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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required(VERSION 2.8.0 FATAL_ERROR)
project(CoupledCells)
set(PROJECT_NAME "Coupled Arterial Cells")
set(PROJECT_COPYRIGHT "UC HPC, University of Canterbury, NZ")
set(PROJECT_VERSION_MAJOR 1)
set(PROJECT_VERSION_MINOR 0)
set(PROJECT_VERSION ${PROJECT_VERSION_MAJOR}.${PROJECT_VERSION_MINOR})
set(PROJECT_DESCRIPTION "Large-scale simulation of chemical species transport in coupled arterial cells.")
# Build type defaults to Release unless specified
if (NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release")
endif (NOT CMAKE_BUILD_TYPE)
# Add local CMake directory to CMake module path to load project-specific modules.
set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake ${CMAKE_MODULE_PATH})
# Take care of the non-standard location of malloc includes on Mac.
if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
# Location of malloc.h on OS X.
include_directories(/usr/include/malloc/)
endif(${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
if (${CMAKE_SYSTEM_NAME} STREQUAL "AIX")
# AIX (fitzroy) needs some help
set(POE "/usr/lpp/ppe.poe")
if(EXISTS "${POE}/include" AND EXISTS "${POE}/lib")
set(MPI_INCLUDE_PATH "${POE}/include")
set(MPI_LIBRARIES "${POE}/lib/libmpi_r.a;${POE}/lib/libvtd_r.a")
set(MPI_C_INCLUDE_PATH "${MPI_INCLUDE_PATH}")
set(MPI_C_LIBRARIES "${MPI_LIBRARIES}")
set(MPI_CXX_INCLUDE_PATH "${MPI_INCLUDE_PATH}")
set(MPI_CXX_LIBRARIES "${MPI_LIBRARIES}")
set(MPI_CXX_COMPILER "mpCC_r")
message(STATUS "Setting MPI_CXX_INCLUDE_PATH=${MPI_CXX_INCLUDE_PATH}")
message(STATUS "Setting MPI_CXX_LIBRARIES=${MPI_CXX_LIBRARIES}")
if (CMAKE_BUILD_TYPE STREQUAL "Release")
set(ADD_FLAGS "-q64 -O3 -qstrict -qmaxmem=-1 -qtune=pwr6 -qarch=pwr6 -qcache=auto -qhot -qipa -qsimd -qreport")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${ADD_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${ADD_FLAGS}")
set(CMAKE_Fortran_FLAGS "${CMAKE_CXX_FLAGS} ${ADD_FLAGS}")
endif (CMAKE_BUILD_TYPE STREQUAL "Release")
endif(EXISTS "${POE}/include" AND EXISTS "${POE}/lib")
endif(${CMAKE_SYSTEM_NAME} STREQUAL "AIX")
if (${CMAKE_SYSTEM_NAME} STREQUAL "Linux")
if (CMAKE_BUILD_TYPE STREQUAL "gprof")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
endif()
if (CMAKE_BUILD_TYPE STREQUAL "Report")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -ftree-vectorize -fopt-info-vec-missed -fopt-info-inline-missed")
endif()
endif()
# Unable to run without MPI.
find_package(MPI REQUIRED)
include_directories(${MPI_CXX_INCLUDE_PATH})
set(CMAKE_C_COMPILER "${MPI_C_COMPILER}")
set(CMAKE_CXX_COMPILER "${MPI_CXX_COMPILER}")
option(ENABLE_OPENMP "Turn OpenMP on/off" OFF)
if (ENABLE_OPENMP)
find_package(OpenMP)
if (OPENMP_FOUND)
add_definitions(-DHAVE_OPENMP)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
message(STATUS "c++ flags: ${CMAKE_CXX_FLAGS}")
message(STATUS "openmp flags: ${OpenMP_CXX_FLAGS}")
endif()
endif()
# Unable to run without HDF5.
find_package(HDF5 REQUIRED)
include_directories(${HDF5_INCLUDE_DIR})
# ODE implementation choice.
set(ODE_SOLVER "RK_suite" CACHE STRING
"ODE solver implementation to be used in the simulations.")
# Available options for ODE implementation.
set(ODE_SOLVER_CHOICES "RK_suite;SUNDIALS_arkode;BOOST_odeint" CACHE INTERNAL
"List of values for choosing a solver to be compiled against.")
# Enable ODE choices in the GUI drop-down menue.
# The appropriate choice will have to be typed in when using CLI.
set_property(CACHE ODE_SOLVER PROPERTY STRINGS ${ODE_SOLVER_CHOICES})
# In this case we want to compile RK Suite in the ext/rksuite-1.0 directory.
if(${ODE_SOLVER} STREQUAL "RK_suite")
message(STATUS "Selected ODE solver: Local RK Suite")
# Pass preprocessor macro definition to the compiler.
add_definitions(-DRK_SUITE)
# Add RK Suite library.
include_directories(${PROJECT_SOURCE_DIR}/ext/rksuite-1.0)
add_subdirectory(${PROJECT_SOURCE_DIR}/ext/rksuite-1.0)
# Remember the library for the ODE solver implementation to link in to the executable.
set(ODE_SOLVER_LIBS RKSuite)
set(ODE_SOLVER_WRAPPER src/solver_rk.cpp)
# In this case we want to find the system SUNDIALS libraries, including ARKODE.
elseif(${ODE_SOLVER} STREQUAL "SUNDIALS_arkode")
message(STATUS "Selected ODE solver: system SUNDIALS arkode")
# Pass preprocessor macro definition to the compiler.
add_definitions(-DARK_ODE)
# Find SUNDIALS
find_package(SUNDIALS REQUIRED)
# Add the location of the SUNDIALS headers.
include_directories(${SUNDIALS_INCLUDES})
# Remember the libraries for the ODE solver implementation to link in to the executable.
set(ODE_SOLVER_LIBS ${SUNDIALS_LIBRARIES})
set(ODE_SOLVER_WRAPPER src/solver_arkode.cpp)
# In this case we want to find the system BOOST libraries, including ODEINT.
elseif(${ODE_SOLVER} STREQUAL "BOOST_odeint")
message(STATUS "Selected ODE solver: system Boost odeint")
# Pass preprocessor macro definition to the compiler.
add_definitions(-DBOOST_ODEINT)
# Find Boost
find_package(Boost REQUIRED)
# Add the location of the Boost headers.
include_directories(${Boost_INCLUDE_DIRS})
set(ODE_SOLVER_WRAPPER src/solver_odeint.cpp)
endif(${ODE_SOLVER} STREQUAL "RK_suite")
# Optionally turn on performance monitoring with TAU on AIX
# if ${TAU_MAKEFILE} is set
if (${CMAKE_SYSTEM_NAME} STREQUAL "AIX" AND (NOT "$ENV{TAU_MAKEFILE}" STREQUAL ""))
get_filename_component(TAU_LIBRARY_DIR "$ENV{TAU_MAKEFILE}" DIRECTORY)
get_filename_component(TAU_DIR "${TAU_LIBRARY_DIR}" DIRECTORY)
message(STATUS "**********************************************************")
message(STATUS "Will use TAU compilers:")
message(STATUS "**********************************************************")
set(CMAKE_C_COMPILER "taucc")
set(CMAKE_C_FLAGS
"-optVerbose -O2 -qstrict -qmaxmem=-1 -qarch=pwr6 -qtune=pwr6")
set(CMAKE_CXX_COMPILER "taucxx")
set(CMAKE_CXX_FLAGS
"-optVerbose -O3 -qstrict -qmaxmem=-1 -qarch=pwr6 -qtune=pwr6 -qreport -qhot -qsimd")
set(CMAKE_Fortran_COMPILER "tauf90")
set(CMAKE_Fortran_FLAGS
"-optVerbose ${CMAKE_Fortran_FLAGS} -qstrict -qfixed -O2 -qmaxmem=-1 -qarch=pwr6 -qtune=pwr6")
# POE MPI libraries interfere with TAU
set(MPI_LIBRARIES "")
endif()
# Allow the user to set directory where reference results are stored so
# we can run ctest on the results
set(REF_RESULTS_DIR CACHE FILEPATH "")
set(HAVE_REF_RESULTS "NO")
if(NOT ${REF_RESULTS_DIR} STREQUAL "" AND (EXISTS ${REF_RESULTS_DIR}))
message(STATUS "Reference test results directory set to ${REF_RESULTS_DIR}")
set(HAVE_REF_RESULTS "YES")
endif()
file(GLOB HDRs src/*.h)
set (SRCs
src/time_profiling.cpp
src/koenigsberger_model.cpp
src/update.cpp
src/compute.cpp
src/simulation_main.cpp
src/writeHDF5.cpp
src/debug_helpers.cpp
src/topology.cpp
src/gather.cpp
${ODE_SOLVER_WRAPPER})
add_executable(coupledCellsModel ${SRCs} ${HDRs})
# Can use either set_target_properties or set.
# set_target_properties(coupledCellsModel PROPERTIES COMPILE_FLAGS "${MPI_CXX_COMPILE_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_CXX_COMPILE_FLAGS}")
# Can use either set_target_properties or set.
# set_target_properties(coupledCellsModel PROPERTIES LINK_FLAGS "${MPI_CXX_LINK_FLAGS}")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MPI_CXX_LINK_FLAGS}")
target_link_libraries(coupledCellsModel
${MPI_LIBRARIES}
${HDF5_LIBRARIES}
${ODE_SOLVER_LIBS})
message(STATUS "C++ compiler flags: ${CMAKE_CXX_FLAGS}")
find_package(Doxygen)
find_Package(Graphviz)
if(DOXYGEN_DOT_EXECUTABLE)
set(HAVE_DOT "YES")
set(CALL_GRAPH "YES")
set(CALLER_GRAPH "YES")
else(DOXYGEN_DOT_EXECUTABLE)
set(HAVE_DOT "NO")
set(CALL_GRAPH "NO")
set(CALLER_GRAPH "NO")
endif(DOXYGEN_DOT_EXECUTABLE)
set(DOXY_INPUT_DIR ${PROJECT_SOURCE_DIR}/src)
set(DOXY_OUTPUT_DIR ${PROJECT_BINARY_DIR}/doc/doxygen)
file(MAKE_DIRECTORY ${DOXY_OUTPUT_DIR})
set(DOXY_API_LINK_TAGS ${DOXY_OUTPUT_DIR}/DoxyLink.tag)
configure_file(
${PROJECT_SOURCE_DIR}/doc/doxygen/Doxyfile.in
${PROJECT_BINARY_DIR}/Doxyfile
@ONLY)
if(DOXYGEN_FOUND)
add_custom_target(doxyDocs
COMMAND ${DOXYGEN_EXECUTABLE} ${PROJECT_BINARY_DIR}/Doxyfile
WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
COMMENT "Generating API documentation with Doxygen" VERBATIM)
endif(DOXYGEN_FOUND)
find_package(Sphinx)
if(NOT DEFINED SPHINX_THEME)
set(SPHINX_THEME default)
endif()
if(NOT DEFINED SPHINX_THEME_DIR)
set(SPHINX_THEME_DIR)
endif()
set(SPHINX_BUILD_DIR ${PROJECT_BINARY_DIR}/_sphinxbuild)
# Muffle the warning about missing directory.
# Might have to use _static directory in source to copy files here if necessary.
file(MAKE_DIRECTORY ${SPHINX_BUILD_DIR}/_static)
set(SPHINX_OUTPUT_DIR ${PROJECT_BINARY_DIR}/doc/sphinx)
configure_file(
${PROJECT_SOURCE_DIR}/doc/sphinx/conf.py.in
${SPHINX_BUILD_DIR}/conf.py
@ONLY)
if(SPHINX_FOUND)
add_custom_target(sphinxDocs
COMMAND ${SPHINX_EXECUTABLE}
-q -b html
-c ${SPHINX_BUILD_DIR}
-d ${SPHINX_BUILD_DIR}
${PROJECT_SOURCE_DIR}/doc/sphinx
${SPHINX_OUTPUT_DIR}
COMMENT "Building HTML documentation with Sphinx" VERBATIM)
endif(SPHINX_FOUND)
# CTest
enable_testing()
add_subdirectory(tests)