/
CMakeLists.txt
934 lines (774 loc) · 36.5 KB
/
CMakeLists.txt
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cmake_minimum_required (VERSION 3.16)
###############################################################################
# Get the Current Version Number so that it can be embedded in files later
###############################################################################
file(STRINGS "${CMAKE_CURRENT_LIST_DIR}/VERSION" _VERSION_DATA REGEX ^[0-9]+_[0-9]+_[0-9]+)
string(REPLACE "_" ";" _VERSION_LIST ${_VERSION_DATA})
list(GET _VERSION_LIST 0 MAJOR_VERSION)
list(GET _VERSION_LIST 1 MINOR_VERSION)
list(GET _VERSION_LIST 2 MICRO_VERSION)
set(CMAKE_PROJECT_VERSION ${MAJOR_VERSION}.${MINOR_VERSION}.${MICRO_VERSION})
################################################################################
# TODO: Add licensing and authorship information
# TODO: Test with FEtk build
# TODO: Handle special mac dependencies
# (configure.ac:1306)
################################################################################
#set(CMAKE_VERBOSE_MAKEFILE false)
cmake_policy(SET CMP0042 NEW) # MacOS RPATH on by default
cmake_policy(SET CMP0048 NEW) # project() command manages the VERSION variables
cmake_policy(SET CMP0054 NEW) # Only interpret if() arguments as variables or keywords when unquoted
cmake_policy(SET CMP0077 NEW) # option() honors normal variables (i.e. does nothing if a normal variable with the same name exists)
cmake_policy(SET CMP0083 NEW) # Pass flags needed for position-independent executables
cmake_policy(SET CMP0091 NEW) # MSVC runtime library flags are selected by an abstraction (i.e. CMAKE_MSVC_RUNTIME_LIBRARY)
set(CMAKE_MACOSX_RPATH 1)
################################################################################
# Set up basic project stuff #
################################################################################
include(CheckIncludeFiles)
include(CheckFunctionExists)
include(ExternalProject)
include(FetchContent)
include(FeatureSummary)
include(InstallRequiredSystemLibraries)
set(APBS_VERSION "${MAJOR_VERSION}.${MINOR_VERSION}.${MICRO_VERSION}")
set(PACKAGE_STRING "APBS ${APBS_VERSION}")
set(CMAKE_BUILD_TYPE "RELWITHDEBINFO")
################################################################################
# NOTE: Overwrite the RPATH information during the install from
# https://gitlab.kitware.com/cmake/community/-/wikis/doc/cmake/RPATH-handling
################################################################################
set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
#include(GNUInstallDirs)
#file(RELATIVE_PATH relDir
# ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_INSTALL_BINDIR}
# ${CMAKE_CURRENT_BINARY_DIR}/${CMAKE_INSTALL_LIBDIR}
#)
#set(CMAKE_INSTALL_RPATH $ORIGIN $ORIGIN/${relDir})
project("APBS" VERSION ${APBS_VERSION})
set(CMAKE_PROJECT_DESCRIPTION "Adaptive Poisson-Boltzmann Solver")
set(CMAKE_PROJECT_HOMEPAGE_URL "http://www.poissonboltzmann.org/")
set_package_properties(APBS PROPERTIES
URL "${CMAKE_PROJECT_HOMEPAGE_URL}"
DESCRIPTION "${CMAKE_PROJECT_DESCRIPTION}"
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.")
list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
if(CMAKE_TOOLCHAIN_FILE)
message(STATUS "Toolchain file is set to <${CMAKE_TOOLCHAIN_FILE}>. Including the file.")
include(${CMAKE_TOOLCHAIN_FILE})
endif()
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
set(CMAKE_INSTALL_PREFIX "${CMAKE_BINARY_DIR}" CACHE PATH "Install prefix" FORCE)
endif()
message(STATUS "Install prefix: ${CMAKE_INSTALL_PREFIX}")
set(CMAKE_INSTALL_DATAROOTDIR "share/apbs")
include(GNUInstallDirs)
set(APBS_ROOT ${PROJECT_SOURCE_DIR})
set(APBS_BUILD ${PROJECT_BINARY_DIR})
set(TOOLS_PATH ${APBS_BUILD}/tools)
set(APBS_LIBS)
set(APBS_LIB_DIRS)
set(PYTHON_VERSION 3.6 CACHE STRING "Python version to be used (or compatible)") # Python 3.6 is the lowest version tested so far
find_file(CONTRIB_PATH "contrib"
PATHS "${APBS_ROOT}"
DOC "The path to contributed modules for apbs")
find_file(EXTERNALS_PATH "externals"
PATHS "${APBS_ROOT}"
DOC "The path to the external git submodules")
set(SYS_LIBPATHS /usr/lib64)
#list(APPEND SYS_LIBPATHS /usr/lib64)
# If this option is true: static libraries will be built
# static dependencies will be preferred
# executables will be statically linked
# If this option is false: dynamic libraries will be built
# dynamic libraries of dependencies will be preferred
# executables will be dynamically linked
option(APBS_STATIC_BUILD "Flag to indicate whether a static build should be used (if false, will be dynamic)" ON)
if(APBS_STATIC_BUILD)
set(FETK_STATIC_BUILD ON)
set(BLA_STATIC ON)
set(BUILD_SHARED_LIBS OFF)
set(CMAKE_SKIP_RPATH ON)
set(CMAKE_MACOSX_RPATH OFF)
#set(CMAKE_LINK_SEARCH_START_STATIC ON)
#set(CMAKE_LINK_SEARCH_END_STATIC ON)
if(WIN32)
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
list(PREPEND CMAKE_FIND_LIBRARY_SUFFIXES .lib .a)
else()
list(PREPEND CMAKE_FIND_LIBRARY_SUFFIXES .a)
endif()
set(Python3_USE_STATIC_LIBS TRUE)
else()
set(FETK_STATIC_BUILD OFF)
set(BLA_STATIC OFF)
set(BUILD_SHARED_LIBS ON)
set(CMAKE_SKIP_RPATH OFF)
set(CMAKE_MACOSX_RPATH ON)
#set(CMAKE_LINK_SEARCH_START_STATIC OFF)
#set(CMAKE_LINK_SEARCH_END_STATIC OFF)
if(WIN32)
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreadedDLL$<$<CONFIG:Debug>:Debug>")
list(PREPEND CMAKE_FIND_LIBRARY_SUFFIXES .dll)
elseif(APPLE)
list(PREPEND CMAKE_FIND_LIBRARY_SUFFIXES .dylib .so)
else()
list(PREPEND CMAKE_FIND_LIBRARY_SUFFIXES .so)
endif()
set(Python3_USE_STATIC_LIBS FALSE)
endif()
message(STATUS "")
message(STATUS "APBS Static build: ${APBS_STATIC_BUILD}")
message(STATUS "Building shared libs: ${BUILD_SHARED_LIBS}")
message(STATUS "Find-library suffixes: ${CMAKE_FIND_LIBRARY_SUFFIXES}")
message(STATUS "")
################################################################################
# Handle the Finite Element Toolkit
#
# To use a released version of FETK:
# - Set FETK_VERSION to the version number (e.g. 1.8.0)
# In this case, the binary archive will be downloaded and used.
#
# To use a non-released version of FETK:
# - Set FETK_VERSION to the git branch or commit hash you want to use (e.g. main)
################################################################################
# FETK is currently required, and therefore this option is disabled
#option(ENABLE_FETK "Enable the finite element solver" ON)
set(FETK_VERSION "57195e55351e04ce6ee0ef56a143c996a9aee7e2" CACHE STRING "Version of FETK to use")
include(ImportFETK)
import_fetk(${FETK_VERSION})
###############################################################################
## NOTE: For Debugging and generally nice information to have
###############################################################################
string(TIMESTAMP COMPILE_TIME)
string(TIMESTAMP COMPILE_YEAR "%Y")
message(STATUS "#############################################################")
message(STATUS "** PROJECT NAME: ${CMAKE_PROJECT_NAME}")
message(STATUS "** PROJECT DESC: ${CMAKE_PROJECT_DESCRIPTION}")
message(STATUS "** PROJECT URL: ${CMAKE_PROJECT_HOMEPAGE_URL}")
