I am unable to run Relion jobs with MPI procs on all available threads. For example, if running CTFFIND4 on our 4 core / 8 hyperthread machine, the job runs successfully with 4x MPI procs, but fails with 8x MPI procs. The error message reports: "Either request fewer slots for your application, or make more slots available for use".
One suspicion is that this problem may have arisen during compiling, so I've provided commands for "cmake" and "make" below, used when building Relion. I've also attached the output for the two commands. The system has Relion 3, Centos 7, openmpi3.
sudo cmake -DCUDA_ARCH=61 -DMPI_CXX_COMPILER=/usr/lib64/openmpi3/bin/mpicxx -DMPI_C_COMPILER=/usr/lib64/openmpi3/bin/mpicc ..
sudo make -j 8
Any suggestions on how to solve this?
Thanks,
Joel
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[joel@localhost build]$ sudo cmake -DCUDA_ARCH=61 -DMPI_CXX_COMPILER=/usr/lib64/openmpi3/bin/mpicxx -DMPI_C_COMPILER=/usr/lib64/openmpi3/bin/mpicc ..
-- The C compiler identification is GNU 4.8.5
-- The CXX compiler identification is GNU 4.8.5
-- Check for working C compiler: /bin/cc
-- Check for working C compiler: /bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working CXX compiler: /bin/c++
-- Check for working CXX compiler: /bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - 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
-- Found CUDA: /usr/local/cuda (found version "10.1")
-- Using cuda wrapper to compile....
-- Cuda version is >= 7.5 and single-precision build, enable double usage warning.
-- Found MPI_C: /usr/lib64/openmpi3/lib/libmpi.so
-- Found MPI_CXX: /usr/lib64/openmpi3/lib/libmpi_cxx.so;/usr/lib64/openmpi3/lib/libmpi.so
-- MPI_INCLUDE_PATH : /usr/include/openmpi3-x86_64
-- MPI_LIBRARIES : /usr/lib64/openmpi3/lib/libmpi_cxx.so;/usr/lib64/openmpi3/lib/libmpi.so
-- MPI_CXX_INCLUDE_PATH : /usr/include/openmpi3-x86_64
-- MPI_CXX_LIBRARIES : /usr/lib64/openmpi3/lib/libmpi_cxx.so;/usr/lib64/openmpi3/lib/libmpi.so
-- CMAKE_C_COMPILER : /bin/cc
-- CMAKE_CXX_COMPILER : /bin/c++
-- MPI_C_COMPILER : /usr/lib64/openmpi3/bin/mpicc
-- MPI_CXX_COMPILER : /usr/lib64/openmpi3/bin/mpicxx
-- CMAKE_CXX_COMPILER_ID : GNU
-- CMAKE_C_COMPILER : /usr/lib64/openmpi3/bin/mpicc
-- CMAKE_CXX_COMPILER : /usr/lib64/openmpi3/bin/mpicxx
-- MPI_C_COMPILER : /usr/lib64/openmpi3/bin/mpicc
-- MPI_CXX_COMPILER : /usr/lib64/openmpi3/bin/mpicxx
-- Looking for XOpenDisplay in /usr/lib64/libX11.so
-- Looking for XOpenDisplay in /usr/lib64/libX11.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
-- Found X11: /usr/lib64/libX11.so
-- Could NOT find FLTK (missing: FLTK_LIBRARIES FLTK_INCLUDE_DIR FLTK_FLUID_EXECUTABLE)
-- No FLTK installation was found
-- Found previously built non-system FLTK libraries that will be used.
-- FLTK_INCLUDE_DIR: /usr/local/bin/relion/external/fltk/include
-- FLTK_LIBRARIES: /usr/local/bin/relion/external/fltk/lib/libfltk.so
-- Single-precision FFTW was required but NOT found
-- Double-precision FFTW was required but NOT found
-- Found previously built non-system single precision FFTW libraries that will be used.
-- Found previously built non-system double precision FFTW libraries that will be used.
-- Looking for sincos
-- Looking for sincos - found
-- Looking for __sincos
-- Looking for __sincos - not found
-- Found TIFF: /usr/lib64/libtiff.so (found version "4.0.3")
BUILD_SHARED_LIBS = OFF
-- Building static libs (larger build size and binaries)
Running apps/CMakeLists.txt...
