#
# This file is part of the GROMACS molecular simulation package.
#
-# Copyright (c) 2010,2011,2012,2013,2014,2015, The GROMACS development team.
-# Copyright (c) 2016,2017,2018,2019,2020, by the GROMACS development team, led by
+# Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
+# Copyright (c) 2015,2016,2017,2018,2019 by the GROMACS development team.
+# Copyright (c) 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.
endif()
set_property(GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
-set_property(GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
+set_property(GLOBAL PROPERTY CUDA_SOURCES)
set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
set_property(GLOBAL PROPERTY GMX_AVX_512_SOURCE)
_gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
endfunction ()
-# TODO Reconsider this, as the CUDA driver API is probably a simpler
-# approach, at least for the build system. See Redmine #2530
-function (gmx_compile_cpp_as_cuda)
- _gmx_add_files_to_property(GMX_LIBGROMACS_GPU_IMPL_SOURCES ${ARGN})
-endfunction ()
+# Permit the configuration to disable compiling the many nbnxm kernels
+# and others involved in force calculations. Currently only
+# short-ranged and bonded kernels are disabled this way, but in future
+# others may be appropriate. Thus the cmake option is not specific to
+# nbnxm module.
+option(GMX_USE_SIMD_KERNELS "Whether to compile NBNXM and other SIMD kernels" ON)
+mark_as_advanced(GMX_USE_SIMD_KERNELS)
# Add these contents first because linking their tests can take a lot
# of time, so we want lots of parallel work still available after
add_subdirectory(swap)
add_subdirectory(essentialdynamics)
add_subdirectory(pulling)
-add_subdirectory(awh)
add_subdirectory(simd)
add_subdirectory(imd)
add_subdirectory(compat)
add_subdirectory(mimic)
add_subdirectory(modularsimulator)
-if (NOT GMX_BUILD_MDRUN_ONLY)
- add_subdirectory(gmxana)
- add_subdirectory(gmxpreprocess)
- add_subdirectory(correlationfunctions)
- add_subdirectory(statistics)
- add_subdirectory(analysisdata)
- add_subdirectory(coordinateio)
- add_subdirectory(trajectoryanalysis)
- add_subdirectory(energyanalysis)
- add_subdirectory(tools)
-endif()
+add_subdirectory(gmxana)
+add_subdirectory(gmxpreprocess)
+add_subdirectory(correlationfunctions)
+add_subdirectory(statistics)
+add_subdirectory(analysisdata)
+add_subdirectory(coordinateio)
+add_subdirectory(trajectoryanalysis)
+add_subdirectory(energyanalysis)
+add_subdirectory(tools)
get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
tmpi_get_source_list(THREAD_MPI_SOURCES ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/src)
add_library(thread_mpi OBJECT ${THREAD_MPI_SOURCES})
target_compile_definitions(thread_mpi PRIVATE HAVE_CONFIG_H)
+if(CYGWIN)
+ # Needs POSIX-isms for strdup, not just std-isms
+ target_compile_definitions(thread_mpi PRIVATE _POSIX_C_SOURCE=200809L)
+endif()
gmx_target_compile_options(thread_mpi)
if (WIN32)
gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
endif()
list(APPEND libgromacs_object_library_dependencies thread_mpi)
-configure_file(version.h.cmakein version.h)
if(GMX_INSTALL_LEGACY_API)
install(FILES
- ${CMAKE_CURRENT_BINARY_DIR}/version.h
analysisdata.h
options.h
selection.h
list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
# Mark some shared GPU implementation files to compile with CUDA if needed
-if (GMX_USE_CUDA)
- get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
- set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
+if (GMX_GPU_CUDA)
+ get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
+ set_source_files_properties(${CUDA_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
endif()
-# set up CUDA compilation with clang
-if (GMX_CLANG_CUDA)
- foreach (_file ${LIBGROMACS_SOURCES})
- get_filename_component(_ext ${_file} EXT)
- get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
- if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
- gmx_compile_cuda_file_with_clang(${_file})
- endif()
- endforeach()
-endif()
-
-if (GMX_USE_CUDA)
+if (GMX_GPU_CUDA)
