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

[Kai Szuttor]

----- Forwarded message from David Power <address@hidden> -----

Date: Mon, 17 Sep 2018 15:14:11 +0100
From: David Power <address@hidden>
To: address@hidden
Subject: Re: [ESPResSo-users] espresso-4.0.0 failing to run when compiled with 
mpiicpc

   Thanks Kai,
   I had compiled the boost libraries from source with the intel compiler as
   the apt repository version was lower than the espresso-4.0 required
   version.
   I reread the boost install instructions and it turns out I had to specify
   the mpi compiler wrapper in the boost project-config.jam file. 
   I did this and Espresso is running fine now.
   For anyone else who has this issue, it was resolved by adding the
   following to the boost project-config.jam file:
   using mpi :
   /opt/intel/compilers_and_libraries_2019.0.117/linux/mpi/intel64/bin/mpiicpc
   ;
   Thanks,
   David
   On Mon, 17 Sep 2018 at 13:13, Kai Szuttor <address@hidden>
   wrote:

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

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