Re: [ESPResSo-users] Error when importing espressomd

[Jean-Noël Grad]

Hi,

Discussion was moved to 
https://github.com/espressomd/espresso/issues/3055

Best regards,
JN

On 2019-08-05 17:10, xibei wrote:
> Hi,
> I am installing espresso on my computer. There is no error message in
> the progress of "cmake" and "make". But when I import the espressomd,
> it returns:
> ________________________________________________________
>  File "<stdin>", line 1, in <module>
>   File
> "/remote/pi309a/jia/software/Espresso/src/python/espressomd/__init__.py",
> line 23, in <module>
>     import espressomd._init
> ImportError:
> /remote/pi309a/jia/software/Espresso/src/core/cluster_analysis/libcluster_analysis.so.4:
> undefined symbol: _ZTIN5boost7archive6detail14basic_iarchiveE
> ___________end___________
> The output of cmake is:
> ________________________________________________________
>
>  -- The C compiler identification is GNU 6.3.0
> -- The CXX compiler identification is GNU 6.3.0
> -- 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
> -- Config file:
> /remote/pi309a/jia/espresso/src/core/myconfig-default.hpp
> -- Performing Test result__PRETTY_FUNCTION__
> -- Performing Test result__PRETTY_FUNCTION__ - Success
> -- Found PythonInterp: /usr/bin/python (found version "2.7.13")
> -- Found Cython version 0.25.2
> -- Found Cython: /usr/bin/cython (Required is at least version "0.23")
>
> -- Found NumPy: /usr/lib/python2.7/dist-packages/numpy/core/include
> (found version "1.12.1")
> -- NumPy ver. 1.12.1 found (include:
> /usr/lib/python2.7/dist-packages/numpy/core/include)
> -- Found FFTW3: /usr/lib/x86_64-linux-gnu/libfftw3.so
> -- HDF5: Using hdf5 compiler wrapper to determine C configuration
> -- Found HDF5:
> /usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/x86_64-linux-gnu/libpthread.so;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.so;/usr/lib/x86_64-linux-gnu/libm.so
> (found suitable version "1.10.0.1", minimum required is "1.8") found
> components:  C
> -- Found PkgConfig: /usr/bin/pkg-config (found version "0.29")
> -- Found GSL: /usr/include (found version "2.3")
> -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
> -- Found MPI_CXX:
> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
>
> -- Found Boost 1.70.0 at /opt/boost_1_70_0/lib/cmake/Boost-1.70.0
> --   Requested configuration: QUIET REQUIRED COMPONENTS
> mpi;serialization;filesystem;system;unit_test_framework
> -- Found boost_headers 1.70.0 at
> /opt/boost_1_70_0/lib/cmake/boost_headers-1.70.0
> -- Found boost_mpi 1.70.0 at
> /opt/boost_1_70_0/lib/cmake/boost_mpi-1.70.0
> -- Adding boost_mpi dependencies: headers
> -- Found boost_serialization 1.70.0 at
> /opt/boost_1_70_0/lib/cmake/boost_serialization-1.70.0
> --   libboost_serialization.a
> -- Adding boost_serialization dependencies: headers
> -- Found boost_filesystem 1.70.0 at
> /opt/boost_1_70_0/lib/cmake/boost_filesystem-1.70.0
> --   libboost_filesystem.a
> -- Adding boost_filesystem dependencies: headers
> -- Found boost_system 1.70.0 at
> /opt/boost_1_70_0/lib/cmake/boost_system-1.70.0
> --   libboost_system.a
> -- Adding boost_system dependencies: headers
> -- Found boost_unit_test_framework 1.70.0 at
> /opt/boost_1_70_0/lib/cmake/boost_unit_test_framework-1.70.0
> --   libboost_unit_test_framework.a
> -- Adding boost_unit_test_framework dependencies: headers
> Boost 1.53.0 found.
> Found Boost components:
>    mpi;serialization;filesystem;system;unit_test_framework
> -- Found Doxygen: /usr/bin/doxygen (found version "1.8.13")
> -- Could NOT find Sphinx (missing:  SPHINX_EXECUTABLE
> SPHINX_API_DOC_EXE) (Required is at least version "1.6.6")
> -- writing /remote/pi309a/jia/software/Espresso/myconfig-sample.hpp
> --
> -- The following OPTIONAL packages have been found:
>  * FFTW3
>  * HDF5 (required version >= 1.8)
>  * PkgConfig
>  * GSL
>  * Doxygen
> -- The following REQUIRED packages have been found:
>  * PythonInterp
>  * Cython (required version >= 0.23)
>  * NumPy
>  * MPI
>  * boost_mpi (required version == 1.70.0)
>  * boost_serialization (required version == 1.70.0)
>  * boost_filesystem (required version == 1.70.0)
>  * boost_system (required version == 1.70.0)
>  * boost_headers (required version == 1.70.0)
>  * boost_unit_test_framework (required version == 1.70.0)
>  * Boost (required version >= 1.53.0)
>
> -- The following OPTIONAL packages have not been found:
>
>  * Sphinx (required version >= 1.6.6)
>
> -- Configuring done
> -- Generating done
> -- Build files have been written to:
> /remote/pi309a/jia/software/Espresso
> ___________end___________
>
> The output of make is:
> _________________________________________________________________
>
> Scanning dependencies of target myconfig
> [  0%] Built target myconfig
> Scanning dependencies of target check_myconfig
> [  0%] Built target check_myconfig
> [  0%] Generating config-features.hpp, config-features.cpp
> Reading definitions from
> /remote/pi309a/jia/espresso/src/features.def...
> Done.
> Writing
> /remote/pi309a/jia/software/Espresso/src/core/config-features.hpp...
> Done.
> Writing
> /remote/pi309a/jia/software/Espresso/src/core/config-features.cpp...
> Done.
> Scanning dependencies of target EspressoConfig
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> [  1%] Linking CXX shared library libcluster_analysis.so
> [  1%] Built target cluster_analysis
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>  __________end _______________
>
> I don't know what is going on. Several months ago I installed it, all
> is fine..
> Thanks very much for any help!
> Best Wishes!
> Jia