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CCPEM  June 2020

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Subject:

MPI runtime errors - RELION 3.0 and 3.1 on CentOS 8.1

From:

Guillaume Gaullier <[log in to unmask]>

Reply-To:

Guillaume Gaullier <[log in to unmask]>

Date:

Mon, 1 Jun 2020 15:01:12 +0200

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (25 lines) , run.err (25 lines) , Unknown Name (9 lines) , cmake-log.txt (95 lines)

Hello CCPEM,

I installed RELION 3.0 (commit 5a8f82785e53bc8ed271b096c3f7afff09e5e82f ) and also the latest in branch 3.1 (commit 5997001f75abd0f1fa135ee25e04f92c855e5e29 ). They compile and install fine on a fresh CentOS 8.1, but I get MPI errors at runtime with both versions of RELION. I attached a run.err obtained with RELION 3.1 while trying to go through the tutorial.

I did read the FAQ about MPI runtime errors ( https://www3.mrc-lmb.cam.ac.uk/relion/index.php/FAQs#Program_crashes_showing_MPI_runtime_errors ), and I am pretty sure I compiled and ran with the same MPI, because I only have one version installed. It is OpenMPI 4.0.1, installed with the distribution’s package manager. I also believe the environment is correctly set up both during compilation and at run time, because I use the environment modules system and I use the modulefile provided by the system installation of OpenMPI. I also tested the mpirun command with unrelated programs, and it worked as expected.

So, as far as I can tell, this looks like either a bug in RELION or an incompatibility with this version of OpenMPI (if so, it would be very helpful to list compatible versions of OpenMPI on the wiki).

I would be happy to be told I messed something up during installation and there is an easy fix, so I also attached the output of my fresh cmake just in case it would point to a problem with my installation.

Can someone help me with this issue?

Thank you in advance,

Guillaume


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######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/  
-- The C compiler identification is GNU 8.3.1 -- The CXX compiler identification is GNU 8.3.1 -- 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 -- Detecting C compile features -- Detecting C compile features - 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 -- Detecting CXX compile features -- Detecting CXX compile features - done -- BUILD TYPE set to the default type: 'Release' -- Using provided CUDA_ARCH=75 -- ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2 -- CUDA enabled - Building CUDA-accelerated version of RELION -- Setting cpu precision to double -- Setting accelerated code precision to single -- Looking for pthread.h -- Looking for pthread.h - found -- Looking for pthread_create -- Looking for pthread_create - not found -- Looking for pthread_create in pthreads -- Looking for pthread_create in pthreads - not found -- Looking for pthread_create in pthread -- Looking for pthread_create in pthread - found -- Found Threads: TRUE -- Found CUDA: /opt/cuda-10.2 (found version "10.2") -- 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 version "3.1") -- Found MPI_CXX: /usr/lib64/openmpi/lib/libmpi_cxx.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- 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 -- CMAKE_C_COMPILER : /usr/lib64/openmpi/bin/mpicc -- CMAKE_CXX_COMPILER : /usr/lib64/openmpi/bin/mpicxx -- MPI_C_COMPILER : /usr/lib64/openmpi/bin/mpicc -- MPI_CXX_COMPILER : /usr/lib64/openmpi/bin/mpicxx -- 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_FLUID_EXECUTABLE) -- No FLTK installation was found -- Found previously built non-system FLTK libraries that will be used. -- FLTK_INCLUDE_DIR: /usr/include -- FLTK_LIBRARIES: /usr/lib64/libfltk_images.so;/usr/lib64/libfltk_forms.so;/usr/lib64/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: /usr/lib64/libtiff.so (found version "4.0.9") -- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11") -- Found PNG: /usr/lib64/libpng.so (found version "1.6.34") -- Building static libs (larger build size and binaries) -- CMAKE_BINARY_DIR:/home/guillaume/software/relion/build_3.1_cuda-10.2 -- Git commit ID: 5997001f75abd0f1fa135ee25e04f92c855e5e29 -- Found OpenMP_C: -fopenmp (found version "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- Configuring done -- Generating done -- Build files have been written to: /home/guillaume/software/relion/build_3.1_cuda-10.2 ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCPEM&A=1 This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/

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