[SOLVED] Geant4 input with MPI not compiling

Geant4 input with MPI not compiling

I am trying to compile a Geant4 Input in multiple cores using MPI (G4MPI). But the make command is yielding following error:

/usr/bin/ld: CMakeFiles/exMPI01.dir/exMPI01.cc.o: undefined reference to symbol '_ZNSt8ios_base4InitD1Ev@@GLIBCXX_3.4'
/usr/lib/x86_64-linux-gnu/libstdc++.so.6: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status

Though I am able to compile Inputs without MPI

My cmakelist file is:

# - CmakeLists.txt for building an application

#----------------------------------------------------------------------------
# Setup the project
cmake_minimum_required(VERSION 2.6 FATAL_ERROR)
project(exMPI01)

#----------------------------------------------------------------------------
# check MPI package...
find_package(MPI REQUIRED)

# modify these variables if needed
#set(CMAKE_CXX_COMPILER mpicxx)
#set(CMAKE_CXX_COMPILER mpiicpc)

#set(CMAKE_CXX_INCLUDE_PATH )

#------------------------------------------------------------------------------
# Find Geant4 package, activating all available UI and Vis drivers by default
# You can set WITH_GEANT4_UIVIS to OFF via the command line or ccmake/cmake-gui
# to build a batch mode only executable
option(WITH_GEANT4_UIVIS "Build example with Geant4 UI and Vis drivers" ON)
if(WITH_GEANT4_UIVIS)
  find_package(Geant4 REQUIRED ui_all vis_all)
else()
  find_package(Geant4 REQUIRED)
endif()


find_package(G4mpi REQUIRED)

#----------------------------------------------------------------------------
# Setup Geant4 include directories and compile definitions
#
include(${Geant4_USE_FILE})

#----------------------------------------------------------------------------
# Locate sources and headers for this project
#
include_directories(${PROJECT_SOURCE_DIR}/include)
file(GLOB sources ${PROJECT_SOURCE_DIR}/src/*.cc)
file(GLOB headers ${PROJECT_SOURCE_DIR}/include/*.hh)

include_directories(${CMAKE_CURRENT_SOURCE_DIR}/include
                  ${Geant4_INCLUDE_DIR}
                  ${G4mpi_INCLUDE_DIR})

#----------------------------------------------------------------------------
# Add the executable, and link it to the Geant4 libraries
#
add_executable(exMPI01 exMPI01.cc ${sources} ${headers})
target_link_libraries(exMPI01 ${G4mpi_LIBRARIES} ${Geant4_LIBRARIES})

#----------------------------------------------------------------------------
# Copy all scripts to the build directory, i.e. the directory in which we
# build exMPI01. This is so that we can run the executable directly because it
# relies on these scripts being in the current working directory.
#
set(exMPI01_SCRIPTS
    run.mac
    v.mac
  )

foreach(_script ${exMPI01_SCRIPTS})
  configure_file(
    ${PROJECT_SOURCE_DIR}/${_script}
    ${PROJECT_BINARY_DIR}/${_script}
    COPYONLY
    )
endforeach()

#----------------------------------------------------------------------------
# Install the executable to 'bin' directory under CMAKE_INSTALL_PREFIX
#
install(TARGETS exMPI01 RUNTIME DESTINATION bin)

I have tried using -lstdc++ at the end of the command line but did not work

Any suggestions will be of great help

The complete set of example is in the link: https://drive.google.com/open?id=1gkvUsilp9wKK3WZ9E8SAEzwVg5nVKrJJ

Solution

One solution for this case is to update the target_link_libraries in your CMake so that you manually link to the libstdc++.so library. In addition, you can also update the CMAKE_EXE_LINKER_FLAGS variable as shown here:

target_link_libraries(exMPI01 ${G4mpi_LIBRARIES} ${Geant4_LIBRARIES} stdc++)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -stdlib=libc++ -lc++abi")