Geant4 input with MPI not compiling

Question

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

We can't help you much because you don't tell us enough how you are doing it... Wild guess would be you're using `mpicc` rather than `mpicxx`. — Zulan, Jul 18 '19 at 12:40
You may need to install a different version of `libstdc++.so`. Try to see if GLIBCXX 3.4 is available in your stdc++ library by running `strings /usr/lib/x86_64-linux-gnu/libstdc++.so.6 | grep GLIBC` — Kevin, Jul 18 '19 at 12:48
@squareskittles GLIBCXX3.4 is installed. What to do next to install a different version of libstdc++.so? — SANDIPAN DAWN, Jul 18 '19 at 15:08
@Zulan I have added the cmakelist.txt file through which I am compiling can you please check again. The complete set of example I am tryng to compile is in the link: https://drive.google.com/open?id=1gkvUsilp9wKK3WZ9E8SAEzwVg5nVKrJJ — SANDIPAN DAWN, Jul 18 '19 at 15:16
If `GLIBCXX 3.4` is listed when you ran the `strings` command, then your `libstdc++.so` file is probably OK. — Kevin, Jul 18 '19 at 15:29
Can you run `make VERBOSE=1` and provide the output? Specifically, we should check if `-lstdc++` is present at the link stage. — Kevin, Jul 18 '19 at 15:33
@squareskittles Then what might be the cause of the error message? I am clueless — SANDIPAN DAWN, Jul 18 '19 at 15:35
@squareskittles sure and a big thanks. I will post the message as soon as I am able to run it — SANDIPAN DAWN, Jul 18 '19 at 15:37
Let us [continue this discussion in chat](https://chat.stackoverflow.com/rooms/196650/discussion-between-sandipan-dawn-and-squareskittles). — SANDIPAN DAWN, Jul 18 '19 at 16:57

score 2 · Accepted Answer · answered Jul 18 '19 at 17:39

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")

Geant4 input with MPI not compiling

1 Answers1