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Subject:

Re: Yet another relion 2.0 compile error

From:

"Schulz, Eike-Christian" <[log in to unmask]>

Reply-To:

Schulz, Eike-Christian

Date:

Wed, 15 Feb 2017 19:45:02 +0000

Content-Type:

text/plain

Parts/Attachments:
Parts/Attachments

text/plain (1 lines) 

Hi Björn, 



sorry my bad. Please find the output below: 



Best 



Eike





cfelm-pcx25816:/usr/local/xtal/relion/build> sudo cmake -DCUDA_ARCH=61 ..

-- BUILD TYPE set to the default type:  'Release'

-- Using provided CUDA_ARCH=61

-- Setting cpu precision to double

-- Setting gpu precision to single

-- Using cuda wrapper to compile....

-- Cuda version is >= 7.5 and single-precision build, enable double usage warning.

-- MPI_INCLUDE_PATH : /usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi

-- MPI_LIBRARIES : /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so

-- MPI_CXX_INCLUDE_PATH : /usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent;/usr/lib/openmpi/include/openmpi/opal/mca/event/libevent2021/libevent/include;/usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi

-- MPI_CXX_LIBRARIES : /usr/lib/openmpi/lib/libmpi_cxx.so;/usr/lib/openmpi/lib/libmpi.so

-- -------------------------------------------------

-- ------- WILL USE LOCALLY BUILT FLTK LIBS --------

-- -------------------------------------------------

-- Found previously built external (non-system) FLTK library

-- FLTK_INCLUDE_DIR: /usr/local/xtal/relion/external/fltk/include

-- FLTK_LIBRARIES:   /usr/local/xtal/relion/external/fltk/lib/libfltk.so

-- -------------------------------------------------

-- ------- WILL USE LOCALLY BUILT FFTW LIBS --------

-- -------------------------------------------------

-- Found previously built external (non-system) FFTW library

-- FFTW_INCLUDES:     /usr/local/xtal/relion/external/fftw/include

-- FFTW_LIBRARIES:    /usr/local/xtal/relion/external/fftw/lib/libfftw3.so

-- Building shared libs (smaller build size and binaries)

-- CMAKE_BINARY_DIR:/usr/local/xtal/relion/build

-- added refine...

-- added maingui...

-- added autopick_mpi...

-- added particle_reposition...

-- added project...

-- added particle_polish...

-- added postprocess...

-- added mask_create...

-- added manualpick...

-- added star_compare...

-- added find_tiltpairs...

-- added star_combine...

-- added preprocess...

-- added pipeliner...

-- added display...

-- added helix_toolbox...

-- added particle_polish_mpi...

-- added tiltpair_plot...

-- added run_ctffind...

-- added reconstruct...

-- added autopick...

-- added stack_create...

-- added refine_mpi...

-- added particle_symmetry_expand...

-- added run_ctffind_mpi...

-- added postprocess_mpi...

-- added image_handler...

-- added preprocess_mpi...

-- added particle_sort...

-- added run_motioncorr...

-- added run_motioncorr_mpi...

-- added particle_sort_mpi...

-- Configuring done

-- Generating done

-- Build files have been written to: /usr/local/xtal/relion/build



-----Original Message-----

From: Bjoern Forsberg <[log in to unmask]>

Date: Wednesday 15 February 2017 at 20:14

To: "Schulz, Eike-Christian" <[log in to unmask]>

Subject: Re: [ccpem] Yet another relion 2.0 compile error



    At the risk of repeating myself from earlier today; what was the cmake 

    configuration output?

    

    /Björn

    

    

    On 02/15/2017 07:55 PM, Schulz, Eike-Christian wrote:

    > Dear all,

    >

    > I am trying to compile relion 2.0 with gpu / mpi support on ubuntu 16.04 ... cmake completes without errors but the make process stops early on ... cuda seems to be the problem ...

    >

    >

    > I would be glad if someone could give me a hint how to continue.

    >

    > Thanks and best regards

    >

    > Eike

    >

    > cfelm-pcx25816:/usr/local/xtal/relion/build> sudo make -j 32

    > [  1%] Building NVCC (Device) object

    > src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_ge

    > nerated_cuda_ml_optimiser.cu.o

    > [  2%] Building NVCC (Device) object

    > src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_ge

    > nerated_cuda_backprojector.cu.o

    > [  3%] Building NVCC (Device) object

    > src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/relio

    > n_gpu_util_generated_helper.cu.o

    > [  4%] Building NVCC (Device) object

    > src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_ge

    > nerated_cuda_helper_functions.cu.o

    > [  5%] Building NVCC (Device) object

    > src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_ge

    > nerated_cuda_projector_plan.cu.o

    > [  6%] Building NVCC (Device) object

    > src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_ge

    > nerated_cuda_projector.cu.o

    > [  6%] Building NVCC (Device) object

    > src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_ge

    > nerated_cuda_autopicker.cu.o

    > [  7%] Building NVCC (Device) object

    > src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_ge

    > nerated_cuda_benchmark_utils.cu.o

    > CMake Error at

    > relion_gpu_util_generated_cuda_ml_optimiser.cu.o.cmake:207 (message):

    >    Error generating

    >   

    > /usr/local/xtal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__

    > /gpu_utils/./relion_gpu_util_generated_cuda_ml_optimiser.cu.o

    >

    >

    > CMake Error at relion_gpu_util_generated_helper.cu.o.cmake:207

    > (message):

    >    Error generating

    >   

    > /usr/local/xtal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__

    > /gpu_utils/cuda_kernels/./relion_gpu_util_generated_helper.cu.o

    >

    >

    > src/apps/CMakeFiles/relion_gpu_util.dir/build.make:63: recipe for

    > target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_ml_optimiser.cu.o' failed

    > make[2]: ***

    > [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_ml_optimiser.cu.o] Error 1

    > make[2]: *** Waiting for unfinished jobs....

    > src/apps/CMakeFiles/relion_gpu_util.dir/build.make:112: recipe for

    > target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/reli

    > on_gpu_util_generated_helper.cu.o' failed

    > make[2]: ***

    > [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/cuda_kernels/reli

    > on_gpu_util_generated_helper.cu.o] Error 1

    > CMake Error at

    > relion_gpu_util_generated_cuda_projector_plan.cu.o.cmake:207 (message):

    >    Error generating

    >   

    > /usr/local/xtal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__

    > /gpu_utils/./relion_gpu_util_generated_cuda_projector_plan.cu.o

    >

    >

    > src/apps/CMakeFiles/relion_gpu_util.dir/build.make:98: recipe for

    > target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_projector_plan.cu.o' failed

    > make[2]: ***

    > [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_projector_plan.cu.o] Error 1

    > CMake Error at

    > relion_gpu_util_generated_cuda_helper_functions.cu.o.cmake:207

    > (message):

    >    Error generating

    >   

    > /usr/local/xtal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__

    > /gpu_utils/./relion_gpu_util_generated_cuda_helper_functions.cu.o

    >

    > CMake Error at relion_gpu_util_generated_cuda_autopicker.cu.o.cmake:207

    > (message):

    >    Error generating

    >   

    > /usr/local/xtal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__

    > /gpu_utils/./relion_gpu_util_generated_cuda_autopicker.cu.o

    >

    >

    >

    > CMake Error at

    > relion_gpu_util_generated_cuda_benchmark_utils.cu.o.cmake:207

    > (message):

    >    Error generating

    >   

    > /usr/local/xtal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__

    > /gpu_utils/./relion_gpu_util_generated_cuda_benchmark_utils.cu.o

    >

    >

    > src/apps/CMakeFiles/relion_gpu_util.dir/build.make:91: recipe for

    > target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_autopicker.cu.o' failed

    > make[2]: ***

    > [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_autopicker.cu.o] Error 1

    > src/apps/CMakeFiles/relion_gpu_util.dir/build.make:84: recipe for

    > target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_helper_functions.cu.o' failed

    > make[2]: ***

    > [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_helper_functions.cu.o] Error 1

    > src/apps/CMakeFiles/relion_gpu_util.dir/build.make:77: recipe for

    > target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_benchmark_utils.cu.o' failed

    > make[2]: ***

    > [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_benchmark_utils.cu.o] Error 1

    > CMake Error at relion_gpu_util_generated_cuda_projector.cu.o.cmake:207

    > (message):

    >    Error generating

    >   

    > /usr/local/xtal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__

    > /gpu_utils/./relion_gpu_util_generated_cuda_projector.cu.o

    >

    >

    > CMake Error at

    > relion_gpu_util_generated_cuda_backprojector.cu.o.cmake:207 (message):

    >    Error generating

    >   

    > /usr/local/xtal/relion/build/src/apps/CMakeFiles/relion_gpu_util.dir/__

    > /gpu_utils/./relion_gpu_util_generated_cuda_backprojector.cu.o

    >

    >

    > src/apps/CMakeFiles/relion_gpu_util.dir/build.make:105: recipe for

    > target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_projector.cu.o' failed

    > make[2]: ***

    > [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_projector.cu.o] Error 1

    > src/apps/CMakeFiles/relion_gpu_util.dir/build.make:70: recipe for

    > target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_backprojector.cu.o' failed

    > make[2]: ***

    > [src/apps/CMakeFiles/relion_gpu_util.dir/__/gpu_utils/relion_gpu_util_g

    > enerated_cuda_backprojector.cu.o] Error 1

    > CMakeFiles/Makefile2:909: recipe for target

    > 'src/apps/CMakeFiles/relion_gpu_util.dir/all' failed

    > make[1]: *** [src/apps/CMakeFiles/relion_gpu_util.dir/all] Error 2

    > make[1]: *** Waiting for unfinished jobs....

    > [  7%] Built target copy_scripts

    > Makefile:138: recipe for target 'all' failed

    > make: *** [all] Error 2

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