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CMakeLists.txt
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cmake_minimum_required (VERSION 3.12)
################################################################################
# TODO: Add licensing and authorship information
# TODO: Test with FEtk build
# TODO: Handle special mac dependencies
# (configure.ac:1306)
################################################################################
set(CMAKE_VERBOSE_MAKEFILE true)
cmake_policy(SET CMP0054 OLD)
cmake_policy(SET CMP0042 NEW)
set(CMAKE_MACOSX_RPATH 1)
################################################################################
# Set up basic project stuff #
################################################################################
include(CheckIncludeFiles)
include(CheckFunctionExists)
include(ExternalProject)
include(FeatureSummary)
set(CMAKE_MAJOR_VERSION "3")
set(CMAKE_MINOR_VERSION "0")
set(CMAKE_MICRO_VERSION "0")
set(APBS_VERSION "${CMAKE_MAJOR_VERSION}.${CMAKE_MICRO_VERSION}")
set(PACKAGE_STRING "${APBS_VERSION}")
set(CMAKE_BUILD_TYPE "RELWITHDEBINFO")
################################################################################
# NOTE: Overwrite the RPATH information during the install from
# https://gitlab.kitware.com/cmake/community/-/wikis/doc/cmake/RPATH-handling
################################################################################
set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
project("APBS" VERSION ${CMAKE_MAJOR_VERSION}.${CMAKE_MINOR_VERSION}.${CMAKE_MICRO_VERSION})
set_package_properties(APBS PROPERTIES
URL "http://www.poissonboltzmann.org/"
DESCRIPTION "Adaptive Poisson-Boltzmann Solver"
PURPOSE "APBS solves the equations of continuum electrostatics for large \
biomolecular assemblages. This software was designed 'from the \
ground up' using modern design principles to ensure its ability \
to interface with other computational packages and evolve as \
methods and applications change over time. The APBS code is \
accompanied by extensive documentation for both users and \
programmers and is supported by a variety of utilities for \
preparing calculations and analyzing results. Finally, the free, \
open-source APBS license ensures its accessibility to the entire \
biomedical community.")
OPTION(BUILD_SHARED_LIBS "Build shared libraries." OFF)
################################################################################
# Set project paths #
################################################################################
message(STATUS "Setting project paths")
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Werror -fpermissive -fPIC")
if(WIN32)
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /STACK:100000000")
endif()
if(APPLE AND BUILD_SHARED_LIBS)
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -undefined dynamic_lookup")
endif()
set(APBS_ROOT ${PROJECT_SOURCE_DIR})
set(APBS_BUILD ${PROJECT_BINARY_DIR})
set(EXECUTABLE_OUTPUT_PATH ${APBS_BUILD}/bin)
set(LIBRARY_OUTPUT_PATH ${APBS_BUILD}/lib)
set(TOOLS_PATH ${APBS_BUILD}/tools)
set(APBS_BINARY ${EXECUTABLE_OUTPUT_PATH}/apbs)
set(LIBRARY_INSTALL_PATH lib)
set(HEADER_INSTALL_PATH include/apbs)
set(EXECUTABLE_INSTALL_PATH bin)
set(SHARE_INSTALL_PATH share/apbs)
set(APBS_LIBS)
set(APBS_LIB_DIRS)
find_file(CONTRIB_PATH "contrib"
PATHS "${APBS_ROOT}"
DOC "The path to contributed modules for apbs")
find_file(EXTERNALS_PATH "externals"
PATHS "${APBS_ROOT}"
DOC "The path to the external git submodules")
set(SYS_LIBPATHS /usr/lib64)
#list(APPEND SYS_LIBPATHS /usr/lib64)
###############################################################################
##### Boilerplate Setup
###############################################################################
# include(GNUInstallDirs)
# set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
# set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR})
# set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR})
# message(STATUS "** Project will be installed to ${CMAKE_INSTALL_PREFIX}")
###############################################################################
##### Offer the builder the choice of overriding the installation directories
###############################################################################
# set(INSTALL_LIBDIR ${CMAKE_INSTALL_LIBDIR} CACHE PATH "Installation directory for libraries")
# set(INSTALL_BINDIR ${CMAKE_INSTALL_BINDIR} CACHE PATH "Installation directory for executables")
# set(INSTALL_INCLUDEDIR ${CMAKE_INSTALL_INCLUDEDIR} CACHE PATH "Installation directory for header files")
# set(INSTALL_CMAKEDIR ${DEF_INSTALL_CMAKEDIR} CACHE PATH "Installation directory for CMake files")
###############################################################################
##### Report to builder
###############################################################################
# foreach(p LIB BIN INCLUDE CMAKE)
# file(TO_NATIVE_PATH ${CMAKE_INSTALL_PREFIX}/${INSTALL_${p}DIR} _path )
# message(STATUS "** Installing ${p} components to ${_path}")
# unset(_path)
# endforeach()
################################################################################
# Debian/Ubuntu hack for #
# https://github.com/Electrostatics/apbs-pdb2pqr/issues/364 #
################################################################################
if(EXISTS "/etc/debian_version" AND
"${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -Wl,--no-as-needed")
endif()
################################################################################
# Set up temporary files and directories #
################################################################################
file(MAKE_DIRECTORY ${EXECUTABLE_OUTPUT_PATH}/temp)
################################################################################
# Set the lookup paths for external library dependencies #
################################################################################
message(STATUS "Setting lookup paths for headers and libraries")
set(CMAKE_INCLUDE_PATH "${CMAKE_INCLUDE_PATH}")
list(APPEND CMAKE_INCLUDE_PATH /usr/include)
list(APPEND CMAKE_INCLUDE_PATH /usr/local/include)
################################################################################
# Enable ansi pedantic compiling #
################################################################################
option(ENABLE_PEDANTIC "Enable the pedantic ansi compilation" OFF)
if(ENABLE_PEDANTIC)
ADD_DEFINITIONS("-Wall -pedantic -ansi")
message(STATUS "Pedantic compilation enabled")
endif()
################################################################################
# Determine Machine Epsilon values #
################################################################################
OPTION(CHECK_EPSILON "Compute machine epsilon values" YES)
if(CHECK_EPSILON)
message(STATUS "Computing machine epsilon values")
try_run(
FLOAT_EPSILON_COMPILED
FLOAT_EPSILON_COMPUTED
${EXECUTABLE_OUTPUT_PATH}/temp
${APBS_ROOT}/src/.config/float_epsilon.c
RUN_OUTPUT_VARIABLE FLOAT_EPSILON_OUTPUT
)
if(FLOAT_EPSILON_COMPUTED)
message(STATUS "Floating point epsilon is ${FLOAT_EPSILON_OUTPUT}")
set(FLOAT_EPSILON ${FLOAT_EPSILON_OUTPUT})
else()
message(FATAL_ERROR "Couldn't compute floating point machine epsilon")
endif()
try_run(
DOUBLE_EPSILON_COMPILED
DOUBLE_EPSILON_COMPUTED
${EXECUTABLE_OUTPUT_PATH}/temp
${APBS_ROOT}/src/.config/double_epsilon.c
RUN_OUTPUT_VARIABLE DOUBLE_EPSILON_OUTPUT
)
if(DOUBLE_EPSILON_COMPUTED)
message(STATUS "Double precision epsilon is ${DOUBLE_EPSILON_OUTPUT}")
set(DOUBLE_EPSILON ${DOUBLE_EPSILON_OUTPUT})
else()
message(FATAL_ERROR "Couldn't compute double precision machine epsilon")
endif()
else()
set(FLOAT_EPSILON "1.19209290e-7")
set(DOUBLE_EPSILON "2.2204460492503131e-16")
endif()
################################################################################
# Check for a few required functions #
################################################################################
CHECK_FUNCTION_EXISTS(time HAVE_TIME_FUNC)
if(NOT HAVE_TIME_FUNC)
message(FATAL_ERROR "Required time function not found")
endif()
CHECK_FUNCTION_EXISTS(rand HAVE_RAND_FUNC)
if(NOT HAVE_RAND_FUNC)
message(FATAL_ERROR "Required rand function not found")
endif()
CHECK_FUNCTION_EXISTS(srand HAVE_SRAND_FUNC)
if(NOT HAVE_SRAND_FUNC)
message(FATAL_ERROR "Required srand function not found")
endif()
################################################################################
# Find some libraries; Windows finds these automatically #
################################################################################
if(NOT WIN32)
find_library(MATH_LIBRARY "m")
list(APPEND APBS_LIBS m stdc++)
endif()
################################################################################
# Optionally copy NanoShaper exectutable
# the actual grab is later for PBSAM enable
################################################################################
option(GET_NanoShaper "Put NanoShaper executable in the build directory" OFF)
################################################################################
# Optionally build BEM: TABI-PB method #
################################################################################
option(ENABLE_BEM "Boundary element method using TABIPB" OFF)
if(ENABLE_BEM)
message(STATUS "Building TABIPB")
add_definitions(-DENABLE_BEM)
set(TABI bem)
set(TABI_PATH ${EXTERNALS_PATH}/${TABI})
set(GET_NanoShaper ON) #CACHE BOOL "Grabbing NanoShaper path"
if(WIN32)
ExternalProject_add(${TABI}
SOURCE_DIR ${TABI_PATH}
CMAKE_ARGS -DENABLE_TABIPB_APBS=ON -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
BUILD_COMMAND "${CMAKE_COMMAND}" --build . --config $<CONFIG> --target TABIPBlib
INSTALL_COMMAND "")
else()
ExternalProject_add(${TABI}
SOURCE_DIR ${TABI_PATH}
CMAKE_ARGS -DENABLE_TABIPB_APBS=ON -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
BUILD_COMMAND "${CMAKE_COMMAND}" --build . --target TABIPBlib
INSTALL_COMMAND "")
endif()
ExternalProject_Get_Property(${TABI} binary_dir)
list(APPEND APBS_LIB_DIRS "${binary_dir}")
list(APPEND APBS_LIBS TABIPBlib)
include_directories(${EXTERNALS_PATH}/${TABI})
include_directories(${EXTERNALS_PATH}/${TABI}/src)
if(BUILD_SHARED_LIBS)
install(FILES ${binary_dir}/libTABIPBlib${CMAKE_SHARED_LIBRARY_SUFFIX}
DESTINATION ${LIBRARY_INSTALL_PATH})
endif()
endif() # ENABLE_BEM
################################################################################
# Handle conditional building with MPI Support #
# There may be a better way, but for now this comes before FETK because FETK #
# depends on having the libraries located. #
################################################################################
option(ENABLE_MPI "Enable MPI parallelism" OFF)
if(ENABLE_MPI)
if(NOT ENABLE_DEBUG)
message(STATUS "Checking for MPI")
find_package(MPI)
if(MPI_FOUND)
message(STATUS "MPI support enabled")
set(HAVE_MPI_H 1)
include_directories(${MPI_C_INCLUDE_PATH})
list(APPEND APBS_LIBS ${MPI_C_LIBRARIES})
else()
message(WARNING "MPI was not found; disabling")
endif()
else()
message(WARNING "MPI may not be enabled in debugging mode")
endif()
endif()
################################################################################
# Deal with MALOC #
# Note that we depend exclusively on the MALOC that is in our external FETK #
# repository. Also note, that in order for this to work on Windows, we've had #
# to add CMake support to MALOC, and that FETK has no such support, in general.#
################################################################################
if(NOT ENABLE_FETK)
# We'll use autotools to build MALOC if FETK is enabled.
add_subdirectory(${EXTERNALS_PATH}/fetk/maloc)
include_directories(${EXTERNALS_PATH}/fetk/maloc/src/base
${EXTERNALS_PATH}/fetk/maloc/src/vsys
${EXTERNALS_PATH}/fetk/maloc/src/vsh
${EXTERNALS_PATH}/fetk/maloc/src/psh)
list(APPEND APBS_LIB_DIRS ${EXTERNALS_PATH}/fetk/maloc/lib)
list(APPEND APBS_LIBS maloc)
endif()
################################################################################
# Handle the finite element solver dependencies #
################################################################################
option(ENABLE_FETK "Enable the finite element solver" OFF)
if(ENABLE_FETK)
if(WIN32)
message(FATAL_ERROR "FETK will not built on Windows because it uses autotools!")
else()
message(STATUS "Building FETK components.")
set(CONFIG_OPTS --prefix=<INSTALL_DIR>)
set(MPI_ENV "")
if(HAVE_MPI_H)
list(APPEND CONFIG_OPTS --enable-mpi)
# MALOC just cares about libmpi
foreach(LIB_PATH ${MPI_C_LIBRARIES})
get_filename_component(LIB ${LIB_PATH} NAME_WE)
if(LIB STREQUAL "libmpi")
get_filename_component(MPI_LIB_DIR ${LIB_PATH} DIRECTORY)
endif()
endforeach()
set(MPI_ENV "FETK_MPI_INCLUDE=${MPI_C_INCLUDE_PATH}" "FETK_MPI_LIBRARY=${MPI_LIB_DIR}")
endif()
ExternalProject_Add(fetk-maloc
PREFIX fetk
SOURCE_DIR ${EXTERNALS_PATH}/fetk/maloc/src
CONFIGURE_COMMAND ${MPI_ENV} ${EXTERNALS_PATH}/fetk/maloc/configure ${CONFIG_OPTS}
BUILD_COMMAND ${MAKE})
ExternalProject_Add(fetk-punc
PREFIX fetk
DEPENDS fetk-maloc
SOURCE_DIR ${EXTERNALS_PATH}/fetk/punc/src
CONFIGURE_COMMAND ${MPI_ENV} FETK_INCLUDE=<INSTALL_DIR>/include FETK_LIBRARY=<INSTALL_DIR>/lib ${EXTERNALS_PATH}/fetk/punc/configure ${CONFIG_OPTS}
BUILD_COMMAND ${MAKE})
ExternalProject_Add(fetk-gamer
PREFIX fetk
DEPENDS fetk-maloc
SOURCE_DIR ${EXTERNALS_PATH}/fetk/gamer/src
CONFIGURE_COMMAND ${MPI_ENV} FETK_INCLUDE=<INSTALL_DIR>/include FETK_LIBRARY=<INSTALL_DIR>/lib ${EXTERNALS_PATH}/fetk/gamer/configure ${CONFIG_OPTS}
BUILD_COMMAND ${MAKE})
ExternalProject_Add(fetk-mc
PREFIX fetk
DEPENDS fetk-maloc fetk-punc
SOURCE_DIR ${EXTERNALS_PATH}/fetk/mc/src
CONFIGURE_COMMAND ${MPI_ENV} FETK_INCLUDE=<INSTALL_DIR>/include FETK_LIBRARY=<INSTALL_DIR>/lib ${EXTERNALS_PATH}/fetk/mc/configure ${CONFIG_OPTS}
BUILD_COMMAND ${MAKE})
set(FETK_ENABLED 1)
ExternalProject_Get_Property(fetk-maloc install_dir)
include_directories(${install_dir}/include)
list(APPEND APBS_LIB_DIRS "${install_dir}/lib")
list(APPEND APBS_LIBS
maloc
amd
punc
mc
gamer
superlu
umfpack
blas
vf2c
tetgen
triangle
readline
termcap)
if(BUILD_SHARED_LIBS)
install(DIRECTORY ${install_dir}/lib/
DESTINATION ${LIBRARY_INSTALL_PATH})
endif()
SET(HAVE_MC_H 1)
SET(HAVE_PUNC_H 1)
SET(HAVE_BIOM_H 1)
endif()
endif()
################################################################################
# Optionally build geoflow (git submodule)
################################################################################
option(ENABLE_GEOFLOW "geoflow method" OFF)
if(ENABLE_GEOFLOW)
message(STATUS "Building GEOFLOW")
add_definitions(-DGEOFLOW_APBS)
if(WIN32)
ExternalProject_Add(geoflow
SOURCE_DIR ${EXTERNALS_PATH}/geoflow_c
CMAKE_ARGS -DENABLE_GEOFLOW_APBS=ON -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
BUILD_COMMAND "${CMAKE_COMMAND}" --build . --config $<CONFIG> --target GeometricFlowLib
INSTALL_COMMAND "")
else()
ExternalProject_Add(geoflow
SOURCE_DIR ${EXTERNALS_PATH}/geoflow_c
CMAKE_ARGS -DENABLE_GEOFLOW_APBS=ON -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
BUILD_COMMAND "${CMAKE_COMMAND}" --build . --target GeometricFlowLib
INSTALL_COMMAND "")
endif()
ExternalProject_Get_Property(geoflow binary_dir)
add_definitions(-DENABLE_GEOFLOW)
list(APPEND APBS_LIB_DIRS "${binary_dir}/lib")
list(APPEND APBS_LIBS GeometricFlowLib)
include_directories(${EXTERNALS_PATH}/geoflow_c/src)
if(BUILD_SHARED_LIBS)
install(FILES ${binary_dir}/lib/libGeometricFlowLib${CMAKE_SHARED_LIBRARY_SUFFIX}
DESTINATION ${LIBRARY_INSTALL_PATH})
endif()
endif()
################################################################################
# Optionally build pbam (git submodule)
################################################################################
option(ENABLE_PBAM "pbam method" OFF)
if(ENABLE_PBAM)
message(STATUS "Building PBAM")
add_definitions(-DPBAM_APBS)
if(WIN32)
ExternalProject_Add(pbam
SOURCE_DIR ${EXTERNALS_PATH}/pb_s_am
CMAKE_ARGS -DENABLE_PBAM_APBS=ON -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
BUILD_COMMAND "${CMAKE_COMMAND}" --build . --config $<CONFIG> --target PBAMLib
INSTALL_COMMAND "")
else()
ExternalProject_Add(pbam
SOURCE_DIR ${EXTERNALS_PATH}/pb_s_am
CMAKE_ARGS -DENABLE_PBAM_APBS=ON -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
BUILD_COMMAND "${CMAKE_COMMAND}" --build . --target PBAMLib
INSTALL_COMMAND "")
endif()
ExternalProject_Get_Property(pbam binary_dir)
add_definitions(-DENABLE_PBAM)
list(APPEND APBS_LIB_DIRS "${binary_dir}/pbam/src")
list(APPEND APBS_LIBS PBAMLib)
include_directories(${EXTERNALS_PATH}/pb_s_am/pbam/src)
include_directories(${EXTERNALS_PATH}/pb_s_am/pb_shared/src)
include_directories(${EXTERNALS_PATH}/pb_s_am/pb_wrap/src)
if(BUILD_SHARED_LIBS)
install(FILES ${binary_dir}/pbam/src/libPBAMLib${CMAKE_SHARED_LIBRARY_SUFFIX}
DESTINATION ${LIBRARY_INSTALL_PATH})
endif()
endif()
################################################################################
# Optionally build pbsam (git submodule)
################################################################################
option(ENABLE_PBSAM "pbsam method" OFF)
if(ENABLE_PBSAM)
message(STATUS "Building PBSAM")
add_definitions(-DPBSAM_APBS)
list(APPEND CMAKE_MODULE_PATH ${EXTERNALS_PATH}/pb_s_am/cmake/modules)
include(${EXTERNALS_PATH}/pb_s_am/cmake/Utils.cmake)
include(${EXTERNALS_PATH}/pb_s_am/cmake/Dependencies.cmake)
include(${EXTERNALS_PATH}/pb_s_am/cmake/Summary.cmake)
if(WIN32)
ExternalProject_Add(pbsam
SOURCE_DIR ${EXTERNALS_PATH}/pb_s_am
CMAKE_ARGS -DENABLE_PBSAM_APBS=ON -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
BUILD_COMMAND "${CMAKE_COMMAND}" --build . --config $<CONFIG> --target PBSAMLib
INSTALL_COMMAND "")
else()
ExternalProject_Add(pbsam
SOURCE_DIR ${EXTERNALS_PATH}/pb_s_am
CMAKE_ARGS -DENABLE_PBSAM_APBS=ON -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
BUILD_COMMAND "${CMAKE_COMMAND}" --build . --target PBSAMLib
INSTALL_COMMAND "")
endif()
ExternalProject_Get_Property(pbsam binary_dir)
add_definitions(-DENABLE_PBSAM)
list(APPEND APBS_LIB_DIRS "${binary_dir}/pbsam/src")
if(WIN32)
list(APPEND APBS_LIBS PBSAMLib ${PBSAM_LINKER_LIBS})
else()
list(APPEND APBS_LIBS stdc++ PBSAMLib ${PBSAM_LINKER_LIBS})
endif()
message(STATUS "Adding in " ${PBSAM_LINKER_LIBS} )
include_directories(${EXTERNALS_PATH}/pb_s_am/pbsam/src)
include_directories(${EXTERNALS_PATH}/pb_s_am/pb_shared/src)
include_directories(${EXTERNALS_PATH}/pb_s_am/pb_wrap/src)
if(BUILD_SHARED_LIBS)
install(FILES ${binary_dir}/pbsam/src/libPBSAMLib${CMAKE_SHARED_LIBRARY_SUFFIX}
DESTINATION ${LIBRARY_INSTALL_PATH})
endif()
endif()
################################################################################
# Getting nanoshaper binary
################################################################################
set(MESH_ROOT_URL_PATH "https://github.com/lwwilson1/mesh_routines/releases/download/v1.6")
if(GET_NanoShaper)
set(NANOSHAPER_FULL_URL_PATH)
set(NANOSHAPER_RAW_BINARY_NAME "NanoShaper")
message(STATUS "Copying NanoShaper exectuable")
if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") # Mac OS X specific code
set(NANOSHAPER_FULL_URL_PATH "${MESH_ROOT_URL_PATH}/NanoShaper_OSX")
elseif(${CMAKE_SYSTEM_NAME} MATCHES "Linux") # Linux specific code
set(NANOSHAPER_FULL_URL_PATH "${MESH_ROOT_URL_PATH}/NanoShaper_Linux64")
elseif(${CMAKE_SYSTEM_NAME} MATCHES "Windows") # Windows specific code
set(NANOSHAPER_FULL_URL_PATH "${MESH_ROOT_URL_PATH}/NanoShaper32.exe")
set(NANOSHAPER_RAW_BINARY_NAME "NanoShaper.exe")
endif()
if (NOT EXISTS "${EXECUTABLE_OUTPUT_PATH}/${NANOSHAPER_RAW_BINARY_NAME}")
file(DOWNLOAD ${NANOSHAPER_FULL_URL_PATH} ${EXECUTABLE_OUTPUT_PATH}/${NANOSHAPER_RAW_BINARY_NAME})
message(STATUS "NanoShaper Download: ${NANOSHAPER_FULL_URL_PATH} ${EXECUTABLE_OUTPUT_PATH}/${NANOSHAPER_RAW_BINARY_NAME}")
endif()
install(PROGRAMS ${EXECUTABLE_OUTPUT_PATH}/${NANOSHAPER_RAW_BINARY_NAME}
DESTINATION ${EXECUTABLE_INSTALL_PATH})
message(STATUS "NanoShaper install: ${EXECUTABLE_OUTPUT_PATH}/${NANOSHAPER_RAW_BINARY_NAME} ${EXECUTABLE_INSTALL_PATH}")
endif()
################################################################################
# Handle conditional fast mode #
################################################################################
option(ENABLE_FAST "Enable fast mode" OFF)
if(ENABLE_FAST)
set(APBS_FAST 1)
message(STATUS "Fast mode enabled")
endif()
################################################################################
# Handle conditional TINKER support #
################################################################################
option(ENABLE_TINKER "Enable TINKER support" OFF)
if(ENABLE_TINKER)
set(WITH_TINKER 1)
message(STATUS "Tinker enabled")
endif()
################################################################################
# Handle conditional availability of macro embedding #
################################################################################
try_compile(
HAVE_EMBED
${APBS_BUILD}/build
${APBS_ROOT}/src/.config/embed_test.c
)
# TODO: Determine if the EMBED macro is even used
################################################################################
# Handle conditional debug building #
################################################################################
option(ENABLE_DEBUG "Enable debugging mode" OFF)
if(ENABLE_DEBUG)
set(CMAKE_BUILD_TYPE Debug)
set(DEBUG 1)
message(STATUS "Debugging compilation enabled")
endif()
################################################################################
# Enable inline functions conditionally dependent on debug mode #
################################################################################
option(ENABLE_INLINE "Enable inline functions" ON)
if(ENABLE_INLINE)
set(APBS_NOINLINE 1)
message(STATUS "Inline functions enabled")
endif()
################################################################################
# Handle conditional building with quiet mode #
################################################################################
option(ENABLE_QUIET "Enable quiet mode" OFF)
if(ENABLE_QUIET)
set(VAPBSQUIET 1)
message(STATUS "Quiet mode enabled")
endif()
################################################################################
# Handle conditional building with verbose debugging information printouts #
################################################################################
option(ENABLE_VERBOSE_DEBUG "Enable verbose debugging mode" ON)
if(ENABLE_VERBOSE_DEBUG)
set(VERBOSE_DEBUG 1)
message(STATUS "Verbose debugging mode enabled")
endif()
################################################################################
# Configure Python #
# Buidling the Python goodness happens in the tool/python directory. #
################################################################################
option(ENABLE_PYTHON "Enable python support" OFF)
#If(ENABLE_PYTHON AND UNIX AND NOT APPLE AND NOT BUILD_SHARED_LIBS)
# message(FATAL_ERROR "In order to build the APBS Python shared library, BUILD_SHARED_LIBS must be enabled.")
#elseif(ENABLE_PYTHON AND APPLE AND BUILD_SHARED_LIBS)
# message(FATAL_ERROR "ENABLE_PYTHON option in OSX systems requires the variable BUILD_SHARED_LIBS to be set to off.")
#endif()
################################################################################
# Handle conditional building with OpenMP #
################################################################################
option(ENABLE_OPENMP "Enable OpenMP parallelism" OFF)
if(ENABLE_OPENMP)
if(NOT ENABLE_DEBUG)
message(STATUS "Checking for OpenMP")
find_package(OpenMP)
if(OPENMP_FOUND)
message(STATUS "OpenMP support enabled")
add_definitions("${OpenMP_C_FLAGS}")
list(APPEND APBS_LIBS ${OpenMP_C_FLAGS})
else()
message(WARNING "OpenMP was not found. OpenMP support disabled")
endif()
else()
message(WARNING "OpenMP may not be enabled in debugging mode")
endif()
endif()
################################################################################
# Handle library checks for embedded unix environments in windows #
################################################################################
if(MINGW)
message(STATUS "Checking for wsock32 in MinGW environment")
find_library(MINGW_WSOCK32
NAMES wsock32
PATHS ${SYS_LIBPATHS}
DOC "The wsock32 library")
if(MINGW_WSOCK32)
message(STATUS "The wsock32 library was found: ${MINGW_HAS_WSOCK32}")
else()
message(FATAL_ERROR "The wsock32 library was not fond")
endif()
endif()
if(CYGWIN)
message(STATUS "Checking for wsock32 in Cygwin environment")
find_library(CYGWIN_WSOCK32
NAMES wsock32
PATHS ${SYS_LIBPATHS}
DOC "The wsock32 library")
if(CYGWIN_WSOCK32)
message(STATUS "The wsock32 library was found: ${CYGWIN_WSOCK32}")
list(APPEND APBS_LIBS ${CYGWIN_WSOCK32})
else()
message(FATAL_ERROR "The wsock32 library was not fond")
endif()
set(HAVE_CYGWIN 1)
endif()
if(NOT CYGWIN AND NOT MINGW AND WIN32)
list(APPEND APBS_LIBS wsock32)
ADD_DEFINITIONS("/D _CRT_SECURE_NO_WARNINGS")
endif()
################################################################################
# Build APBS sources #
################################################################################
link_directories(${APBS_LIB_DIRS})
include_directories(${APBS_ROOT}/src ${APBS_BUILD}/src ${APBS_ROOT}/include)
add_subdirectory(src)
################################################################################
# Build APBS documentation #
################################################################################
option(BUILD_DOC "Build/Rebuild documentation using doxygen" OFF)
if(BUILD_DOC)
message(STATUS "Building documentation enabled")
add_subdirectory(docs)
endif()
################################################################################
# Handle conditional building with verbose debugging information printouts #
################################################################################
option(BUILD_TOOLS "Build supplemental tools" ON)
if(BUILD_TOOLS)
message(STATUS "Supplemental tools enabled")
add_subdirectory(tools)
endif()
################################################################################
# Set up additional directories to install #
################################################################################
install(DIRECTORY ${APBS_ROOT}/docs
DESTINATION ${SHARE_INSTALL_PATH}
PATTERN "programmer" EXCLUDE
PATTERN "CMakeLists.txt" EXCLUDE)
if(BUILD_DOC)
install(DIRECTORY ${APBS_BUILD}/docs/programmer
DESTINATION ${SHARE_INSTALL_PATH}/docs
PATTERN "Doxyfile" EXCLUDE
PATTERN "latex" EXCLUDE
PATTERN "mainpage.h" EXCLUDE)
endif()
install(DIRECTORY ${APBS_ROOT}/examples
DESTINATION ${SHARE_INSTALL_PATH})
install(DIRECTORY ${APBS_ROOT}/tests
DESTINATION ${SHARE_INSTALL_PATH}
FILES_MATCHING
PATTERN "*.py"
PATTERN "README")
if(BUILD_TOOLS)
install(DIRECTORY ${APBS_ROOT}/tools
DESTINATION ${SHARE_INSTALL_PATH}
USE_SOURCE_PERMISSIONS
PATTERN "CMakeLists.txt"
PATTERN "matlab" EXCLUDE)
if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}")
install(DIRECTORY ${APBS_BUILD}/tools/bin
DESTINATION ${SHARE_INSTALL_PATH}/tools
USE_SOURCE_PERMISSIONS)
endif()
endif()
################################################################################
# Optionally build iAPBS interface #
################################################################################
option(ENABLE_iAPBS "Enable iAPBS" OFF)
if(ENABLE_iAPBS)
message(STATUS "Building of iAPBS interface enabled")
add_subdirectory(contrib/iapbs/src)
list(APPEND APBS_LIBS ${iAPBS_LIBRARY})
endif()
################################################################################
# Clean up temporary files and directories #
################################################################################
file(REMOVE_RECURSE ${EXECUTABLE_OUTPUT_PATH}/temp)
###############################################################################
##### Do Testing
###############################################################################
option(ENABLE_TESTS "Enable tests" ON)
if(${ENABLE_TESTS})
enable_testing()
add_subdirectory(tests)
endif()
###############################################################################
##### Generate Packages
###############################################################################
# string(TOLOWER ${PROJECT_NAME} PACKAGE_NAME)
set(PACKAGE_NAME "${PROJECT_NAME}")
set(CPACK_PACKAGE_NAME "${PACKAGE_NAME}")
set(CPACK_PACKAGE_DESCRIPTION "APBS - Adaptive Poisson Boltzmann Solver")
set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/COPYING")
set(CPACK_PACKAGE_DESCRIPTION_FILE "${PROJECT_SOURCE_DIR}/README.md")
set(CPACK_SOURCE_IGNORE_FILES "${PROJECT_BINARY_DIR};/.git/;.gitignore;/tools/matlab/")
set(CPACK_PACKAGE_VERSION_MAJOR "${CMAKE_MAJOR_VERSION}")
set(CPACK_PACKAGE_VERSION_MINOR "${CMAKE_MINOR_VERSION}")
set(CPACK_PACKAGE_VERSION_PATCH "${CMAKE_MICRO_VERSION}")
# NOTE: The following is tempting but does not work!
# set(FULL_PACKAGE_NAME "${PACKAGE_NAME}-${MAJOR_VERSION}.${MINOR_VERSION}.${MICRO_VERSION}")
set(CPACK_PACKAGE_VENDOR "PNNL")
set(CPACK_PACKAGE_CONTACT "APBS - https://github.com/Electrostatics/apbs-pdb2pqr")
set(CPACK_PACKAGE_FILE_NAME "${PACKAGE_NAME}-${APBS_VERSION}.${CMAKE_HOST_SYSTEM_NAME}")
set(CPACK_STRIP_FILES True)
list(APPEND CPACK_GENERATOR "ZIP")
set(CPACK_INCLUDE_TOPLEVEL_DIRECTORY True)
if(CPACK_GENERATOR MATCHES "^(7Z|TBZ2|TGZ|TXZ|TZ|TZST|ZIP)$")
set(CPACK_TOPLEVEL_TAG ${CPACK_PACKAGE_NAME})
set(CPACK_SET_DESTDIR False)
set(CPACK_COMPONENT_INCLUDE_TOPLEVEL_DIRECTORY False)
endif()
include (CPack)