-- CMAKE_BINARY_DIR:/usr/local/bin/relion/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/bin/relion/build
########################################################################
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[joel@localhost build]$ sudo make -j 8
Scanning dependencies of target copy_scripts
Scanning dependencies of target relion_lib
[ 0%] Built target copy_scripts
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Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/assembly.cpp.o
Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/args.cpp.o
[ 4%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker.cpp.o
Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/backprojector.cpp.o
Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/autopicker_mpi.cpp.o
Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/complex.cpp.o
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[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner.cpp.o
[ 5%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/ctffind_runner_mpi.cpp.o
[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/error.cpp.o
[ 6%] Building CXX object src/apps/CMakeFiles/relion_lib.dir/__/euler.cpp.o
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[ 81%] Building CXX object src/apps/CMakeFiles/relion_gui_lib.dir/__/Healpix_2.15a/healpix_base.cc.o
[ 81%] Built target flex_analyse_mpi
Scanning dependencies of target localsym
[ 81%] Building CXX object src/apps/CMakeFiles/localsym.dir/localsym.cpp.o
Scanning dependencies of target localsym_mpi
[ 82%] Building CXX object src/apps/CMakeFiles/localsym_mpi.dir/localsym_mpi.cpp.o
Scanning dependencies of target mask_create
Scanning dependencies of target motion_refine
Scanning dependencies of target motion_refine_mpi
[ 82%] Linking CXX executable ../../bin/relion_localsym
Building CXX object src/apps/CMakeFiles/mask_create.dir/mask_create.cpp.o
[ 83%] Building CXX object src/apps/CMakeFiles/motion_refine.dir/motion_refine.cpp.o
[ 83%] Building CXX object src/apps/CMakeFiles/motion_refine_mpi.dir/motion_refine_mpi.cpp.o
[ 83%] Built target localsym
Scanning dependencies of target motion_stats
[ 84%] Building CXX object src/apps/CMakeFiles/motion_stats.dir/motion_stats.cpp.o
Linking CXX executable ../../bin/relion_helix_toolbox
[ 84%] Built target helix_toolbox
Scanning dependencies of target mrc2vtk
[ 84%] Building CXX object src/apps/CMakeFiles/mrc2vtk.dir/mrc2vtk.cpp.o
Linking CXX executable ../../bin/relion_localsym_mpi
[ 84%] Built target localsym_mpi
Scanning dependencies of target particle_polish
Linking CXX executable ../../bin/relion_motion_stats
[ 85%] Building CXX object src/apps/CMakeFiles/particle_polish.dir/particle_polish.cpp.o
Linking CXX executable ../../bin/relion_motion_refine
[ 85%] Built target motion_stats
Scanning dependencies of target particle_polish_mpi
[ 85%] Building CXX object src/apps/CMakeFiles/particle_polish_mpi.dir/particle_polish_mpi.cpp.o
[ 85%] Built target motion_refine
Scanning dependencies of target particle_reposition
[ 86%] Building CXX object src/apps/CMakeFiles/particle_reposition.dir/particle_reposition.cpp.o
Linking CXX executable ../../bin/relion_motion_refine_mpi
Linking CXX executable ../../bin/relion_image_handler
[ 86%] Built target image_handler
[ 86%] Scanning dependencies of target particle_sort
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[ 86%] Building CXX object src/apps/CMakeFiles/particle_sort.dir/particle_sort.cpp.o
[ 87%] Building CXX object src/apps/CMakeFiles/particle_sort_mpi.dir/particle_sort_mpi.cpp.o
Linking CXX executable ../../bin/relion_mask_create
[ 87%] Built target mask_create
Scanning dependencies of target particle_symmetry_expand
[ 87%] Building CXX object src/apps/CMakeFiles/particle_symmetry_expand.dir/particle_symmetry_expand.cpp.o
Linking CXX executable ../../bin/relion_particle_sort
Linking CXX executable ../../bin/relion_particle_polish
Linking CXX executable ../../bin/relion_mrc2vtk
[ 87%] Built target particle_sort
Linking CXX executable ../../bin/relion_particle_polish_mpi
Scanning dependencies of target postprocess
[ 87%] Building CXX object src/apps/CMakeFiles/postprocess.dir/postprocess.cpp.o
[ 87%] Built target mrc2vtk
Scanning dependencies of target postprocess_mpi
[ 88%] [ 88%] Building CXX object src/apps/CMakeFiles/postprocess_mpi.dir/postprocess_mpi.cpp.o
Built target particle_polish
Scanning dependencies of target prepare_subtomo
[ 88%] [ 88%] Building CXX object src/apps/CMakeFiles/prepare_subtomo.dir/prepare_subtomo.cpp.o
Built target particle_polish_mpi
Scanning dependencies of target preprocess
[ 89%] Building CXX object src/apps/CMakeFiles/preprocess.dir/preprocess.cpp.o
Linking CXX executable ../../bin/relion_particle_sort_mpi
Linking CXX static library ../../lib/librelion_gui_lib.a