message(STATUS "** VERSION_DATA: ${CMAKE_PROJECT_VERSION}")
message(STATUS "** CURRENT_TIME: ${COMPILE_TIME}")
message(STATUS "** CURRENT_YEAR: ${COMPILE_YEAR}")
################################################################################
# Set project paths #
################################################################################
message(STATUS "Setting project paths")
set(CMAKE_CXX_STANDARD 17)
if(WIN32)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -W4")
set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /LARGEADDRESSAWARE /STACK:100000000")
set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} /LARGEADDRESSAWARE")
else()
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -fPIC")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wpedantic -fpermissive -fPIC")
endif()
if(APPLE AND BUILD_SHARED_LIBS AND (${CMAKE_CXX_COMPILER_ID} MATCHES "GNU"))
set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -undefined dynamic_lookup")
endif()
###############################################################################
##### 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 ${_path}")
# unset(_path)
# endforeach()
################################################################################
# Debian/Ubuntu hack #
################################################################################
if(EXISTS "/etc/os-release" AND
"${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 #
################################################################################
set(TEMP_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/temp)
file(MAKE_DIRECTORY ${TEMP_OUTPUT_DIR})
################################################################################
# Set the lookup paths for external library dependencies #
################################################################################
message(STATUS "Setting lookup paths for headers and libraries")
set(CMAKE_INCLUDE_PATH "${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
${TEMP_OUTPUT_DIR}
${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
${TEMP_OUTPUT_DIR}
${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 #
################################################################################
if(NOT WIN32)
find_library(MATH_LIBRARY "m")
find_package(Intl REQUIRED)
find_package(Iconv REQUIRED)
list(APPEND APBS_LIBS
util
dl
m
stdc++
${Intl_LIBRARIES}
${Iconv_LIBRARIES}
)
set(MORE_INCLUDE_DIRS
${Intl_INCLUDE_DIRS}
${Iconv_INCLUDE_DIRS}
)
if(MORE_INCLUDE_DIRS)
include_directories(${MORE_INCLUDE_DIRS})
endif()
endif()
find_package( Threads REQUIRED )
list(APPEND APBS_LIBS ${CMAKE_THREAD_LIBS_INIT})
find_package( UMFPACK REQUIRED )
find_package( SuiteSparse REQUIRED )
message(STATUS "UMFPack libraries: ${UMFPACK_LIBRARIES}")
message(STATUS "SUITESPARSE_INCLUDE_DIRS: ${SUITESPARSE_INCLUDE_DIRS}")
message(STATUS "SUITESPARSE_LIBRARIES: ${SUITESPARSE_LIBRARIES}")
list(APPEND APBS_LIBS
${UMFPACK_LIBRARIES}
${SUITESPARSE_LIBRARIES}
)
################################################################################
# Optionally copy NanoShaper executable #
# the actual grab is later for BEM enable #
################################################################################
option(GET_NanoShaper "Put NanoShaper executable in the build directory" OFF)
################################################################################
# Optionally build PYGBE: PYGBE method #
################################################################################
option(ENABLE_PYGBE "Boundary element method using PYGBE" OFF)
if(ENABLE_PYGBE)
message(STATUS "Building PYGBE")
add_definitions(-DENABLE_PYGBE)
#set (Python3_FIND_ABI "OFF" "ANY" "ANY")
find_package(Python3 ${PYTHON_VERSION} EXACT REQUIRED COMPONENTS Interpreter Development)
message(STATUS "******** PYTHON3_VERSION ${Python3_VERSION}")
message(STATUS "******** PYTHON_INCLUDE_DIRS ${Python3_INCLUDE_DIRS}")
message(STATUS "******** PYTHON_LIBRARIES ${Python3_LIBRARIES}")
include_directories(${Python3_INCLUDE_DIRS})
list(APPEND APBS_LIBS ${Python3_LIBRARIES})
# make sure we have PYGBE
# detect virtualenv and set pip args accordingly
if(DEFINED ENV{VIRTUAL_ENV} OR DEFINED ENV{CONDA_PREFIX})
set(_pip_args)
else()
set(_pip_args "--user")
endif()
# then install PYGBE with pip
execute_process(COMMAND ${Python3_EXECUTABLE} -m pip install pygbe ${_pip_args})
endif() # ENABLE_PYGBE
################################################################################
# Optionally build BEM: TABI-PB method #
################################################################################
option(ENABLE_BEM "Boundary element method using TABIPB" OFF)
if(ENABLE_BEM)
message(STATUS "Building TABIPB")
#set(TABI bem)
#set(TABI_PATH ${EXTERNALS_PATH}/${TABI})
set(GET_NanoShaper ON) #CACHE BOOL "Grabbing NanoShaper path"
add_definitions(-DENABLE_BEM)
# We turn the TABIPB/APBS wrapper off and build here instead
set(ENABLE_TABIPB_APBS OFF CACHE BOOL "Turn off TABIPB/APBS wrapper" FORCE)
#add_subdirectory(${EXTERNALS_PATH}/${TABI})
FetchContent_Declare( tabi
GIT_REPOSITORY https://github.com/Treecodes/TABI-PB.git
GIT_TAG fe1c237b057418fed48535db125394607040d9de
)
FetchContent_MakeAvailable( tabi )
include_directories(${tabi_SOURCE_DIR}/src)
include_directories(${tabi_SOURCE_DIR}/src/tabipb_wrap)
add_definitions(-DTABIPB_APBS)
set(TABIPB_LIBFILES
${tabi_SOURCE_DIR}/src/params.cpp
${tabi_SOURCE_DIR}/src/molecule.cpp
${tabi_SOURCE_DIR}/src/particles.cpp
${tabi_SOURCE_DIR}/src/tree.cpp
${tabi_SOURCE_DIR}/src/clusters.cpp
${tabi_SOURCE_DIR}/src/interaction_list.cpp
${tabi_SOURCE_DIR}/src/boundary_element.cpp
${tabi_SOURCE_DIR}/src/gmres.cpp
${tabi_SOURCE_DIR}/src/precondition.cpp
${tabi_SOURCE_DIR}/src/output.cpp
${tabi_SOURCE_DIR}/src/tabipb_wrap/TABIPBWrap.cpp
${tabi_SOURCE_DIR}/src/tabipb_wrap/params_apbs_ctor.cpp
${tabi_SOURCE_DIR}/src/tabipb_wrap/molecule_apbs_ctor.cpp
)
set(TABIPB_HEADERS
${tabi_SOURCE_DIR}/src/boundary_element.h
${tabi_SOURCE_DIR}/src/clusters.h
${tabi_SOURCE_DIR}/src/constants.h
${tabi_SOURCE_DIR}/src/interaction_list.h
${tabi_SOURCE_DIR}/src/molecule.h
${tabi_SOURCE_DIR}/src/output.h
${tabi_SOURCE_DIR}/src/params.h
${tabi_SOURCE_DIR}/src/particles.h
${tabi_SOURCE_DIR}/src/partition.h
${tabi_SOURCE_DIR}/src/tabipb_timers.h
${tabi_SOURCE_DIR}/src/timer.h
${tabi_SOURCE_DIR}/src/tree.h
${tabi_SOURCE_DIR}/src/tabipb_wrap/TABIPBStruct.h
${tabi_SOURCE_DIR}/src/tabipb_wrap/TABIPBWrap.h)
set(TABIPB_LIBNAME TABIPBlib)
add_library(${TABIPB_LIBNAME} ${TABIPB_LIBFILES})
target_link_libraries(${TABIPB_LIBNAME} ${APBS_LIBS})
target_compile_features(${TABIPB_LIBNAME} PRIVATE cxx_std_11)
target_compile_options(${TABIPB_LIBNAME} PRIVATE
$<$<CONFIG:RELEASE>:-O3>
$<$<CONFIG:RELWITHDEBINFO>:-O3>
$<$<CONFIG:DEBUG>:-O0 -Wall>)
install(FILES ${TABIPB_HEADERS} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/tabi COMPONENT headers)
install(TARGETS ${TABIPB_LIBNAME} DESTINATION ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
list(APPEND APBS_LIB_DIRS "${tabi_BINARY_DIR}/lib")
list(APPEND APBS_LIBS TABIPBlib)
endif() # ENABLE_BEM
################################################################################
# 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 executable")
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 "${TEMP_OUTPUT_DIR}/${NANOSHAPER_RAW_BINARY_NAME}")
file(DOWNLOAD ${NANOSHAPER_FULL_URL_PATH} ${TEMP_OUTPUT_DIR}/${NANOSHAPER_RAW_BINARY_NAME})
