Hei,
I tried to create my own CMakeLists-file, in order to include a second 
project (which provides a shared library, which should be coupled to the 
main executable). Thus my CMakeLists-file looks now like
# Set the name of the project and target:
set(CMAKE_C_COMPILER /usr/lib64/mpi/gcc/openmpi3/bin/mpicc)
set(CMAKE_CXX_COMPILER /usr/lib64/mpi/gcc/openmpi3/bin/mpic++)
set(TARGET "main")
PROJECT(${TARGET})
set(CMAKE_BUILD_TYPE Debug)
cmake_policy(SET CMP0015 NEW)
cmake_policy(SET CMP0003 NEW)
include_directories("include" 
            "../pulse_propagation/include"
            "/opt/dealii/include"
            "/opt/trilinos/include"
            "/opt/intel/tbb/include"
            "/opt/petsc/include"
            "/opt/slepc/include"
            "/opt/p4est/include")
file(GLOB_RECURSE TARGET_SRC  "source/*.cpp")
file(GLOB_RECURSE TARGET_INC  "include/*.h" )

SET(TARGET_SRC ${TARGET_SRC}  ${TARGET_INC})
add_executable(${TARGET} ${TARGET_SRC})
find_library(PULSE_LIBRARY pulse_propagation HINT ../pulse_propagation/)
find_library(FILESYSTEM boost_filesystem)
target_link_libraries(${TARGET} ${FILESYSTEM} ${PULSE_LIBRARY})
# Usually, you will not need to modify anything beyond this point...

CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12)

FIND_PACKAGE(deal.II 9.0.0 QUIET
  HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR}
  )
IF(NOT ${deal.II_FOUND})
  MESSAGE(FATAL_ERROR "\n"
    "*** Could not locate a (sufficiently recent) version of deal.II. 
***\n\n"
    "You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to 
cmake\n"
    "or set an environment variable \"DEAL_II_DIR\" that contains this 
path."
    )
ENDIF()


DEAL_II_INITIALIZE_CACHED_VARIABLES()
SET(CLEAN_UP_FILES *.log *.*tu* *.gmv *.gnuplot *.gpl *.eps *.pov *.vtk *.ucd 
*.d2 *.vtu *.pvtu)
#PROJECT(${TARGET})
DEAL_II_INVOKE_AUTOPILOT()
But now the command "DEAL_II_INVOKE_AUTOPILOT()" results in the error 
  ADD_EXECUTABLE cannot create target "main" because another target with the
  same name already exists.  The existing target is an executable created in
  source directory
  "~/Documents/heat_equation_with_pulse_propagation/heat_equation".
  See documentation for policy CMP0002 for more details.
Call Stack (most recent call first):
  CMakeLists.txt:44 (DEAL_II_INVOKE_AUTOPILOT)

Removing the command "add_executable" results in 
CMake Error at CMakeLists.txt:24 (target_link_libraries):
  Cannot specify link libraries for target "main" which is not built by this
  project.

What do I have to fix in order to remove the collision with 
DEAL_II_INVOKE_AUTOPILOT?
Thanks!



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