#
# 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, by the GROMACS development team, led by
+# 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.
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 >=10.9 helps to find modern C++ compatibility,
+ # 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 10.9 CACHE STRING
- "OS X deployment target affects default SDK version and compiler flags."
- FORCE)
+ 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."
project(Gromacs)
-set(CMAKE_CXX_STANDARD 14)
+set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
set(CMAKE_CXX_EXTENSIONS OFF)
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
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." FORCE)
+ 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")
+ "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile" "TSAN" "ASAN" "MSAN" "UBSAN")
endif()
if(CMAKE_CONFIGURATION_TYPES)
# Add appropriate GROMACS-specific build types for the Visual
mark_as_advanced(GMX_COOL_QUOTES)
gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
-option(GMX_USE_OPENCL "Enable OpenCL acceleration" OFF)
-
option(GMX_INSTALL_LEGACY_API "Install legacy headers" OFF)
-# The earliest version of the CUDA toolkit that supports c++14 is 9.0
-set(REQUIRED_CUDA_VERSION 9.0)
-set(REQUIRED_CUDA_COMPUTE_CAPABILITY 3.0)
-
-# OpenCL required version: 1.2 or newer
-set(REQUIRED_OPENCL_MIN_VERSION_MAJOR 1)
-set(REQUIRED_OPENCL_MIN_VERSION_MINOR 2)
-set(REQUIRED_OPENCL_MIN_VERSION ${REQUIRED_OPENCL_MIN_VERSION_MAJOR}.${REQUIRED_OPENCL_MIN_VERSION_MINOR})
-
-if(NOT GMX_USE_OPENCL)
- # CUDA detection is done only if GMX_USE_OPENCL is OFF.
- include(gmxManageGPU)
- set(GMX_USE_CUDA ${GMX_GPU})
- if(GMX_GPU)
- set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_CUDA")
- else()
- set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_NONE")
- endif()
-else()
- #Now the OpenCL path (for both AMD and NVIDIA)
- if(GMX_GPU)
- include(gmxManageOpenCL)
- set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_OPENCL")
- else()
- message(FATAL_ERROR "OpenCL requested but GPU option is not enabled (try -DGMX_GPU=on) ")
- endif()
-endif()
+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 IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
+ 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")
# These need to be done early (before further tests).
#####################################################################
+include(gmxTestIntelLLVM)
include(gmxCFlags)
gmx_c_flags()
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;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE64)
+ 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)
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 #
########################################################################
# set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
#endif()
-gmx_option_trivalue(
- GMX_HWLOC
- "Use hwloc portable hardware locality library"
- "AUTO")
+option(GMX_HWLOC "Use hwloc portable hardware locality library" OFF)
if (GMX_HWLOC)
# Find quietly the second time.
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()
include(gmxManageLmfit)
if(GMX_GPU)
- # now that we have detected the dependencies, do the second configure pass
- gmx_gpu_setup()
- if (GMX_CLANG_CUDA)
- list(APPEND GMX_EXTRA_LIBRARIES ${GMX_CUDA_CLANG_LINK_LIBS})
- link_directories("${GMX_CUDA_CLANG_LINK_DIRS}")
+
+ 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)
########################################################################
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 ${CMAKE_BINARY_DIR}/src)
include(gmxSetBuildInformation)
gmx_set_build_information()
-gmx_option_multichoice(
- GMX_USE_RDTSCP
- "Use low-latency RDTSCP instruction for CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments)"
- "AUTO"
- OFF ON AUTO DETECT)
+# Anything but truly ancient x86 hardware should support rdtscp, so we enable it by default.
+# The inline assembly calling it is only ever compiled on x86, so defaulting to ON is OK.
+option(GMX_USE_RDTSCP "Use low-latency RDTSCP instruction for x86 CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments" ON)
mark_as_advanced(GMX_USE_RDTSCP)
-macro(gmx_check_rdtscp)
- if (CPU_DETECTION_FEATURES MATCHES "rdtscp")
- set(HAVE_RDTSCP 1)
- set(RDTSCP_DETECTION_MESSAGE " - detected on the build host")
- else()
- set(RDTSCP_DETECTION_MESSAGE " - not detected on the build host")
- endif()
-endmacro()
-
-set(HAVE_RDTSCP 0)
-if (GMX_USE_RDTSCP STREQUAL "ON")
- set(HAVE_RDTSCP 1)
-elseif(GMX_USE_RDTSCP STREQUAL "DETECT")
- gmx_check_rdtscp()
-elseif(GMX_USE_RDTSCP STREQUAL "AUTO")
- # If the user specified automated SIMD selection, that the choice
- # is made based on detection on the build host. If so, then RDTSCP
- # should be chosen the same way.
- #
- # If the user specified an AVX SIMD level (e.g. when
- # cross-compiling GROMACS) then they will get our best guess, ie
- # that in practice AVX mostly correlates with rdtscp (and anyway
- # is only relevant in rather old x86 hardware).
- if (GMX_SIMD STREQUAL "AUTO")
- gmx_check_rdtscp()
- elseif (GMX_SIMD MATCHES "AVX")
- set(HAVE_RDTSCP 1)
- endif()
-endif()
-gmx_check_if_changed(HAVE_RDTSCP_CHANGED HAVE_RDTSCP)
-if (HAVE_RDTSCP_CHANGED)
- if (HAVE_RDTSCP)
- message(STATUS "Enabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
- else()
- message(STATUS "Disabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
- endif()
-endif()
-
include(gmxTestLargeFiles)
gmx_test_large_files(GMX_LARGEFILES)
include(gmxManageLinearAlgebraLibraries)
include(gmxManagePluginSupport)
+gmx_manage_plugin_support()
-if (GMX_USE_PLUGINS)
+if(GMX_USE_PLUGINS)
if(NOT GMX_VMD_PLUGIN_PATH)
find_package(VMD)
endif()
endif()
+# People might want to customize the default location for the DSSP binary
+set(GMX_DSSP_PROGRAM_PATH "/usr/local/bin/dssp"
+ CACHE PATH
+ "The default location to use for the DSSP binary")
+mark_as_advanced(GMX_DSSP_PROGRAM_PATH)
+
# Link real-time library for POSIX timers. The check for clock_gettime
# confirms the linkability of rt.
if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
include_directories(${COREWRAP_INCLUDE_DIR})
endif()
-# Value of GMX_BUILD_HELP=AUTO tries to generate things, but will only
-# produce warnings if that fails.
-set(build_help_default AUTO)
-if (SOURCE_IS_SOURCE_DISTRIBUTION OR CMAKE_CROSSCOMPILING)
- set(build_help_default OFF)
-endif()
-gmx_option_trivalue(GMX_BUILD_HELP "Build completions automatically (requires that compiled binaries can be executed on the build host) and install man pages if built (requires building the 'man' target manually)" ${build_help_default})
+option(GMX_BUILD_HELP "Build completions (requires that compiled binaries can be executed on build host) and install man pages if built (requires building the 'man' target manually)" OFF)
mark_as_advanced(GMX_BUILD_HELP)
if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND BUILD_IS_INSOURCE)
message(FATAL_ERROR
# # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
# these are set after everything else
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
- set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
- set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
+ set(CMAKE_EXE_LINKER_FLAGS "${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}")
# Allow `admin` directory to be easily conveyed to nested CMake commands.
set(GMX_ADMIN_DIR ${CMAKE_SOURCE_DIR}/admin)
-########################################################################
-# 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)
-set(GMX_INSTALL_OCLDIR ${GMX_INSTALL_GMXDATADIR}/opencl)
-
-list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${CMAKE_INSTALL_INCLUDEDIR})
-
-# Binary and library suffix options
-include(gmxManageSuffixes)
-
################################################################
# Shared library load path settings
################################################################
mark_as_advanced(GMX_PYTHON_PACKAGE)
if (NOT GMX_BUILD_MDRUN_ONLY)
- # Note: Though only documented as an output variable, PYTHON_EXECUTABLE is
- # also effective as a CMake input variable to effectively hint the location
- # of the Python interpreter. This may be helpful in environments with both
- # Python 2 and Python 3 on the default PATH.
- # Ref: https://cmake.org/cmake/help/latest/module/FindPythonInterp.html
- if(FIND_PACKAGE_MESSAGE_DETAILS_PythonInterp)
- # Keep quiet on subsequent runs of cmake
- set(PythonInterp_FIND_QUIETLY ON)
- endif()
- # Older CMake versions might not search for Python newer than 3.7.
- set(Python_ADDITIONAL_VERSIONS 3.8)
- if(GMX_PYTHON_PACKAGE)
- find_package(PythonInterp 3.6 REQUIRED)
- # Note: PythonLibs will be found later by pybind11.
- # TODO: (Issue #2998) When CMake >= 3.12 is required, update detection.
- # I.e. find_package(Python3 3.6 COMPONENTS Interpreter Development REQUIRED)
- else()
- find_package(PythonInterp 3.6)
- endif()
find_package(ImageMagick QUIET COMPONENTS convert)
include(gmxTestImageMagick)
GMX_TEST_IMAGEMAGICK(IMAGE_CONVERT_POSSIBLE)
add_subdirectory(share)
add_subdirectory(scripts)
endif()
+add_subdirectory(api)
add_subdirectory(src)
if (BUILD_TESTING)
gmx_cpack_write_config()
-# Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
-# Don't bother the user after the first configure pass.
-if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
- message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
-endif()
-set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
-
#######################
## uninstall target
#######################
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff