Hi,
Please delete your build directory and start again from
the 'cmake' step, with "-DFORCE_OWN_FFTW=ON -DFORCE_OWN_FLTK=ON".
Also avoid "-j" option in make so that the errors are
displayed in order.
Best regards,
Takanori Nakane
On 2019/06/21 17:58, Schulz, Eike-Christian wrote:
> 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
> > >
> >
> >
> >
> >
>
>
>
>
>
> ########################################################################
>
> 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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