Hi Takanori,
I had attached the output files, but maybe they get filtered on the mailing list. Here is the output:
-- 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
-- Using cuda wrapper to compile....
-- Cuda version is >= 7.5 and single-precision build, enable double usage warning.
-- MPI_INCLUDE_PATH : /opts/openmpi4/include
-- MPI_LIBRARIES : /opts/openmpi4/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH : /opts/openmpi4/include
-- MPI_CXX_LIBRARIES : /opts/openmpi4/lib/libmpi.so
-- CMAKE_C_COMPILER : /usr/bin/cc
-- CMAKE_CXX_COMPILER : /usr/bin/c++
-- MPI_C_COMPILER : /opts/openmpi4/bin/mpicc
-- MPI_CXX_COMPILER : /opts/openmpi4/bin/mpicxxa
-- CMAKE_CXX_COMPILER_ID : GNU
-- CMAKE_C_COMPILER : /opts/openmpi4/bin/mpicc
-- CMAKE_CXX_COMPILER : /opts/openmpi4/bin/mpicxx
-- MPI_C_COMPILER : /opts/openmpi4/bin/mpicc
-- MPI_CXX_COMPILER : /opts/openmpi4/bin/mpicxx
-- X11 and FLTK were found
-- FLTK_LIBRARIES: fltk_images;fltk_forms;fltk;/usr/lib/x86_64-linux-gnu/libSM.so;/usr/lib/x86_64-linux-gnu/libICE.so;/usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so;/usr/lib/x86_64-linux-gnu/libm.so
-- Found FFTW
-- FFTW_PATH: /usr/include
-- FFTW_INCLUDES: /usr/include
-- FFTW_LIBRARIES: /usr/lib/x86_64-linux-gnu/libfftw3f.so;/usr/lib/x86_64-linux-gnu/libfftw3.so
-- Building static libs (larger build size and binaries)
-- CMAKE_BINARY_DIR:/opts/INSTALLFILES/relion/build
-- Found OpenMP_C: -fopenmp
-- Found OpenMP_CXX: -fopenmp
-- Found OpenMP: TRUE
-- Configuring done
-- Generating done
-- Build files have been written to: /opts/INSTALLFILES/relion/build
[ 0%] Built target copy_scripts
[ 54%] Built target relion_lib
[ 55%] Linking CXX static library ../../lib/librelion_gpu_util.a
[ 58%] Built target relion_gpu_util
[ 60%] Linking CXX executable ../../bin/relion_star_handler
[ 60%] Linking CXX executable ../../bin/relion_tiltpair_plot
[ 60%] Linking CXX executable ../../bin/relion_project
[ 60%] Linking CXX executable ../../bin/relion_run_motioncorr_mpi
[ 60%] Linking CXX executable ../../bin/relion_refine
[ 62%] Linking CXX executable ../../bin/relion_reconstruct_mpi
[ 62%] Linking CXX executable ../../bin/relion_ref_aberration_plot
[ 62%] Linking CXX executable ../../bin/relion_reconstruct
[ 62%] Linking CXX executable ../../bin/relion_helix_toolbox
[ 64%] Linking CXX executable ../../bin/relion_flex_analyse_mpi
[ 64%] Linking CXX executable ../../bin/relion_particle_sort
[ 64%] Linking CXX executable ../../bin/relion_autopick_mpi
[ 66%] Linking CXX executable ../../bin/relion_autopick
[ 68%] Linking CXX executable ../../bin/relion_find_tiltpairs
[ 65%] Linking CXX executable ../../bin/relion_refine_mpi
[ 69%] Linking CXX executable ../../bin/relion_run_ctffind
[ 70%] Linking CXX executable ../../bin/relion_localsym
[ 70%] Linking CXX executable ../../bin/relion_postprocess
[ 70%] Linking CXX executable ../../bin/relion_align_symmetry
[ 74%] Linking CXX executable ../../bin/relion_flex_analyse
[ 75%] Linking CXX executable ../../bin/relion_stack_create
[ 75%] Linking CXX executable ../../bin/relion_particle_polish
[ 75%] Linking CXX executable ../../bin/relion_preprocess_mpi
[ 69%] Linking CXX executable ../../bin/relion_preprocess
[ 75%] Linking CXX executable ../../bin/relion_star_combine
[ 75%] Linking CXX executable ../../bin/relion_ctf_refine
[ 76%] Linking CXX executable ../../bin/relion_motion_refine
[ 76%] Linking CXX executable ../../bin/relion_image_handler
[ 77%] Linking CXX executable ../../bin/relion_motion_refine_mpi
[ 77%] Linking CXX executable ../../bin/relion_particle_reposition
[ 77%] Linking CXX executable ../../bin/relion_ctf_refine_mpi
[ 77%] Built target relion_gui_lib
[ 77%] Linking CXX executable ../../bin/relion_mrc2vtk
[ 77%] Linking CXX executable ../../bin/relion_motion_stats
[ 77%] Linking CXX executable ../../bin/relion_star_compare
[ 77%] Linking CXX executable ../../bin/relion_run_ctffind_mpi
[ 77%] Linking CXX executable ../../bin/relion_localsym_mpi
[ 74%] Linking CXX executable ../../bin/relion_particle_polish_mpi
[ 72%] Linking CXX executable ../../bin/relion_mask_create
[ 76%] Linking CXX executable ../../bin/relion_particle_sort_mpi
[ 77%] Linking CXX executable ../../bin/relion_particle_symmetry_expand
[ 77%] Built target particle_sort
[ 78%] Built target tiltpair_plot
[ 78%] Built target star_handler
[ 78%] Built target find_tiltpairs
[ 79%] Built target stack_create
[ 80%] Built target star_combine
[ 82%] Built target postprocess
[ 82%] Built target mask_create
[ 82%] Built target align_symmetry
[ 82%] Built target particle_sort_mpi
[ 83%] Built target mrc2vtk
[ 83%] Built target star_compare
[ 82%] Built target localsym
[ 84%] Built target preprocess_mpi
[ 84%] Built target particle_polish
[ 84%] Built target image_handler
[ 83%] Built target helix_toolbox
[ 85%] Built target run_ctffind_mpi
[ 85%] Built target preprocess
[ 85%] Built target run_ctffind
[ 84%] Built target run_motioncorr_mpi
[ 84%] Built target particle_symmetry_expand
[ 86%] Built target motion_stats
[ 86%] Built target reconstruct_mpi
[ 86%] Built target ctf_refine
[ 86%] Built target particle_polish_mpi
[ 85%] Built target ref_aberration_plot
Scanning dependencies of target pipeliner
Scanning dependencies of target maingui
[ 87%] Built target reconstruct
[ 89%] Built target project
[ 89%] Linking CXX executable ../../bin/relion_postprocess_mpi
[ 89%] Linking CXX executable ../../bin/relion_run_motioncorr
[ 88%] Linking CXX executable ../../bin/relion_ctf_toolbox
[ 89%] Built target flex_analyse
src/apps/CMakeFiles/refine_mpi.dir/build.make:97: recipe for target 'bin/relion_refine_mpi' failed
CMakeFiles/Makefile2:338: recipe for target 'src/apps/CMakeFiles/refine_mpi.dir/all' failed
[ 91%] Built target ctf_refine_mpi
[ 91%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o
[ 91%] Linking CXX executable ../../bin/relion_prepare_subtomo
[ 91%] Building CXX object src/apps/CMakeFiles/maingui.dir/maingui.cpp.o
[ 93%] Built target flex_analyse_mpi
[ 93%] Built target motion_refine_mpi
[ 93%] Built target motion_refine
[ 93%] Built target localsym_mpi
src/apps/CMakeFiles/refine.dir/build.make:97: recipe for target 'bin/relion_refine' failed
CMakeFiles/Makefile2:412: recipe for target 'src/apps/CMakeFiles/refine.dir/all' failed
src/apps/CMakeFiles/particle_reposition.dir/build.make:97: recipe for target 'bin/relion_particle_reposition' failed
CMakeFiles/Makefile2:1524: recipe for target 'src/apps/CMakeFiles/particle_reposition.dir/all' failed
Scanning dependencies of target display
Scanning dependencies of target manualpick
[ 93%] Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o
[ 94%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o
src/apps/CMakeFiles/autopick.dir/build.make:97: recipe for target 'bin/relion_autopick' failed
CMakeFiles/Makefile2:745: recipe for target 'src/apps/CMakeFiles/autopick.dir/all' failed
src/apps/CMakeFiles/autopick_mpi.dir/build.make:97: recipe for target 'bin/relion_autopick_mpi' failed
CMakeFiles/Makefile2:1263: recipe for target 'src/apps/CMakeFiles/autopick_mpi.dir/all' failed
[ 94%] Built target postprocess_mpi
[ 94%] Built target ctf_toolbox
[ 94%] Built target prepare_subtomo
[ 94%] Built target run_motioncorr
[ 95%] Linking CXX executable ../../bin/relion_manualpick
[ 96%] Linking CXX executable ../../bin/relion_maingui
[ 96%] Linking CXX executable ../../bin/relion_display
[ 96%] Linking CXX executable ../../bin/relion_pipeliner
[ 96%] Built target manualpick
[ 96%] Built target display
[ 96%] Built target maingui
[ 96%] Built target pipeliner
Makefile:140: recipe for target 'all' failed
-----Original Message-----
From: Takanori Nakane <[log in to unmask]>
Date: Friday, 21. June 2019 at 18:52
To: Eike-Christian Schulz <[log in to unmask]>
Cc: CCPEM <[log in to unmask]>
Subject: Re: [ccpem] Relion3.0 MPI error during 3D autorefine
Please show the FULL message from make.
Takanori
> Hi Takanori,
>
> thanks for your quick response. Upon re-compilation I ran into errors at
> 96% of the make step. Could you help me out here ?
>
> Best,
>
> Eike
>
>
> ?-----Original Message-----
> From: Takanori Nakane <[log in to unmask]>
> Date: Thursday, 20. June 2019 at 23:26
> To: Eike-Christian Schulz <[log in to unmask]>, CCPEM
> <[log in to unmask]>
> Subject: Re: [ccpem] Relion3.0 MPI error during 3D autorefine
>
> Hi,
>
> We need more information!
>
> > segmentation faults
>
> Where did it happen? E step or M step? Anything in run.err?
>
> > I tired updating to openmpi4.
>
> Did you recompile RELION with OpenMPI4?
> Did you make sure cmake find the right version of OpenMPI?
>
> Best regards,
>
> Takanori Nakane
>
> On 2019/06/20 22:14, Schulz, Eike-Christian wrote:
> > Hi everyone,
> >
> > When using MPI I was getting segmentation faults. MPI is obviously
> required for map splitting in 3D-autorefine. Thus, I tired updating
> to openmpi4. Now 3D-autorefine does not start at all - there is no
> output, that is also no error messages whatsoever.
> >
> > I would be very happy for suggestions,
> >
> > Thanks and best regards,
> >
> > Eike
> >
> >
> > Ubuntu 16.04, Cuda8, OpenMPI4.01
> >
> >
> >
> >
> > ########################################################################
> >
> > To unsubscribe from the CCPEM list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1
> >
>
>
>
>
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