message(STATUS "NanoShaper Download: ${NANOSHAPER_FULL_URL_PATH} ${TEMP_OUTPUT_DIR}/${NANOSHAPER_RAW_BINARY_NAME}")
endif()
if(NOT ENABLE_BEM)
install(PROGRAMS ${TEMP_OUTPUT_DIR}/${NANOSHAPER_RAW_BINARY_NAME}
DESTINATION ${CMAKE_INSTALL_BINDIR}
COMPONENT executables)
message(STATUS "NanoShaper install: ${TEMP_OUTPUT_DIR}/${NANOSHAPER_RAW_BINARY_NAME} ${CMAKE_INSTALL_BINDIR}")
endif()
endif()
################################################################################
# Handle conditional building with MPI Support #
# There may be a better way, but for now this comes before FETK because FETK #
# depends on having the libraries located. #
################################################################################
option(ENABLE_MPI "Enable MPI parallelism" OFF)
if(ENABLE_MPI)
if(NOT ENABLE_DEBUG)
message(STATUS "Checking for MPI")
find_package(MPI)
if(MPI_FOUND)
message(STATUS "MPI support enabled")
set(HAVE_MPI_H 1)
include_directories(${MPI_C_INCLUDE_PATH})
list(APPEND APBS_LIBS ${MPI_C_LIBRARIES})
else()
message(WARNING "MPI was not found; disabling")
endif()
else()
message(WARNING "MPI may not be enabled in debugging mode")
endif()
endif()
################################################################################
# Optionally build geoflow (git submodule)
################################################################################
option(ENABLE_GEOFLOW "geoflow method" OFF)
if(ENABLE_GEOFLOW)
message(STATUS "Building GEOFLOW")
#add_definitions(-DGEOFLOW_APBS)
#set(ENABLE_GEOFLOW_APBS ON CACHE BOOL "Enable the APBS-Geoflow connection")
#add_subdirectory(${EXTERNALS_PATH}/geoflow_c)
FetchContent_Declare( geoflow
GIT_REPOSITORY https://github.com/Electrostatics/geoflow_c.git
GIT_TAG 39d53269c084f1dc1caa71de95dca77f19da739e
)
FetchContent_MakeAvailable( geoflow )
add_definitions(-DENABLE_GEOFLOW)
list(APPEND APBS_LIBS GeometricFlowLib)
include_directories(${geoflow_SOURCE_DIR}/src)
find_package(Eigen3 REQUIRED)
include_directories(${EIGEN3_INCLUDE_DIR})
endif()
################################################################################
# Optionally build pbam and pbsam (git submodule)
################################################################################
option(ENABLE_PBAM "pbam method" OFF)
option(ENABLE_PBSAM "pbsam method" OFF)
if(ENABLE_PBAM OR ENABLE_PBSAM)
if(ENABLE_PBAM)
message(STATUS "Building PBAM")
set(ENABLE_PBAM_APBS ON CACHE BOOL "Enable the APBS-PBAM connection")
add_definitions(
-DENABLE_PBAM
-DPBAM_APBS
)
list(APPEND APBS_LIBS PBAMLib)
endif()
if(ENABLE_PBSAM)
message(STATUS "Building PBSAM")
set(ENABLE_PBSAM_APBS ON CACHE BOOL "Enable the APBS-PBSAM connection")
find_package(BLAS REQUIRED)
add_definitions(
-DENABLE_PBSAM
-DPBSAM_APBS
)
list(APPEND APBS_LIBS PBSAMLib)
endif()
FetchContent_Declare( pb_s_am
GIT_REPOSITORY https://github.com/Electrostatics/pb_solvers.git
GIT_TAG d3ba994d7ec2b2cad5b3e843784c7cb9f41ace37
)
#add_subdirectory(${EXTERNALS_PATH}/pb_s_am)
FetchContent_MakeAvailable( pb_s_am )
endif()
if(ENABLE_PBAM)
include_directories(${pb_s_am_SOURCE_DIR}/pbam/src)
endif()
if(ENABLE_PBSAM)
include_directories(${pb_s_am_SOURCE_DIR}/pbam/src)
if(ENABLE_PBAM)
include(${pb_s_am_SOURCE_DIR}/cmake/Utils.cmake)
include(${pb_s_am_SOURCE_DIR}/cmake/Dependencies.cmake)
include(${pb_s_am_SOURCE_DIR}/cmake/Summary.cmake)
endif()
endif()
if(ENABLE_PBAM OR ENABLE_PBSAM)
include_directories(${pb_s_am_SOURCE_DIR}/pb_shared/src)
include_directories(${pb_s_am_SOURCE_DIR}/pb_wrap/src)
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 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(FATAL_ERROR "OpenMP was not found. OpenMP support disabled")
endif()
else()
message(WARNING "OpenMP may not be enabled in debugging mode")
endif()
if(NOT BUILD_SHARED_LIBS)