# Work around FindCUDA that prevents using target_link_libraries()
# with keywords otherwise...
set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
add_library(libgromacs ${LIBGROMACS_SOURCES})
endif()
+if (TARGET Heffte::Heffte)
+ target_link_libraries(libgromacs PRIVATE Heffte::Heffte)
+endif()
+
+if (GMX_SYCL_HIPSYCL AND GMX_HIPSYCL_HAVE_HIP_TARGET)
+ target_link_libraries(libgromacs PUBLIC roc::rocfft)
+endif()
+
+target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:common>)
+# As long as the libgromacs target has source files that reference headers from
+# modules that don't provide CMake targets, libgromacs needs to use `src/`
+# amongst its include directories (to support `#include "gromacs/module/header.h"`).
+add_library(legacy_modules INTERFACE)
+target_include_directories(legacy_modules INTERFACE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
+target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:legacy_modules>)
+
# Add these contents first because linking their tests can take a lot
# of time, so we want lots of parallel work still available after
# linking starts.
add_subdirectory(fileio)
add_subdirectory(selection)
-# Suppress a warning about our abuse of t_inputrec
-gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
-
# Handle the object libraries that contain the source file
# dependencies that need special handling because they are generated
# or external code.
set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
endif()
target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
+ target_link_libraries(${object_library} PRIVATE common)
# Add the sources from the object libraries to the main library.
target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
-if (GMX_USE_OPENCL)
+if (GMX_GPU_OPENCL)
option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
mark_as_advanced(GMX_EXTERNAL_CLFFT)
set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
endif()
+# Do any special handling needed for .cpp files that use
+# CUDA runtime headers
+if (GMX_GPU_CUDA AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+ foreach(_compile_flag ${NVCC_CLANG_SUPPRESSIONS_CXXFLAGS})
+ set(GMX_CUDA_CLANG_FLAGS "${GMX_CUDA_CLANG_FLAGS} ${_compile_flag}")
+ endforeach()
+ if (GMX_CLANG_CUDA)
+ foreach (_file ${LIBGROMACS_SOURCES})
+ get_filename_component(_ext ${_file} EXT)
+ get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
+ if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
+ gmx_compile_cuda_file_with_clang(${_file})
+ endif()
+ endforeach()
+ else()
+ get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
+ set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS ${GMX_CUDA_CLANG_FLAGS})
+ endif()
+endif()
+
+# Only add the -fsycl flag to sources that really need it
+if (GMX_GPU_SYCL)
+ get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
+ add_sycl_to_target(TARGET libgromacs SOURCES ${SYCL_SOURCES})
+endif()
+
gmx_setup_tng_for_libgromacs()
+# We apply the SYCL flag explicitly just for libgromacs, since bugs in the beta versions of
+# icpx/dpcpp leads to crashes if we try to link an library without any SYCL code with the
+# -fsycl flag enabled. Once that bug is fixed, we should change it to simply add
+# SYCL_CXX_FLAGS to GMX_SHARED_LINKER_FLAGS.
target_link_libraries(libgromacs
PRIVATE
${EXTRAE_LIBRARIES}
${GMX_COMMON_LIBRARIES}
${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
+ ${SYCL_CXX_FLAGS}
${OpenCL_LIBRARIES}
$<$<PLATFORM_ID:SunOS>:socket>
PUBLIC
${GMX_PUBLIC_LIBRARIES}
)
+target_link_libraries(libgromacs PUBLIC legacy_api)
+# Dependencies from libgromacs to the modules are set up here, but
+# once the add_subdirectory() commands are re-ordered then
+# responsibility for setting this up will move to the respective
+# modules.