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[ 89%] Built target particle_sort_mpi
Scanning dependencies of target project
[ 89%] Building CXX object src/apps/CMakeFiles/preprocess_mpi.dir/preprocess_mpi.cpp.o
[ 90%] Building CXX object src/apps/CMakeFiles/project.dir/project.cpp.o
Linking CXX executable ../../bin/relion_preprocess
Linking CXX executable ../../bin/relion_particle_symmetry_expand
[ 90%] Built target preprocess
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[ 90%] Built target particle_symmetry_expand
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[ 90%] Building CXX object src/apps/CMakeFiles/reconstruct.dir/reconstruct.cpp.o
[ 91%] Building CXX object src/apps/CMakeFiles/reconstruct_mpi.dir/reconstruct_mpi.cpp.o
Linking CXX executable ../../bin/relion_postprocess
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[ 91%] Built target postprocess
Scanning dependencies of target ref_aberration_plot
[ 91%] [ 91%] Built target postprocess_mpi
Building CXX object src/apps/CMakeFiles/ref_aberration_plot.dir/ref_aberration_plot.cpp.o
Scanning dependencies of target refine
[ 92%] Building CXX object src/apps/CMakeFiles/refine.dir/refine.cpp.o
Linking CXX executable ../../bin/relion_preprocess_mpi
[ 92%] Built target preprocess_mpi
Scanning dependencies of target refine_mpi
[ 93%] Building CXX object src/apps/CMakeFiles/refine_mpi.dir/refine_mpi.cpp.o
Linking CXX executable ../../bin/relion_particle_reposition
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Scanning dependencies of target run_ctffind
Linking CXX executable ../../bin/relion_reconstruct
[ 93%] Building CXX object src/apps/CMakeFiles/run_ctffind.dir/run_ctffind.cpp.o
[ 93%] Built target reconstruct
Scanning dependencies of target run_ctffind_mpi
[ 94%] Building CXX object src/apps/CMakeFiles/run_ctffind_mpi.dir/run_ctffind_mpi.cpp.o
Linking CXX executable ../../bin/relion_reconstruct_mpi
Linking CXX executable ../../bin/relion_run_ctffind
[ 94%] Built target reconstruct_mpi
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Building CXX object src/apps/CMakeFiles/run_motioncorr.dir/run_motioncorr.cpp.o
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[ 95%] Building CXX object src/apps/CMakeFiles/run_motioncorr_mpi.dir/run_motioncorr_mpi.cpp.o
Linking CXX executable ../../bin/relion_refine
[ 95%] Built target refine
Scanning dependencies of target stack_create
[ 95%] Building CXX object src/apps/CMakeFiles/stack_create.dir/stack_create.cpp.o
Linking CXX executable ../../bin/relion_run_ctffind_mpi
Linking CXX executable ../../bin/relion_ref_aberration_plot
Linking CXX executable ../../bin/relion_project
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Linking CXX executable ../../bin/relion_run_motioncorr
[ 96%] Building CXX object src/apps/CMakeFiles/star_combine.dir/star_combine.cpp.o
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Scanning dependencies of target star_compare
[ 96%] Building CXX object src/apps/CMakeFiles/star_compare.dir/star_compare.cpp.o
[ 96%] Built target project
[ 96%] Built target run_motioncorr
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[ 97%] Building CXX object src/apps/CMakeFiles/tiltpair_plot.dir/tiltpair_plot.cpp.o
[ 98%] Building CXX object src/apps/CMakeFiles/star_handler.dir/star_handler.cpp.o
Linking CXX executable ../../bin/relion_run_motioncorr_mpi
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[ 98%] Built target run_motioncorr_mpi
Scanning dependencies of target display
[ 98%] Building CXX object src/apps/CMakeFiles/display.dir/display.cpp.o
[ 98%] Built target refine_mpi
Scanning dependencies of target maingui
[ 98%] Building CXX object src/apps/CMakeFiles/maingui.dir/maingui.cpp.o
Linking CXX executable ../../bin/relion_prepare_subtomo
Linking CXX executable ../../bin/relion_star_combine
Linking CXX executable ../../bin/relion_star_compare
[ 98%] Built target prepare_subtomo
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[ 98%] Built target star_combine
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[ 99%] [100%] Building CXX object src/apps/CMakeFiles/pipeliner.dir/pipeliner.cpp.o
Building CXX object src/apps/CMakeFiles/manualpick.dir/manualpick.cpp.o
[100%] Built target star_compare
Linking CXX executable ../../bin/relion_display
[100%] Linking CXX executable ../../bin/relion_maingui
Built target display
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[100%] Built target maingui
Linking CXX executable ../../bin/relion_manualpick
[100%] Built target tiltpair_plot
[100%] Built target manualpick
Linking CXX executable ../../bin/relion_pipeliner
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Linking CXX executable ../../bin/relion_stack_create
[100%] Built target stack_create
Linking CXX executable ../../bin/relion_star_handler
[100%] Built target star_handler
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