#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2009,2010,2011,2012,2013 by the GROMACS development team.
# Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
# Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
# as published by the Free Software Foundation; either version 2.1
# of the License, or (at your option) any later version.
#
# GROMACS is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
# consider that scientific software is very special. Version
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# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
cmake_minimum_required(VERSION 3.13)
cmake_policy(SET CMP0074 NEW) # From CMake 3.12
cmake_policy(SET CMP0068 NEW) # From CMake-3.9
# CMake modules/macros are in a subdirectory to keep this file cleaner
# This needs to be set before project() in order to pick up toolchain files
list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
if(CMAKE_SYSTEM_NAME STREQUAL "Darwin")
# Providing a default value >=10.14 helps to find modern C++ compatibility,
# such as by defaulting to the Clang libc++ instead of libstdc++.
set(CMAKE_OSX_DEPLOYMENT_TARGET 10.14 CACHE STRING
"OS X deployment target affects default SDK version and compiler flags.")
# By default, limit the binary architecture to a single 64-bit build.
set(CMAKE_OSX_ARCHITECTURES x86_64 CACHE STRING
"OS X architecture affects the compatibility of the (potentially fat) binaries produced."
FORCE)
endif()
project(Gromacs)
set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
include(gmxManageCcache)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
find_package(LibStdCpp)
# Python is first referenced in gmxVersionInfo, so we perform the search early
# to find a suitable installation for all components.
include(gmxPythonDiscovery)
# Set up common version variables, as well as general information about
# the build tree (whether the build is from a source package or from a git
# repository). Also declares a few functions that will be used for generating
# version info files later.
include(gmxBuildTreeInfo)
include(gmxVersionInfo)
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
endif()
if("${CMAKE_INSTALL_PREFIX}" STREQUAL "${CMAKE_BINARY_DIR}")
message(FATAL_ERROR "GROMACS cannot be installed into the build tree, choose a different location for CMAKE_INSTALL_PREFIX")
endif()
include(gmxBuildTypeReference)
include(gmxBuildTypeProfile)
include(gmxBuildTypeTSAN)
include(gmxBuildTypeASAN)
include(gmxBuildTypeMSAN)
include(gmxBuildTypeUBSAN)
include(gmxBuildTypeReleaseWithAssert)
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile TSAN ASAN MSAN UBSAN." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
"MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile" "TSAN" "ASAN" "MSAN" "UBSAN")
endif()
if(CMAKE_CONFIGURATION_TYPES)
# Add appropriate GROMACS-specific build types for the Visual
# Studio generator (Debug, Release, MinSizeRel and RelWithDebInfo
# are already present by default).
list(APPEND CMAKE_CONFIGURATION_TYPES "RelWithAssert" "Reference")
list(REMOVE_DUPLICATES CMAKE_CONFIGURATION_TYPES)
set(CMAKE_CONFIGURATION_TYPES "${CMAKE_CONFIGURATION_TYPES}" CACHE STRING
"List of configuration types"
FORCE)
endif()
set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBINFO RELWITHASSERT MINSIZEREL PROFILE)
set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
include(gmxCTestUtilities)
gmx_ctest_init()
include(gmxCPackUtilities)
gmx_cpack_init()
# Variables that accumulate stuff influencing the installed headers
set(INSTALLED_HEADER_INCLUDE_DIRS "")
set(INSTALLED_HEADER_DEFINITIONS "")
########################################################################
# Global non-cache variables for implementing the build system
########################################################################
# These variables collect libraries that GROMACS requires for
# linking. They should be appended to with list(APPEND ${name}
# new-library) calls. They are:
# - Libraries that are required for libgromacs (only)
set(GMX_EXTRA_LIBRARIES "")
# - Libraries that are required for all code in the repository
set(GMX_COMMON_LIBRARIES "")
# - Libraries that all code linked against libgromacs needs
# (i.e., something that is exposed in installed headers).
set(GMX_PUBLIC_LIBRARIES "")
########################################################################
# Check and warn if cache generated on a different host is being reused
########################################################################
if(CMAKE_HOST_UNIX)
execute_process(COMMAND hostname
OUTPUT_VARIABLE TMP_HOSTNAME
OUTPUT_STRIP_TRAILING_WHITESPACE)
# Only check for host name if not running in a CI environment, as the cache might
# be reused there between different machines in different stages
if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}"
AND NOT DEFINED ENV{CI_JOB_ID})
message(WARNING "
The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
is being reused! This could lead to inconsistencies; therefore, it is
recommended to regenerate the cache!")
endif()
set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
"Hostname of the machine where the cache was generated.")
endif()
########################################################################
# Detect architecture before setting options so we can alter defaults
########################################################################
# Detect the architecture the compiler is targetting, detect
# SIMD instructions possibilities on that hardware, suggest SIMD instruction set
# to use if none is specified, and populate the cache option for CPU
# SIMD.
include(gmxDetectTargetArchitecture)
gmx_detect_target_architecture()
########################################################################
# User input options #
########################################################################
include(gmxOptionUtilities)
set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
# Fujitsu only has SIMD in double precision, so this will be faster
gmx_set_boolean(GMX_DOUBLE_DEFAULT GMX_TARGET_FUJITSU_SPARC64)
option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" ${GMX_DOUBLE_DEFAULT})
option(GMX_RELAXED_DOUBLE_PRECISION "Accept single precision 1/sqrt(x) when using Fujitsu HPC-ACE SIMD" OFF)
mark_as_advanced(GMX_RELAXED_DOUBLE_PRECISION)
option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
gmx_dependent_option(
GMX_MPI_IN_PLACE
"Enable MPI_IN_PLACE for MPIs that have it defined"
ON
GMX_MPI)
mark_as_advanced(GMX_MPI_IN_PLACE)
option(GMX_MIMIC "Enable MiMiC QM/MM interface (CPMD is required)" OFF)
option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
mark_as_advanced(GMX_FAHCORE)
option(GMX_COOL_QUOTES "Enable GROMACS cool quotes" ON)
mark_as_advanced(GMX_COOL_QUOTES)
gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
option(GMX_INSTALL_LEGACY_API "Install legacy headers" OFF)
gmx_option_multichoice(
GMX_GPU
"Framework for GPU acceleration"
OFF
OFF CUDA OpenCL SYCL)
gmx_option_multichoice(
GMX_SIMD
"SIMD instruction set for CPU kernels and compiler optimization"
"AUTO"
AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD ARM_SVE IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
if(GMX_TARGET_MIC)
set(GMX_FFT_LIBRARY_DEFAULT "mkl")
else()
set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
endif()
gmx_option_multichoice(
GMX_FFT_LIBRARY
"FFT library"
"${GMX_FFT_LIBRARY_DEFAULT}"
fftw3 mkl "fftpack[built-in]")
gmx_dependent_option(
GMX_BUILD_OWN_FFTW
"Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
OFF
"GMX_FFT_LIBRARY STREQUAL FFTW3")
gmx_dependent_option(
GMX_DISABLE_FFTW_MEASURE
"Do not optimize FFTW setups (not needed with SSE)"
OFF
"GMX_FFT_LIBRARY STREQUAL FFTW3")
mark_as_advanced(GMX_BUILD_OWN_FFTW)
mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
# This should be moved to a separate NBNXN cmake module when that code is cleaned up and modularized
option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
mark_as_advanced(GMX_BROKEN_CALLOC)
option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
option(GMX_BUILD_FOR_COVERAGE
"Tune build for better code coverage metrics (e.g., disable asserts)"
OFF)
mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
option(GMX_DEVELOPER_BUILD
"Enable Developer convenience features: always build unit-tests"
OFF)
mark_as_advanced(GMX_DEVELOPER_BUILD)
gmx_set_boolean(GMX_COMPILER_WARNINGS_DEFAULT "NOT SOURCE_IS_SOURCE_DISTRIBUTION")
option(GMX_COMPILER_WARNINGS
"Enable a default set of compiler warnings"
${GMX_COMPILER_WARNINGS_DEFAULT})
mark_as_advanced(GMX_COMPILER_WARNINGS)
# Always turn on compiler warnings with a developer build.
gmx_add_cache_dependency(GMX_COMPILER_WARNINGS BOOL "NOT GMX_DEVELOPER_BUILD" ON)
option(GMX_BUILD_SHARED_EXE
"Build exectuables as shared binaries. If not set, this disables rpath and dynamic linker flags in an attempt to build a static binary, but this may require setting up the toolchain properly and making appropriate libraries available."
ON)
mark_as_advanced(GMX_BUILD_SHARED_EXE)
option(GMX_PHYSICAL_VALIDATION
"Include physical validation tests in ctest environment. These can then be called using 'make check-phys' or
'make check-all'. Warning: Running the physical validation tests takes significantly more time than other tests!"
OFF)
mark_as_advanced(GMX_PHYSICAL_VALIDATION)
######################################################################
# Detect OpenMP support
######################################################################
# The OpenMP detection _must_ come before tests for other CFLAGS.
include(gmxManageOpenMP)
######################################################################
# Compiler tests
# These need to be done early (before further tests).
#####################################################################
include(gmxTestIntelLLVM)
include(gmxCFlags)
gmx_c_flags()
# These variables should be used for CMake-style lists (ie. separated
# by semicolons) of additional compiler flags which are not generated
# in gmxCFlags nor are SIMD or MPI related.
#
# TODO These variables should be consolidated into
# EXTRA_COMPILER_FLAGS so that we we don't perpetrate bugs where
# things that work in C compilation (e.g. merging from old branches)
# might not also work for C++ compilation.
set(EXTRA_C_FLAGS "")
set(EXTRA_CXX_FLAGS "")
# Run through a number of tests for buggy compilers and other issues
include(gmxTestCompilerProblems)
gmx_test_compiler_problems()
# Implement double-precision option. This is complicated because we
# need installed headers to use the precision mode of the build that
# produced the library, but cannot use config.h in that case. We also
# want such variables to always have a definition, because #if is more
# robust than #ifdef. So, we put this value on the compiler command
# line in all cases.
#
# GMX_RELAXED_DOUBLE_PRECISION does not need to be handled here,
# because no installed header needs it
if(GMX_DOUBLE)
set(GMX_DOUBLE_VALUE 1)
else()
set(GMX_DOUBLE_VALUE 0)
endif()
add_definitions(-DGMX_DOUBLE=${GMX_DOUBLE_VALUE})
list(APPEND INSTALLED_HEADER_DEFINITIONS "-DGMX_DOUBLE=${GMX_DOUBLE_VALUE}")
option(GMX_IMD "Enable Interactive Molecular Dynamics (IMD) sessions, e.g. with VMD" ON)
if(GMX_IMD AND WIN32)
list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
endif()
########################################################################
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
include(CheckIncludeFiles)
include(CheckIncludeFileCXX)
check_include_files(unistd.h HAVE_UNISTD_H)
check_include_files(pwd.h HAVE_PWD_H)
check_include_files(dirent.h HAVE_DIRENT_H)
check_include_files(time.h HAVE_TIME_H)
check_include_files(sys/time.h HAVE_SYS_TIME_H)
check_include_files(io.h HAVE_IO_H)
check_include_files(sched.h HAVE_SCHED_H)
check_include_files(xmmintrin.h HAVE_XMMINTRIN_H)
include(CheckCXXSymbolExists)
check_cxx_symbol_exists(gettimeofday sys/time.h HAVE_GETTIMEOFDAY)
check_cxx_symbol_exists(sysconf unistd.h HAVE_SYSCONF)
check_cxx_symbol_exists(nice unistd.h HAVE_NICE)
check_cxx_symbol_exists(fsync unistd.h HAVE_FSYNC)
check_cxx_symbol_exists(_fileno stdio.h HAVE__FILENO)
check_cxx_symbol_exists(fileno stdio.h HAVE_FILENO)
check_cxx_symbol_exists(_commit io.h HAVE__COMMIT)
check_cxx_symbol_exists(sigaction signal.h HAVE_SIGACTION)
# We cannot check for the __builtins as symbols, but check if code compiles
check_cxx_source_compiles("int main(){ return __builtin_clz(1);}" HAVE_BUILTIN_CLZ)
check_cxx_source_compiles("int main(){ return __builtin_clzll(1);}" HAVE_BUILTIN_CLZLL)
if(MSVC)
check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned long i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE)
check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned __int64 i=1;_BitScanReverse64(&r,i);return r;}" HAVE_BITSCANREVERSE64)
elseif(CMAKE_CXX_COMPILER_ID MATCHES "XL")
check_cxx_source_compiles("int main(){ return __cntlz4(1);}" HAVE_CNTLZ4)
check_cxx_source_compiles("int main(){ return __cntlz8(1);}" HAVE_CNTLZ8)
endif()
include(CheckLibraryExists)
find_library(HAVE_LIBM m)
mark_as_advanced(HAVE_LIBM)
check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
check_library_exists(m feenableexcept "" HAVE_FEENABLEEXCEPT)
check_library_exists(m fedisableexcept "" HAVE_FEDISABLEEXCEPT)
include(TestSchedAffinity)
test_sched_affinity(HAVE_SCHED_AFFINITY)
# Aligned memory allocation. We need to check for both mm_malloc(),
# posix_memalign(), memalign(), and on windows also _aligned_malloc()
include(gmxTestMMMalloc)
gmx_test_mm_malloc(HAVE__MM_MALLOC)
check_cxx_symbol_exists(posix_memalign stdlib.h HAVE_POSIX_MEMALIGN)
check_cxx_symbol_exists(memalign stdlib.h HAVE_MEMALIGN)
if(MSVC)
# No need to waste time on this test on platforms where it will never be true
check_cxx_symbol_exists(_aligned_malloc stdlib.h HAVE__ALIGNED_MALLOC)
endif()
include(TestBigEndian)
test_big_endian(GMX_INTEGER_BIG_ENDIAN)
gmx_set_boolean(GMX_USE_NICE "HAVE_UNISTD_H AND HAVE_NICE")
# Management of GROMACS options for specific toolchains should go
# here. Because the initial settings for some of the main options have
# already happened, but things like library detection and MPI compiler
# feature detection have not, the docstrings for any over-rides of
# GROMACS defaults or user settings will make sense. Also, any
# toolchain-related reasons for choosing whether to detect various
# things can be sorted out now, before the detection takes place.
if(GMX_TARGET_FUJITSU_SPARC64)
include(gmxManageFujitsuSparc64)
endif()
########################################################################
#Process MPI settings
########################################################################
include(gmxManageMPI)
########################################################################
#Process MiMiC settings
########################################################################
include(gmxManageMimic)
########################################################################
#Process shared/static library settings
########################################################################
include(gmxManageSharedLibraries)
########################################################################
# Specify install locations
########################################################################
# Use GNUInstallDirs to set paths on multiarch systems.
include(GNUInstallDirs)
set(GMX_INSTALL_DATASUBDIR "gromacs" CACHE STRING "Subdirectory for GROMACS data under CMAKE_INSTALL_DATADIR")
mark_as_advanced(GMX_INSTALL_DATASUBDIR)
# Internal convenience so we do not have to join two path segments in the code
set(GMX_INSTALL_GMXDATADIR ${CMAKE_INSTALL_DATADIR}/${GMX_INSTALL_DATASUBDIR})
# If the nesting level wrt. the installation root is changed,
# gromacs-config.cmake.cmakein needs to be adapted.
set(GMX_INSTALL_CMAKEDIR ${CMAKE_INSTALL_DATAROOTDIR}/cmake)
# TODO: Make GMXRC adapt if this is changed
set(GMX_INSTALL_PKGCONFIGDIR ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${CMAKE_INSTALL_INCLUDEDIR})
# Binary and library suffix options
include(gmxManageSuffixes)
########################################################################
# Find external packages #
########################################################################
# Unconditionally find the package, as it is also required for unit
# tests. This exports LIBXML2_FOUND, which we should not use because
# it does not tell us that linking will succeed. Instead, we test that
# next.
#if(DEFINED LIBXML2_LIBRARIES)
# set(LibXml2_FIND_QUIETLY TRUE)
#endif()
#find_package(LibXml2)
#include(gmxTestLibXml2)
#gmx_test_libxml2(HAVE_LIBXML2)
#option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${HAVE_LIBXML2})
#set(PKG_XML "")
#mark_as_advanced(GMX_XML)
# Don't actually do anything, since libxml2 is currently not used by libgromacs
#if(GMX_XML AND NOT HAVE_LIBXML2)
# message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
#endif()
#if(GMX_XML)
# include_directories(${LIBXML2_INCLUDE_DIR})
# set(PKG_XML libxml-2.0)
# set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
#endif()
option(GMX_HWLOC "Use hwloc portable hardware locality library" OFF)
if (GMX_HWLOC)
# Find quietly the second time.
if (HWLOC_FIND_QUIETLY_AFTER_FIRST_RUN)
set(HWLOC_FIND_QUIETLY TRUE)
endif()
find_package(HWLOC 1.5)
if (HWLOC_FOUND)
if (HWLOC_LIBRARIES MATCHES ".a$")
set(_STATIC_HWLOC TRUE)
endif()
gmx_check_if_changed(HWLOC_FOUND_CHANGED HWLOC_FOUND)
if (_STATIC_HWLOC AND HWLOC_FOUND_CHANGED AND NOT GMX_HWLOC_FORCE)
message(STATUS "Static hwloc library found, will not attempt using it as it could lead to link-time errors. To use the detected library, manually set GMX_HWLOC=ON and you will likely have to pass appropriate linker flags too to satisfy the link-time dependencies of your hwloc library. Try \"pkg-config --libs --static hwloc\" for suggestions on what you will need.")
set(GMX_USE_HWLOC OFF)
else()
set(GMX_USE_HWLOC ON)
endif()
if (GMX_USE_HWLOC)
include_directories(SYSTEM ${HWLOC_INCLUDE_DIRS})
list(APPEND GMX_EXTRA_LIBRARIES ${HWLOC_LIBRARIES})
endif()
elseif(GMX_HWLOC_FORCE)
message(FATAL_ERROR "HWLOC package support required, but not found.")
endif()
if (HWLOC_FOUND AND HWLOC_VERSION VERSION_LESS "2")
message(STATUS "Support for hwloc versions 1.x is deprecated")
endif()
set(HWLOC_FIND_QUIETLY_AFTER_FIRST_RUN TRUE CACHE INTERNAL "Be quiet during future attempts to find HWLOC")
endif()
option(GMX_EXTERNAL_TINYXML2 "Use external TinyXML-2 instead of compiling the version bundled with GROMACS." OFF)
mark_as_advanced(GMX_EXTERNAL_TINYXML2)
if(GMX_EXTERNAL_TINYXML2)
# Find an external TinyXML-2 library.
find_package(TinyXML-2 3.0.0)
set(HAVE_TINYXML2 ${TinyXML2_FOUND})
if(NOT HAVE_TINYXML2)
message(FATAL_ERROR "External TinyXML-2 could not be found, please adjust your search paths")
endif()
endif()
option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
mark_as_advanced(GMX_EXTRAE)
if (GMX_EXTRAE)
find_package(EXTRAE)
if(EXTRAE_FOUND)
include_directories(SYSTEM ${EXTRAE_INCLUDE_DIR})
set(HAVE_EXTRAE 1)
else()
message(FATAL_ERROR "EXTRAE library was not found. Please add the correct path to CMAKE_PREFIX_PATH")
endif()
endif()
option(GMX_X11 "Use X window system" OFF)
if (GMX_X11)
find_package(X11)
# X11 includes/libraries are only set in the ngmx subdirectory!
if(NOT X11_FOUND)
message(FATAL_ERROR
"X11 include files and/or libraries were not found. "
"Set GMX_X11=OFF to compile without X11 support. "
"gmx view will not be available.")
endif()
include_directories(SYSTEM ${X11_INCLUDE_DIR})
endif()
include(ThreadMPI)
# Enable core threading facilities
tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include")
if(GMX_THREAD_MPI)
# enable MPI functions
tmpi_enable()
set(MPI_IN_PLACE_EXISTS 1)
endif()
# If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
if (TMPI_ATOMICS_DISABLED)
add_definitions(-DTMPI_ATOMICS_DISABLED)
endif()
include(gmxManageTNG)
include(gmxManageLmfit)
if(GMX_GPU)
string(TOUPPER "${GMX_GPU}" _gmx_gpu_uppercase)
if(${_gmx_gpu_uppercase} STREQUAL "CUDA")
include(gmxManageCuda)
elseif(${_gmx_gpu_uppercase} STREQUAL "OPENCL")
message(STATUS "GPU support with OpenCL is deprecated. It is still fully supported (and "
"recommended for AMD and Intel GPUs). It may be replaced by different approaches in "
"future releases of GROMACS.")
include(gmxManageOpenCL)
elseif(${_gmx_gpu_uppercase} STREQUAL "SYCL")
include(gmxManageSYCL)
endif()
if(NOT GMX_OPENMP)
message(WARNING "To use GPU acceleration efficiently, mdrun requires OpenMP multi-threading, which is currently not enabled.")
endif()
endif()
if(CYGWIN)
set(GMX_CYGWIN 1)
endif()
if(WIN32)
set(GMX_NATIVE_WINDOWS 1)
# This makes windows.h not declare min/max as macros that would break
# C++ code using std::min/std::max.
add_definitions(-DNOMINMAX)
endif()
option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING" ON)
mark_as_advanced(GMX_BUILD_UNITTESTS)
gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
########################################################################
# Our own GROMACS tests
########################################################################
include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
include_directories(SYSTEM ${CMAKE_SOURCE_DIR}/src/external)
# Required for config.h, maybe should only be set in src/CMakeLists.txt
include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
include(gmxSetBuildInformation)
gmx_set_build_information()
# Anything but truly ancient x86 hardware should support rdtscp, so we enable it by default.
# The inline assembly calling it is only ever compiled on x86, so defaulting to ON is OK.
option(GMX_USE_RDTSCP "Use low-latency RDTSCP instruction for x86 CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments" ON)
mark_as_advanced(GMX_USE_RDTSCP)
include(gmxTestLargeFiles)
gmx_test_large_files(GMX_LARGEFILES)
include(gmxTestSignal)
gmx_test_sigusr1(HAVE_SIGUSR1)
include(gmxTestPipes)
gmx_test_pipes(HAVE_PIPES)
include(gmxTestXDR)
gmx_test_xdr(GMX_SYSTEM_XDR)
# Darwin has system XDR, but it uses a three-argument flavour of
# xdrproc_t that it guarantees will still work if you pass the normal
# two-argument xdr filters, but gcc 8 warns about the cast necessary
# to do that, so it's simpler to just use our own XDR library.
#
# TODO It would be better to craft a cmake test which fails if such
# XDR operations cause warnings, and succeeds otherwise, because it is
# generally preferable to use system libraries where possible.
if(NOT GMX_SYSTEM_XDR OR CMAKE_SYSTEM_NAME STREQUAL "Darwin")
set(GMX_INTERNAL_XDR 1)
endif()
##################################################
# Process SIMD instruction settings
##################################################
# This checks what flags to add in order to
# support the SIMD instructions we need, it sets
# correct defines for the SIMD instructions supported,
# and adds advanced options to control accuracy
# for SIMD math operations.
include(gmxManageSimd)
gmx_manage_simd()
##################################################
# Process FFT library settings
##################################################
include(gmxManageFFTLibraries)
include(gmxManageLinearAlgebraLibraries)
include(gmxManagePluginSupport)
gmx_manage_plugin_support()
if(GMX_USE_PLUGINS)
if(NOT GMX_VMD_PLUGIN_PATH)
find_package(VMD)
endif()
endif()
# People might want to customize the default location for the DSSP binary
set(GMX_DSSP_PROGRAM_PATH "/usr/local/bin/dssp"
CACHE PATH
"The default location to use for the DSSP binary")
mark_as_advanced(GMX_DSSP_PROGRAM_PATH)
# Link real-time library for POSIX timers. The check for clock_gettime
# confirms the linkability of rt.
if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
list(APPEND GMX_EXTRA_LIBRARIES rt)
endif()
# Math and thread libraries must often come after all others when linking...
if (HAVE_LIBM)
list(APPEND GMX_PUBLIC_LIBRARIES m)
endif()
option(GMX_NACL "Configure for Native Client builds" OFF)
if (GMX_NACL)
list(APPEND GMX_EXTRA_LIBRARIES nosys)
set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
# TODO: Is this still necessary with the check for its presence?
set(GMX_USE_NICE 0)
set(GMX_NO_RENAME 1)
endif()
mark_as_advanced(GMX_NACL)
if(GMX_FAHCORE)
set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
"Path to swindirect.h")
include_directories(${COREWRAP_INCLUDE_DIR})
endif()
option(GMX_BUILD_HELP "Build completions (requires that compiled binaries can be executed on build host) and install man pages if built (requires building the 'man' target manually)" OFF)
mark_as_advanced(GMX_BUILD_HELP)
if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND BUILD_IS_INSOURCE)
message(FATAL_ERROR
"Rebuilding shell completions or man pages is not supported for "
"in-source builds from a source distribution. "
"Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
endif()
# # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
# these are set after everything else
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS} ${DISABLE_SYCL_CXX_FLAGS}")
set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS} ${DISABLE_SYCL_CXX_FLAGS}")
else()
message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS};${MPI_COMPILE_FLAGS};${EXTRA_C_FLAGS};${GMXC_CFLAGS}")
foreach(build_type ${build_types_with_explicit_flags})
message("CMAKE_C_FLAGS_${build_type}: ${GMXC_CFLAGS_${build_type}}")
endforeach()
message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS};${MPI_COMPILE_FLAGS};${EXTRA_CXX_FLAGS};${GMXC_CXXFLAGS}")
foreach(build_type ${build_types_with_explicit_flags})
message("CMAKE_CXX_FLAGS_${build_type}: ${GMXC_CXXFLAGS_${build_type}}")
endforeach()
message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
message("CMAKE_SHARED_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
endif()
# Allow `admin` directory to be easily conveyed to nested CMake commands.
set(GMX_ADMIN_DIR ${CMAKE_SOURCE_DIR}/admin)
################################################################
# Shared library load path settings
################################################################
if(NOT GMX_BUILD_SHARED_EXE)
# No rpath
set(CMAKE_SKIP_RPATH TRUE)
set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) # remove -Wl,-Bdynamic
set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
else()
# The build folder always has bin/ and lib/; if we are also going to
# install to lib/, then the installation RPATH works also in the build
# tree. This makes installation slightly faster (no need to rewrite the
# RPATHs), and makes the binaries in the build tree relocatable.
if(CMAKE_INSTALL_LIBDIR STREQUAL "lib")
set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
set(CMAKE_BUILD_WITH_INSTALL_NAME_DIR TRUE)
endif()
# Set the RPATH as relative to the executable location to make the
# binaries relocatable.
if(CMAKE_SYSTEM_NAME STREQUAL "Darwin") #Assume OS X >=10.5
set(CMAKE_INSTALL_RPATH "@loader_path/../${CMAKE_INSTALL_LIBDIR}")
set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_RPATH})
else()
set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${CMAKE_INSTALL_LIBDIR}")
endif()
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
set(CMAKE_MACOSX_RPATH 1)
endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
install(FILES COPYING DESTINATION ${GMX_INSTALL_GMXDATADIR} COMPONENT data)
if (GMX_BUILD_FOR_COVERAGE)
# Code heavy with asserts makes conditional coverage close to useless metric,
# as by design most of the false branches are impossible to trigger in
# correctly functioning code. And the benefit of testing those that could
# be triggered by using an API against its specification isn't usually
# worth the effort.
add_definitions(-DNDEBUG -DGMX_DISABLE_ASSERTS)
endif()
if (BUILD_TESTING)
include(tests/CheckTarget.cmake)
endif()
# TODO: Determine control flow and defaults for package installation and testing use cases.
# Ref: https://gitlab.com/gromacs/gromacs/-/issues/2896
option(GMX_PYTHON_PACKAGE "Configure gmxapi Python package" OFF)
mark_as_advanced(GMX_PYTHON_PACKAGE)
if (NOT GMX_BUILD_MDRUN_ONLY)
find_package(ImageMagick QUIET COMPONENTS convert)
include(gmxTestImageMagick)
GMX_TEST_IMAGEMAGICK(IMAGE_CONVERT_POSSIBLE)
# TODO: Resolve circular dependency between docs, gromacs, and python_packaging
add_subdirectory(docs)
add_subdirectory(share)
add_subdirectory(scripts)
endif()
add_subdirectory(api)
add_subdirectory(src)
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
if(GMX_PYTHON_PACKAGE AND NOT GMX_BUILD_MDRUN_ONLY)
add_subdirectory(python_packaging)
endif()
gmx_cpack_write_config()
#######################
## uninstall target
#######################
CONFIGURE_FILE( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
"${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
IMMEDIATE @ONLY)
###########################
ADD_CUSTOM_TARGET(uninstall
"${CMAKE_COMMAND}" -P
"${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
###########################
set_directory_properties(PROPERTIES
ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")