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Re: [ESPResSo-users] espresso-4.0.0 failing to run when compiled with mp
From: |
Kai Szuttor |
Subject: |
Re: [ESPResSo-users] espresso-4.0.0 failing to run when compiled with mpiicpc |
Date: |
Mon, 17 Sep 2018 14:13:39 +0200 |
User-agent: |
NeoMutt/20170714-126-deb55f (1.8.3) |
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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