#
# 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.
# 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_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
# 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."
- FORCE)
+ "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)
+# 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 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)
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
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)
gmx_option_multichoice(
GMX_GPU
"Framework for GPU acceleration"
- None
- None CUDA OpenCL)
+ 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)
+
+include(gmxTestIntelLLVM)
-if(GMX_TARGET_MIC)
+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_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)
# 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_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
########################################################################
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()
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)
-string(TOUPPER "${GMX_GPU}" _gmx_gpu_uppercase)
-if(NOT ${_gmx_gpu_uppercase} STREQUAL "NONE")
+include(gmxManageMuparser)
+##################################################
+# Process SIMD instruction settings
+##################################################
+# This checks what flags to add in order to
+# support the SIMD instructions we need, it sets
+# correct defines for the SIMD instructions supported,
+# and adds advanced options to control accuracy
+# for SIMD math operations.
+include(gmxManageSimd)
+gmx_manage_simd()
+
+
+if(GMX_GPU)
+
+ string(TOUPPER "${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 ${_gmx_gpu_nb_cluster_size_value} CACHE STRING "Cluster size used by the nonbonded kernel. Set to 4 for Intel GPUs.")
+ mark_as_advanced(GMX_GPU_NB_CLUSTER_SIZE)
+ endif()
+
endif()
-# Not ideal to set this without the GPU acceleration, but the source presently requires GMX_GPU
-# to be set to GMX_GPU_None for a non-GPU build to work.
-set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_${_gmx_gpu_uppercase}")
+# 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
# 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 ${CMAKE_BINARY_DIR}/src)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
set(GMX_INTERNAL_XDR 1)
endif()
-
-##################################################
-# Process SIMD instruction settings
-##################################################
-# This checks what flags to add in order to
-# support the SIMD instructions we need, it sets
-# correct defines for the SIMD instructions supported,
-# and adds advanced options to control accuracy
-# for SIMD math operations.
-include(gmxManageSimd)
-gmx_manage_simd()
-
##################################################
# Process FFT library settings
##################################################
endif()
endif()
+# People might want to customize the default location for the DSSP binary
+set(GMX_DSSP_PROGRAM_PATH "/usr/local/bin/dssp"
+ CACHE PATH
+ "The default location to use for the DSSP binary")
+mark_as_advanced(GMX_DSSP_PROGRAM_PATH)
+
# Link real-time library for POSIX timers. The check for clock_gettime
# confirms the linkability of rt.
if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
"Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
endif()
+if (GMX_BUILD_FOR_COVERAGE)
+ # Set flags for coverage build here instead having to do so manually
+ set(CMAKE_C_FLAGS "-g --coverage")
+ set(CMAKE_CXX_FLAGS "-g --coverage")
+endif()
+
# # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
# these are set after everything else
if (NOT GMX_SKIP_DEFAULT_CFLAGS)
- set(CMAKE_EXE_LINKER_FLAGS "${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}")
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}")
+ 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)
#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)
+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)
-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()
+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)
add_subdirectory(tests)
endif()
-if(GMX_PYTHON_PACKAGE AND NOT GMX_BUILD_MDRUN_ONLY)
+if(GMX_PYTHON_PACKAGE)
add_subdirectory(python_packaging)
endif()
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff