#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+# 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.
# 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 3.9.6)
-if(POLICY CMP0074) #3.12
- cmake_policy(SET CMP0074 NEW)
-endif()
+cmake_minimum_required(VERSION 3.16.3)
+cmake_policy(SET CMP0074 NEW) # From CMake 3.12
+cmake_policy(SET CMP0068 NEW) # From CMake-3.9
+cmake_policy(SET CMP0048 NEW) # As of CMake 3.22, default is still "OLD"
# 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)
-project(Gromacs)
+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()
+
+# The GROMACS convention is that these are the version number of the next
+# release that is going to be made from this branch.
+project(Gromacs VERSION 2022.0)
-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
execute_process(COMMAND hostname
OUTPUT_VARIABLE TMP_HOSTNAME
OUTPUT_STRIP_TRAILING_WHITESPACE)
- if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
+ # Only check for host name if not running in a CI environment, as the cache might
+ # be reused there between different machines in different stages
+ if(GMX_BUILD_HOSTNAME AND NOT "${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
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_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
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_CP2K "Enable CP2K QM/MM interface (CP2K 8.1 or later is required)" OFF)
+
+# We need to enable Fortran, because CP2K will be linked
+if(GMX_CP2K)
+ enable_language(Fortran)
+endif()
+
option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
mark_as_advanced(GMX_FAHCORE)
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)
-
-# 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)
+option(GMX_INSTALL_LEGACY_API "Install legacy headers" OFF)
-# 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 ARM_NEON_ASIMD ARM_SVE IBM_VSX Reference)
-if(GMX_TARGET_MIC)
+include(gmxTestIntelLLVM)
+
+if (GMX_INTEL_LLVM)
set(GMX_FFT_LIBRARY_DEFAULT "mkl")
else()
set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
mark_as_advanced(GMX_BUILD_OWN_FFTW)
mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
-gmx_option_multichoice(
- GMX_QMMM_PROGRAM
- "QM package for QM/MM"
- None
- none gaussian mopac gamess orca)
+gmx_dependent_option(
+ GMX_USE_HEFFTE
+ "Use HeFFTe for FFT support. Used with CUDA backend"
+ OFF
+ "GMX_GPU STREQUAL CUDA;GMX_MPI")
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")
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)
include(gmxCFlags)
gmx_c_flags()
-# This variable should be used for additional compiler flags which are not
-# generated in gmxCFlags nor are SIMD or MPI related.
+# 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)
-# also work for C++ compilation.
+# might not also work for C++ compilation.
set(EXTRA_C_FLAGS "")
set(EXTRA_CXX_FLAGS "")
# 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()
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_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)
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(gmxManageMimic)
+########################################################################
+#Process CP2K settings
+########################################################################
+include(gmxManageCP2K)
+
########################################################################
#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 #
########################################################################
# set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
#endif()
-gmx_option_trivalue(
- GMX_HWLOC
- "Use hwloc portable hardware locality library"
- "AUTO")
+option(GMX_HWLOC "Use hwloc portable hardware locality library" OFF)
if (GMX_HWLOC)
# Find quietly the second time.
- if(HWLOC_VERSION)
+ if (HWLOC_FIND_QUIETLY_AFTER_FIRST_RUN)
set(HWLOC_FIND_QUIETLY TRUE)
endif()
- find_package(Hwloc 1.5)
+ find_package(HWLOC 1.5)
if (HWLOC_FOUND)
if (HWLOC_LIBRARIES MATCHES ".a$")
list(APPEND GMX_EXTRA_LIBRARIES ${HWLOC_LIBRARIES})
endif()
elseif(GMX_HWLOC_FORCE)
- message(FATAL_ERROR "Hwloc package support required, but not found.")
+ 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)
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)
include(gmxManageLmfit)
+include(gmxManageMuparser)
+
+##################################################
+# 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()
+
+
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()
+
+ if (GMX_OPENCL_NB_CLUSTER_SIZE)
+ message(WARNING "GMX_OPENCL_NB_CLUSTER_SIZE is deprecated, use GMX_GPU_NB_CLUSTER_SIZE instead")
+ endif()
+ if (GMX_OPENCL_NB_CLUSTER_SIZE AND GMX_GPU_NB_CLUSTER_SIZE)
+ if (NOT ${GMX_OPENCL_NB_CLUSTER_SIZE} EQUAL ${GMX_GPU_NB_CLUSTER_SIZE})
+ message(FATAL_ERROR "Mismatching values passed to GMX_OPENCL_NB_CLUSTER_SIZE and GMX_GPU_NB_CLUSTER_SIZE; the former is deprecated, use only the latter!")
+ endif()
+ endif()
+ # Only OpenCL and SYCL support changing the default cluster size
+ if (${_gmx_gpu_uppercase} STREQUAL "CUDA")
+ if (GMX_GPU_NB_CLUSTER_SIZE AND NOT "${GMX_GPU_NB_CLUSTER_SIZE}" EQUAL 8)
+ message(FATAL_ERROR "Setting GMX_GPU_NB_CLUSTER_SIZE is not supported in CUDA (the default GMX_GPU_NB_CLUSTER_SIZE=8 is used)")
+ endif()
+ else()
+ # use the legacy GMX_OPENCL_NB_CLUSTER_SIZE variable if set, otherwise set the defaults
+ if (GMX_OPENCL_NB_CLUSTER_SIZE)
+ set(_gmx_gpu_nb_cluster_size_value ${GMX_OPENCL_NB_CLUSTER_SIZE})
+ else()
+ # default cluster size is 8 with OpenCL and 4 with SYCL for now
+ if(${_gmx_gpu_uppercase} STREQUAL "OPENCL")
+ set(_gmx_gpu_nb_cluster_size_value 8)
+ elseif(GMX_GPU_SYCL)
+ if (GMX_SYCL_HIPSYCL AND NOT GMX_HIPSYCL_HAVE_LEVELZERO_TARGET)
+ set(_gmx_gpu_nb_cluster_size_value 8)
+ else()
+ # Either DPCPP or hipSYCL targeting Intel Level0
+ set(_gmx_gpu_nb_cluster_size_value 4)
+ endif()
+ endif()
+ endif()
+ set(GMX_GPU_NB_CLUSTER_SIZE ${_gmx_gpu_nb_cluster_size_value} CACHE STRING "Cluster size used by the nonbonded kernel. Set to 4 for Intel GPUs.")
+ mark_as_advanced(GMX_GPU_NB_CLUSTER_SIZE)
endif()
+
+endif()
+
+# For build with CUDA and Lib-MPI, check if underlying MPI implementation is CUDA-aware
+# CUDA-aware MPI allows direct GPU communication without staging data through host
+if(GMX_GPU_CUDA AND GMX_LIB_MPI)
+ include(gmxManageCudaAwareMPI)
+else()
+ set(HAVE_CUDA_AWARE_MPI 0)
endif()
if(CYGWIN)
set(GMX_CYGWIN 1)
endif()
+if(GMX_USE_HEFFTE)
+ if(NOT GMX_GPU_CUDA)
+ message(FATAL_ERROR "HeFFTe support requires a CUDA build")
+ endif()
+ if(NOT GMX_LIB_MPI)
+ message(FATAL_ERROR "HeFFTe support requires a library MPI build")
+ endif()
+ find_package(Heffte 2.1.0 REQUIRED CUDA)
+endif()
+
if(WIN32)
set(GMX_NATIVE_WINDOWS 1)
# This makes windows.h not declare min/max as macros that would break
add_definitions(-DNOMINMAX)
endif()
-if(CMAKE_SYSTEM_NAME STREQUAL "Darwin") #Work-around for cmake bug #10837
- if (CMAKE_COMPILER_IS_GNUCC OR CMAKE_C_COMPILER_ID MATCHES "Intel" OR CMAKE_C_COMPILER_ID MATCHES "Clang")
- set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
- endif()
- if (CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Intel" OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
- set(CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem ")
- endif()
-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
########################################################################
-add_definitions( -DHAVE_CONFIG_H )
-include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
-# TODO required at high level because both libgromacs and progs/mdrun
-# require it, both for thread-MPI and its atomics and mutexes.
-include_directories(BEFORE SYSTEM ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
-# Required for config.h, maybe should only be set in src/CMakeLists.txt
-include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
+include_directories(SYSTEM ${CMAKE_SOURCE_DIR}/src/external)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
include(gmxSetBuildInformation)
gmx_set_build_information()
-gmx_option_multichoice(
- GMX_USE_RDTSCP
- "Use low-latency RDTSCP instruction for CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments)"
- "AUTO"
- OFF ON AUTO DETECT)
+# Anything but truly ancient x86 hardware should support rdtscp, so we enable it by default.
+# The inline assembly calling it is only ever compiled on x86, so defaulting to ON is OK.
+option(GMX_USE_RDTSCP "Use low-latency RDTSCP instruction for x86 CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments" ON)
mark_as_advanced(GMX_USE_RDTSCP)
-macro(gmx_check_rdtscp)
- if (CPU_DETECTION_FEATURES MATCHES "rdtscp")
- set(HAVE_RDTSCP 1)
- set(RDTSCP_DETECTION_MESSAGE " - detected on the build host")
- else()
- set(RDTSCP_DETECTION_MESSAGE " - not detected on the build host")
- endif()
-endmacro()
-
-set(HAVE_RDTSCP 0)
-if (GMX_USE_RDTSCP STREQUAL "ON")
- set(HAVE_RDTSCP 1)
-elseif(GMX_USE_RDTSCP STREQUAL "DETECT")
- gmx_check_rdtscp()
-elseif(GMX_USE_RDTSCP STREQUAL "AUTO")
- # If the user specified automated SIMD selection, that the choice
- # is made based on detection on the build host. If so, then RDTSCP
- # should be chosen the same way.
- #
- # If the user specified an AVX SIMD level (e.g. when
- # cross-compiling GROMACS) then they will get our best guess, ie
- # that in practice AVX mostly correlates with rdtscp (and anyway
- # is only relevant in rather old x86 hardware).
- if (GMX_SIMD STREQUAL "AUTO")
- gmx_check_rdtscp()
- elseif (GMX_SIMD MATCHES "AVX")
- set(HAVE_RDTSCP 1)
- endif()
-endif()
-gmx_check_if_changed(HAVE_RDTSCP_CHANGED HAVE_RDTSCP)
-if (HAVE_RDTSCP_CHANGED)
- if (HAVE_RDTSCP)
- message(STATUS "Enabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
- else()
- message(STATUS "Disabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
- endif()
-endif()
-
include(gmxTestLargeFiles)
gmx_test_large_files(GMX_LARGEFILES)
set(GMX_INTERNAL_XDR 1)
endif()
-
-##################################################
-# Process SIMD instruction settings
-##################################################
-# This checks what flags to add in order to
-# support the SIMD instructions we need, it sets
-# correct defines for the SIMD instructions supported,
-# and adds advanced options to control accuracy
-# for SIMD math operations.
-include(gmxManageSimd)
-gmx_manage_simd()
-
-include(gmxManageCycleCounters)
-gmx_manage_cycle_counters()
-
-# Process QM/MM Settings
-if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
- set(GMX_QMMM_GAUSSIAN 1)
-elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
- set(GMX_QMMM_MOPAC 1)
-elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
- set(GMX_QMMM_GAMESS 1)
-elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
- set(GMX_QMMM_ORCA 1)
-elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
- # nothing to do
-else()
- gmx_invalid_option_value(GMX_QMMM_PROGRAM)
-endif()
-
-
##################################################
# Process FFT library settings
##################################################
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)" ${build_help_default})
+option(GMX_BUILD_HELP "Build completions (requires that compiled binaries can be executed on build host) and install man pages if built (requires building the 'man' target manually)" OFF)
mark_as_advanced(GMX_BUILD_HELP)
if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND BUILD_IS_INSOURCE)
message(FATAL_ERROR
"Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
endif()
+if (GMX_BUILD_FOR_COVERAGE)
+ # Set flags for coverage build here instead having to do so manually
+ set(CMAKE_C_FLAGS "-g --coverage")
+ set(CMAKE_CXX_FLAGS "-g --coverage")
+endif()
+
# # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
# these are set after everything else
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
- set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
- set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
- set(CMAKE_EXE_LINKER_FLAGS "${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}")
+ #TODO(#3672): Use target_link_libraries(... MPI::MPI_CXX) instead of ${MPI_CXX_LINK_FLAGS}
+ set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_CXX_LINK_FLAGS} ${CMAKE_EXE_LINKER_FLAGS} ${DISABLE_SYCL_CXX_FLAGS}")
+ set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_CXX_LINK_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}")
- message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
- message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
- message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
- message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
- message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
- message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
- message("CMAKE_SHARED_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
-endif()
-
-########################################################################
-# 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)
+ 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_CXX_LINK_FLAGS}")
+ message("CMAKE_SHARED_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_CXX_LINK_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
# RPATHs), and makes the binaries in the build tree relocatable.
if(CMAKE_INSTALL_LIBDIR STREQUAL "lib")
set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
- if(POLICY CMP0068)
- cmake_policy(SET CMP0068 NEW) # From CMake-3.9
- set(CMAKE_BUILD_WITH_INSTALL_NAME_DIR TRUE)
- endif()
+ set(CMAKE_BUILD_WITH_INSTALL_NAME_DIR TRUE)
endif()
# Set the RPATH as relative to the executable location to make the
# binaries relocatable.
#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()
-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)
- find_package(PythonInterp 3.5)
- find_package(ImageMagick QUIET COMPONENTS convert)
- include(gmxTestImageMagick)
- GMX_TEST_IMAGEMAGICK(IMAGE_CONVERT_POSSIBLE)
- add_subdirectory(docs)
- add_subdirectory(share)
- add_subdirectory(scripts)
-endif()
+option(GMX_PYTHON_PACKAGE
+ "Configure gmxapi Python package for use in build tree. Requires pybind11 installed for project Python interpreter."
+ OFF)
+mark_as_advanced(GMX_PYTHON_PACKAGE)
+
+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)
+add_subdirectory(api)
add_subdirectory(src)
if (BUILD_TESTING)
add_subdirectory(tests)
endif()
-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}")
+if(GMX_PYTHON_PACKAGE)
+ add_subdirectory(python_packaging)
endif()
-set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
+
+gmx_cpack_write_config()
#######################
## uninstall target
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff