/relion -I/localhome/bssfh/relion4/relion/external/fltk/include -I/usr/local/cuda/include
> -o CMakeFiles/relion_lib.dir/__/assembly.cpp.o -c /localhome/bssfh/relion4/relion/src/assembly.cpp
> /usr/bin/cmake -E cmake_progress_report /localhome/bssfh/relion4/relion/build/CMakeFiles
> [ 1%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o
> cd /localhome/bssfh/relion4/relion/build/src/apps && /usr/lib64/openmpi/bin/mpicxx -DACC_CPU=1 -DACC_CUDA=2 -DHAVE_PNG -DHAVE_SINCOS -DHAVE_TIFF
> -DINSTALL_LIBRARY_DIR=/usr/local/lib/ -DSOURCE_DIR=/localhome/bssfh/relion4/relion/src/ -D_CUDA_ENABLED -fopenmp -std=c++11 -O3 -DNDEBUG
> -I/usr/include/openmpi-x86_64 -I/localhome/bssfh/relion4/relion -I/localhome/bssfh/relion4/relion/external/fltk/include -I/usr/local/cuda/include
> -o CMakeFiles/relion_lib.dir/__/autopicker.cpp.o -c /localhome/bssfh/relion4/relion/src/autopicker.cpp
> In file included from /localhome/bssfh/relion4/relion/src/autopicker.h:11:0,
> from /localhome/bssfh/relion4/relion/src/autopicker.cpp:21:
> /localhome/bssfh/relion4/relion/src/image.h:58:20: fatal error: tiffio.h: No such file or directory
> #include <tiffio.h>
> ^
> compilation terminated.
> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o] Error 1
> make[2]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> make[1]: *** [src/apps/CMakeFiles/relion_lib.dir/all] Error 2
> make[1]: Leaving directory `/localhome/bssfh/relion4/relion/build'
> make: *** [all] Error 2
>
> If it helps, I installed libtiff from the following gitlab repository: https://gitlab.com/libtiff/libtiff <https://gitlab.com/libtiff/libtiff>
> I assumed this would correspond to the libtiff-devel package from the package manager as it has an include/ directory and the missing file, however if
> that is wrong please let me know.
>
> Kind regards,
> Sam
>
>
>> On 9 Jun 2022, at 23:59, Takanori Nakane <[log in to unmask] <mailto:[log in to unmask]>> wrote:
>>
>> Hi,
>>
>> Did you re-run cmake after deleting your old build directory?
>>
>> Also try "VERBOSE=1 make -j1" to get more verbose diagnostics.
>>
>> Best regards,
>>
>> Takanori Nakane
>>
>> On 2022/06/10 3:56, Samuel Haysom [RPG] wrote:
>>> Hello,
>>> I am encountering an error that I cannot solve while attempting to compile relion4 on a linux workstation running CentOS 7. Whenever I run the
>>> compilation I get errors that look like this:
>>> In file included from /localhome/bssfh/relion4/relion/src/image.cpp:20:0:
>>> /localhome/bssfh/relion4/relion/src/image.h:58:20: fatal error: tiffio.h: No such file or directory
>>> #include <tiffio.h>
>>> ^
>>> compilation terminated.
>>> I get otherwise identical errors for other files during compilation with the full list of errors below:
>>> compilation terminated.
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/preprocessing.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/preprocessing_mpi.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/flex_analyser.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/micrograph_model.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/exp_model.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/helix_inimodel2d.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/healpix_sampling.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/motioncorr_runner_mpi.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/ml_model.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/ctf.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/local_symmetry_mpi.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/particle_subtractor.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/projector.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/helix.cpp.o] Error 1
>>> make[2]: *** [src/apps/CMakeFiles/relion_lib.dir/__/ml_optimiser_mpi.cpp.o] Error 1
>>> make[1]: *** [src/apps/CMakeFiles/relion_lib.dir/all] Error 2
>>> make: *** [all] Error 2
>>> As this seemed to be related to tifflib, I tried compiling my own version of the library and explicitly linking to this library when I call cmake
>>> (unfortunately I do not have root access on this machine and so cannot simply install it using the system package manager).
>>> $ cmake .. -DTIFF_INCLUDE_DIR="/localhome/bssfh/libtiff/usr/local/include/" -DTIFF_LIBRARY="/localhome/bssfh/libtiff/usr/local/lib64/libtiff.so.5”
>>> However this doesn’t seem to help. When I look at the location specified by DTIFF_INCLUDE_DIR I can see a file called tiffio.h in that directory so
>>> the compilation process should also be able to see this file. However it is entirely possible I’ve misunderstood the process and the error relates
>>> to something else.
>>> Any help deeply appreciated!
>>> Kind regards,
>>> SAm
>>> ------------------------------------------------------------------------------------------------------------------------------------------------------
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