message(FATAL_ERROR "OpenMP cannot be used with a static build")
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 WS2_32)
ADD_DEFINITIONS("/D _CRT_SECURE_NO_WARNINGS")
endif()
################################################################################
# Create APBS configuration file
################################################################################
configure_file(
src/.config/apbscfg.h.in
${APBS_BUILD}/src/apbscfg.h
@ONLY
)
if(ENABLE_iAPBS)
INSTALL(FILES ${APBS_BUILD}/src/apbscfg.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} COMPONENT headers)
endif()
################################################################################
# Optionally build iAPBS interface #
# Note that this requires apbscfg.h, #
# and so must follow the APBS config file section #
################################################################################
option(ENABLE_iAPBS "Enable iAPBS" OFF)
if(ENABLE_iAPBS)
message(STATUS "Building of iAPBS interface enabled")
set(iAPBS_LIBRARY iapbs)
include_directories(${APBS_BUILD}/src)
add_subdirectory(contrib/iapbs/src)
if(NOT TARGET ${iAPBS_LIBRARY})
message(FATAL_ERROR "iAPBS target does not exist: <${iAPBS_LIBRARY}>")
endif()
list(APPEND APBS_LIBS ${iAPBS_LIBRARY})
else()
message(STATUS "Building of iAPBS interface disabled")
endif()
################################################################################
# Build APBS sources #
################################################################################
link_directories(${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" ON)
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 ${CMAKE_INSTALL_DATADIR}
COMPONENT docs
PATTERN "programmer" EXCLUDE
PATTERN "CMakeLists.txt" EXCLUDE)
install(DIRECTORY ${APBS_ROOT}/examples
DESTINATION ${CMAKE_INSTALL_DATADIR}
USE_SOURCE_PERMISSIONS
COMPONENT examples)
install(DIRECTORY ${APBS_ROOT}/tests
DESTINATION ${CMAKE_INSTALL_DATADIR}
COMPONENT tests
FILES_MATCHING
PATTERN "*.py"
PATTERN "*.cfg"
PATTERN "README.*")
if(BUILD_TOOLS)
install(DIRECTORY ${APBS_ROOT}/tools
DESTINATION ${CMAKE_INSTALL_DATADIR}
USE_SOURCE_PERMISSIONS
COMPONENT tools
PATTERN "CMakeLists.txt"
PATTERN "matlab" EXCLUDE
PATTERN "__pycache__" EXCLUDE
PATTERN "*.py[co]" EXCLUDE)
if(NOT "${APBS_ROOT}" STREQUAL "${APBS_BUILD}")
install(DIRECTORY ${APBS_BUILD}/tools/bin
DESTINATION ${CMAKE_INSTALL_DATADIR}/tools
USE_SOURCE_PERMISSIONS
COMPONENT tools)
endif()
endif()
###############################################################################
##### Do Testing
###############################################################################
option(ENABLE_TESTS "Enable tests" ON)
if(${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_VERBATIM_VARIABLES YES)
set(CPACK_SOURCE_IGNORE_FILES ${PROJECT_BINARY_DIR}
.gitignore
/.git/
/tools/matlab/
io.mc
\\.dx
\\.err
\\.log
\\.out
\\.vtk
)
set(CPACK_PACKAGE_VERSION_MAJOR "${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")
set(CPACK_PACKAGE_FILE_NAME "${PACKAGE_NAME}-${APBS_VERSION}.${CMAKE_HOST_SYSTEM_NAME}")
set(CPACK_STRIP_FILES True)
list(APPEND CPACK_GENERATOR "ZIP")
set(CPACK_INCLUDE_TOPLEVEL_DIRECTORY True)
# Control which components get included in the package
# Components in use are: executables, libraries, headers, docs, examples, tests, tools, python
set(CPACK_ARCHIVE_COMPONENT_INSTALL ON)
set(CPACK_COMPONENTS_GROUPING ALL_COMPONENTS_IN_ONE)
get_cmake_property(CPACK_COMPONENTS_ALL COMPONENTS)
#list(REMOVE_ITEM CPACK_COMPONENTS_ALL "libraries" "headers" "docs" )
list(REMOVE_ITEM CPACK_COMPONENTS_ALL "docs" )
if(CPACK_GENERATOR MATCHES "^(7Z|TBZ2|TGZ|TXZ|TZ|TZST|ZIP)$")
set(CPACK_TOPLEVEL_TAG ${CPACK_PACKAGE_NAME})
set(CPACK_SET_DESTDIR False)
set(CPACK_COMPONENT_INCLUDE_TOPLEVEL_DIRECTORY True)
endif()
include (CPack)