Re: [ESPResSo-users] espresso-4.0.0 failing to run when compiled with mpiicpc

[Kai Szuttor]

Did you check if your boost-mpi is linked against the same MPI lib?

Best,

Kai
On Mon, Sep 17, 2018 at 12:00:18PM +0000, David Power wrote:
>    I am able to compile are run pypresso with just fine using the gnu
>    compilers and mpirun. However, after compiling with the intel compilers, I
>    get the following error ImportError when I run pypresso with the intel
>    version of mpirun:
>    ImportError: <path>/libcluster_analysis.so.4: undefined symbol:
>    
> _ZN5boost3mpi6detail19packed_archive_recvEiiiRNS0_15packed_iarchiveER10MPI_Status
>    I checked the archive and a similar issue occurred when the user was
>    loading in the wrong version of MPI
>    (https://github.com/espressomd/espresso/issues/2023). But from what I can
>    see from my cmake output, I am selecting the intel version of mpi and my
>    libcluster_analysis.so was build against (see below). Any suggestions as
>    to what is going wrong?
>    ### cmake output ###
>    build-intel> ${CMAKE_PATH}/cmake ../.
>    -- Config file: <path>/espresso-4.0.0/myconfig.hpp
>    -- Found Cython version 0.26
>    -- NumPy ver. 1.15.1 found (include:
>    /home/<user>/.local/lib/python2.7/site-packages/numpy/core/include)
>    -- Checking for module 'scafacos'
>    --Â  Â No package 'scafacos' found
>    -- Boost version: 1.68.0
>    -- Found the following Boost libraries:
>    --Â  Â mpi
>    --Â  Â serialization
>    --Â  Â filesystem
>    --Â  Â system
>    --Â  Â unit_test_framework
>    -- writing
>    
> /home/<user>/Desktop/CompetitiveAdsorptionSimulations/espresso-4.0.0/build-intel/myconfig-sample.hpp
>    -- The following OPTIONAL packages have been found:
>    Â * FFTW3
>    Â * PkgConfig
>    Â * GSL
>    Â * Doxygen
>    Â * Sphinx (required version >= 1.6.6)
>    -- The following REQUIRED packages have been found:
>    Â * PythonInterp
>    Â * Cython (required version >= 0.23)
>    Â * NumPy
>    Â * MPI
>    Â * Boost (required version >= 1.65.0)
>    -- Configuring done
>    -- Generating done
>    -- Build files have been written to:
>    
> /home/<user>/Desktop/CompetitiveAdsorptionSimulations/espresso-4.0.0/build-intel
>    ### ldd output ###
>    ldd /usr/local/lib/libcluster_analysis.so.4
>    linux-vdso.so.1 (0x00007fffb39e3000)
>    libmpicxx.so.12 =>
>    
> /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpicxx.so.12
>    (0x00007f2f1eb32000)
>    libmpifort.so.12 =>
>    
> /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/libmpifort.so.12
>    (0x00007f2f1e786000)
>    libmpi.so.12 =>
>    
> /opt/intel//compilers_and_libraries_2019.0.117/linux/mpi/intel64/lib/release/libmpi.so.12
>    (0x00007f2f1cf67000)
>    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f2f1cd63000)
>    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f2f1cb5b000)
>    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
>    (0x00007f2f1c93c000)
>    libimf.so =>
>    
> /opt/intel/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64_lin/libimf.so
>    (0x00007f2f1c39c000)
>    libsvml.so =>
>    
> /opt/intel/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64_lin/libsvml.so
>    (0x00007f2f1a9f9000)
>    libirng.so =>
>    
> /opt/intel/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64_lin/libirng.so
>    (0x00007f2f1a687000)
>    libstdc++.so.6 => /usr/lib/x86_64-linux-gnu/libstdc++.so.6
>    (0x00007f2f1a2f9000)
>    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2f19f5b000)
>    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007f2f19d43000)
>    libintlc.so.5 =>
>    
> /opt/intel/compilers_and_libraries_2019.0.117/linux/compiler/lib/intel64_lin/libintlc.so.5
>    (0x00007f2f19ad1000)
>    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2f196e0000)
>    libfabric.so.1 => /usr/lib/x86_64-linux-gnu/libfabric.so.1
>    (0x00007f2f19433000)
>    /lib64/ld-linux-x86-64.so.2 (0x00007f2f1ef8d000)
>    librdmacm.so.1 => /usr/lib/x86_64-linux-gnu/librdmacm.so.1
>    (0x00007f2f1921d000)
>    libibverbs.so.1 => /usr/lib/x86_64-linux-gnu/libibverbs.so.1
>    (0x00007f2f19007000)
>    libpsm_infinipath.so.1 => /usr/lib/x86_64-linux-gnu/libpsm_infinipath.so.1
>    (0x00007f2f18dae000)
>    libnl-route-3.so.200 => /usr/lib/x86_64-linux-gnu/libnl-route-3.so.200
>    (0x00007f2f18b39000)
>    libnl-3.so.200 => /lib/x86_64-linux-gnu/libnl-3.so.200
>    (0x00007f2f18919000)
>    libinfinipath.so.4 => /usr/lib/x86_64-linux-gnu/libinfinipath.so.4
>    (0x00007f2f1870a000)
>    libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00007f2f18503000)
>    Â

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