+target_link_libraries(libgromacs PRIVATE
+ $<BUILD_INTERFACE:analysisdata>
+ $<BUILD_INTERFACE:applied_forces>
+ $<BUILD_INTERFACE:commandline>
+ $<BUILD_INTERFACE:compat>
+ $<BUILD_INTERFACE:coordinateio>
+ $<BUILD_INTERFACE:correlationfunctions>
+ $<BUILD_INTERFACE:domdec>
+# $<BUILD_INTERFACE:energyanalysis>
+ $<BUILD_INTERFACE:essentialdynamics>
+ $<BUILD_INTERFACE:ewald>
+ $<BUILD_INTERFACE:fft>
+ $<BUILD_INTERFACE:fileio>
+ $<BUILD_INTERFACE:gmxana>
+ $<BUILD_INTERFACE:gmxlib>
+ $<BUILD_INTERFACE:gmxpreprocess>
+ $<BUILD_INTERFACE:gpu_utils>
+ $<BUILD_INTERFACE:hardware>
+ $<BUILD_INTERFACE:imd>
+ $<BUILD_INTERFACE:linearalgebra>
+ $<BUILD_INTERFACE:listed_forces>
+ $<BUILD_INTERFACE:math>
+ $<BUILD_INTERFACE:mdlib>
+ $<BUILD_INTERFACE:mdrun>
+ $<BUILD_INTERFACE:mdrunutility>
+ $<BUILD_INTERFACE:mdspan>
+ $<BUILD_INTERFACE:mdtypes>
+ $<BUILD_INTERFACE:mimic>
+ $<BUILD_INTERFACE:modularsimulator>
+ $<BUILD_INTERFACE:nbnxm>
+ $<BUILD_INTERFACE:onlinehelp>
+ $<BUILD_INTERFACE:options>
+ $<BUILD_INTERFACE:pbcutil>
+ $<BUILD_INTERFACE:pulling>
+ $<BUILD_INTERFACE:random>
+ $<BUILD_INTERFACE:restraint>
+ $<BUILD_INTERFACE:selection>
+ $<BUILD_INTERFACE:simd>
+ $<BUILD_INTERFACE:statistics>
+ $<BUILD_INTERFACE:swap>
+ $<BUILD_INTERFACE:tables>
+ $<BUILD_INTERFACE:taskassignment>
+ $<BUILD_INTERFACE:timing>
+ $<BUILD_INTERFACE:tools>
+ $<BUILD_INTERFACE:topology>
+ $<BUILD_INTERFACE:trajectory>
+ $<BUILD_INTERFACE:trajectoryanalysis>
+ $<BUILD_INTERFACE:utility>
+ )
if (GMX_OPENMP)
target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
endif()
gmx_manage_lmfit()
target_link_libraries(libgromacs PRIVATE lmfit)
+gmx_manage_muparser()
+target_link_libraries(libgromacs PRIVATE muparser)
-# Fix everything found by the latest version of clang that we use in
-# Jenkins testing. This should be updated when we update the latest
-# tested version of clang.
-if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^7\.0")
- target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
-endif()
+# Make sure we fix "everything" found by compilers that support that
+gmx_warn_on_everything(libgromacs)
if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
#Control flow warnings are disabled because the commond line output is insufficient. There is no tool
target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
endif()
-# Only install the library in mdrun-only mode if it is actually necessary
-# for the binary
-if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
+# TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
+if (BUILD_SHARED_LIBS)
install(TARGETS libgromacs
EXPORT libgromacs
LIBRARY
DESTINATION ${CMAKE_INSTALL_LIBDIR}
COMPONENT libraries
INCLUDES DESTINATION include)
+ target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
+ # legacy headers use c++17 features, so consumer codes need to use that standard, too
+ if(GMX_INSTALL_LEGACY_API)
+ target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
+ endif()
endif()
+add_library(Gromacs::libgromacs ALIAS libgromacs)
-if (NOT GMX_BUILD_MDRUN_ONLY)
- include(InstallLibInfo.cmake)
-endif()
+include(InstallLibInfo.cmake)
# Technically, the user could want to do this for an OpenCL build
# using the CUDA runtime, but currently there's no reason to want to
# do that.
if (INSTALL_CUDART_LIB) #can be set manual by user
- if (GMX_USE_CUDA)
+ if (GMX_GPU_CUDA)
foreach(CUDA_LIB ${CUDA_LIBRARIES})
string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
if(IS_CUDART) #libcuda should not be installed
endif()
endif()
-if(GMX_USE_OPENCL)
+if(GMX_GPU_OPENCL)
# Install the utility headers
file(GLOB OPENCL_INSTALLED_FILES
gpu_utils/vectype_ops.clh
ewald/pme_spread.clh
ewald/pme_solve.clh
ewald/pme_gather.clh
- ewald/pme_gpu_utils.clh
+ ewald/pme_gpu_calculate_splines.clh
ewald/pme_program.cl
ewald/pme_gpu_types.h
)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff