2 # This file is part of the GROMACS molecular simulation package.
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34 # the research papers on the package. Check out http://www.gromacs.org.
36 set(LIBGROMACS_SOURCES)
39 include(gmxClangCudaUtils)
42 set_property(GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
43 set_property(GLOBAL PROPERTY CUDA_SOURCES)
44 set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
45 set_property(GLOBAL PROPERTY GMX_AVX_512_SOURCE)
47 set(libgromacs_object_library_dependencies "")
48 function (_gmx_add_files_to_property PROPERTY)
49 foreach (_file ${ARGN})
50 if (IS_ABSOLUTE "${_file}")
51 set_property(GLOBAL APPEND PROPERTY ${PROPERTY} ${_file})
53 set_property(GLOBAL APPEND PROPERTY ${PROPERTY}
54 ${CMAKE_CURRENT_LIST_DIR}/${_file})
59 function (gmx_add_libgromacs_sources)
60 _gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
63 # Permit the configuration to disable compiling the many nbnxm kernels
64 # and others involved in force calculations. Currently only
65 # short-ranged and bonded kernels are disabled this way, but in future
66 # others may be appropriate. Thus the cmake option is not specific to
68 option(GMX_USE_SIMD_KERNELS "Whether to compile NBNXM and other SIMD kernels" ON)
69 mark_as_advanced(GMX_USE_SIMD_KERNELS)
71 # Add these contents first because linking their tests can take a lot
72 # of time, so we want lots of parallel work still available after
74 add_subdirectory(utility)
76 add_subdirectory(gmxlib)
77 add_subdirectory(mdlib)
78 add_subdirectory(applied_forces)
79 add_subdirectory(listed_forces)
80 add_subdirectory(nbnxm)
81 add_subdirectory(commandline)
82 add_subdirectory(domdec)
83 add_subdirectory(ewald)
85 add_subdirectory(gpu_utils)
86 add_subdirectory(hardware)
87 add_subdirectory(linearalgebra)
88 add_subdirectory(math)
89 add_subdirectory(mdrun)
90 add_subdirectory(mdrunutility)
91 add_subdirectory(mdspan)
92 add_subdirectory(mdtypes)
93 add_subdirectory(onlinehelp)
94 add_subdirectory(options)
95 add_subdirectory(pbcutil)
96 add_subdirectory(random)
97 add_subdirectory(restraint)
98 add_subdirectory(tables)
99 add_subdirectory(taskassignment)
100 add_subdirectory(timing)
101 add_subdirectory(topology)
102 add_subdirectory(trajectory)
103 add_subdirectory(swap)
104 add_subdirectory(essentialdynamics)
105 add_subdirectory(pulling)
106 add_subdirectory(simd)
107 add_subdirectory(imd)
108 add_subdirectory(compat)
109 add_subdirectory(mimic)
110 add_subdirectory(modularsimulator)
111 if (NOT GMX_BUILD_MDRUN_ONLY)
112 add_subdirectory(gmxana)
113 add_subdirectory(gmxpreprocess)
114 add_subdirectory(correlationfunctions)
115 add_subdirectory(statistics)
116 add_subdirectory(analysisdata)
117 add_subdirectory(coordinateio)
118 add_subdirectory(trajectoryanalysis)
119 add_subdirectory(energyanalysis)
120 add_subdirectory(tools)
123 get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
124 list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
126 # This would be the standard way to include thread_mpi, but
127 # we want libgromacs to link the functions directly
129 # add_subdirectory(thread_mpi)
131 #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
132 tmpi_get_source_list(THREAD_MPI_SOURCES ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/src)
133 add_library(thread_mpi OBJECT ${THREAD_MPI_SOURCES})
134 target_compile_definitions(thread_mpi PRIVATE HAVE_CONFIG_H)
136 # Needs POSIX-isms for strdup, not just std-isms
137 target_compile_definitions(thread_mpi PRIVATE _POSIX_C_SOURCE=200809L)
139 gmx_target_compile_options(thread_mpi)
141 gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
143 list(APPEND libgromacs_object_library_dependencies thread_mpi)
145 if(GMX_INSTALL_LEGACY_API)
151 DESTINATION include/gromacs)
154 # This code is here instead of utility/CMakeLists.txt, because CMake
155 # custom commands and source file properties can only be set in the directory
156 # that contains the target that uses them.
157 # TODO: Generate a header instead that can be included from baseversion.cpp.
158 # That probably simplifies things somewhat.
159 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
160 gmx_configure_version_file(
161 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
168 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
170 # Mark some shared GPU implementation files to compile with CUDA if needed
172 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
173 set_source_files_properties(${CUDA_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
177 # Work around FindCUDA that prevents using target_link_libraries()
178 # with keywords otherwise...
179 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
180 if (NOT GMX_CLANG_CUDA)
181 gmx_cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
183 add_library(libgromacs ${LIBGROMACS_SOURCES})
185 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
187 add_library(libgromacs ${LIBGROMACS_SOURCES})
189 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:common>)
190 # As long as the libgromacs target has source files that reference headers from
191 # modules that don't provide CMake targets, libgromacs needs to use `src/`
192 # amongst its include directories (to support `#include "gromacs/module/header.h"`).
193 add_library(legacy_modules INTERFACE)
194 target_include_directories(legacy_modules INTERFACE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
195 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:legacy_modules>)
197 # Add these contents first because linking their tests can take a lot
198 # of time, so we want lots of parallel work still available after
200 add_subdirectory(fileio)
201 add_subdirectory(selection)
203 # Suppress a warning about our abuse of t_inputrec
204 gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
206 # Handle the object libraries that contain the source file
207 # dependencies that need special handling because they are generated
209 foreach(object_library ${libgromacs_object_library_dependencies})
210 if (BUILD_SHARED_LIBS)
211 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
213 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
214 target_link_libraries(${object_library} PRIVATE common)
216 # Add the sources from the object libraries to the main library.
217 target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
219 gmx_target_compile_options(libgromacs)
220 target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
221 target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
224 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
225 mark_as_advanced(GMX_EXTERNAL_CLFFT)
227 # Default to using clFFT found on the system
228 # switch to quiet at the second run.
229 if (DEFINED clFFT_LIBRARY)
230 set (clFFT_FIND_QUIETLY TRUE)
234 if (GMX_EXTERNAL_CLFFT)
235 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
240 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
241 requires clFFT, which was not found on your system. GROMACS does bundle
242 clFFT to help with building for OpenCL, but that clFFT has not yet been
243 ported to the more recent versions of that compiler that GROMACS itself
244 requires. Thus for now, OpenCL is not available with MSVC and the internal
245 build of clFFT in GROMACS 2019. Either change compiler, try installing
246 a clFFT package, or use the latest GROMACS 2018 point release.")
249 # Fall back on the internal version
250 set (_clFFT_dir ../external/clFFT/src)
251 add_subdirectory(${_clFFT_dir} clFFT-build)
252 target_sources(libgromacs PRIVATE
253 $<TARGET_OBJECTS:clFFT>
255 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
256 # Use the magic variable for how to link any library needed for
257 # dlopen, etc. which is -ldl where needed, and empty otherwise
258 # (e.g. Windows, BSD, Mac).
259 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
261 target_link_libraries(libgromacs PRIVATE clFFT)
265 # Permit GROMACS code to include externally developed headers, such as
266 # the functionality from the nonstd project that we use for
267 # gmx::compat::optional. These are included as system headers so that
268 # no warnings are issued from them.
270 # TODO Perhaps generalize this for all headers from src/external
271 target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
273 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
274 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
275 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
276 # with the SIMD_AVX_512_CXX_FLAGS flags.
277 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
280 # Do any special handling needed for .cpp files that use
281 # CUDA runtime headers
282 if (GMX_GPU_CUDA AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
283 # CUDA header cuda_runtime_api.h in at least CUDA 10.1 uses 0
284 # where nullptr would be preferable. GROMACS can't fix these, so
285 # must suppress them.
286 GMX_TEST_CXXFLAG(CXXFLAGS_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
288 foreach(_compile_flag ${NVCC_CLANG_SUPPRESSIONS_CXXFLAGS})
289 set(GMX_CUDA_CLANG_FLAGS "${GMX_CUDA_CLANG_FLAGS} ${_compile_flag}")
292 foreach (_file ${LIBGROMACS_SOURCES})
293 get_filename_component(_ext ${_file} EXT)
294 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
295 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
296 gmx_compile_cuda_file_with_clang(${_file})
300 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
301 set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS ${GMX_CUDA_CLANG_FLAGS})
305 # Only add the -fsycl flag to sources that really need it
307 get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
308 set_source_files_properties(${SYCL_SOURCES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
311 gmx_setup_tng_for_libgromacs()
313 # We apply the SYCL flag explicitly just for libgromacs, since bugs in the beta versions of
314 # icpx/dpcpp leads to crashes if we try to link an library without any SYCL code with the
315 # -fsycl flag enabled. Once that bug is fixed, we should change it to simply add
316 # SYCL_CXX_FLAGS to GMX_SHARED_LINKER_FLAGS.
317 target_link_libraries(libgromacs
320 ${GMX_EXTRA_LIBRARIES}
321 ${GMX_COMMON_LIBRARIES}
322 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
323 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
326 $<$<PLATFORM_ID:SunOS>:socket>
328 ${GMX_PUBLIC_LIBRARIES}
330 target_link_libraries(libgromacs PUBLIC legacy_api)
333 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
335 set_target_properties(libgromacs PROPERTIES
336 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
337 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
338 VERSION ${LIBRARY_VERSION}
342 target_link_libraries(libgromacs PRIVATE lmfit)
344 # Make sure we fix "everything" found by more recent versions of clang.
345 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "7")
346 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
348 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
349 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
350 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
351 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
352 /wd6001 #unitialized memory
353 /wd6011 #derefencing NULL
354 /wd6053 #prior call not zero-terminate
355 /wd6054 #might not be zero-terminated
356 /wd6385 #reading invalid data
357 /wd6386 #buffer overrun
358 /wd6387 #could be '0'
359 /wd28199 #uninitialized memory
360 # For compile time constant (e.g. templates) the following warnings have flase postives
361 /wd6239 #(<non-zero> && <expr>)
362 /wd6240 #(<expr> && <non-zero>)
363 /wd6294 #Ill-defined for-loop
364 /wd6326 #comparison of constant with other constant
365 /wd28020 #expression involving paramter is not true
367 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
368 /wd6993 #OpenMP ignored
370 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
371 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
372 /wd6246 #hides declaration
378 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
379 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
382 # clang-3.6 warns about a number of issues that are not reported by more modern compilers
383 # and we know they are not real issues. So we only check that it can compile without error
384 # but ignore all warnings.
385 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
386 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
389 # Only install the library in mdrun-only mode if it is actually necessary
391 # TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
392 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
393 install(TARGETS libgromacs
396 DESTINATION ${CMAKE_INSTALL_LIBDIR}
399 DESTINATION ${CMAKE_INSTALL_BINDIR}
402 DESTINATION ${CMAKE_INSTALL_LIBDIR}
404 INCLUDES DESTINATION include)
405 target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
406 # legacy headers use c++17 features, so consumer codes need to use that standard, too
407 if(GMX_INSTALL_LEGACY_API)
408 target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
411 add_library(Gromacs::libgromacs ALIAS libgromacs)
413 if (NOT GMX_BUILD_MDRUN_ONLY)
414 include(InstallLibInfo.cmake)
417 # Technically, the user could want to do this for an OpenCL build
418 # using the CUDA runtime, but currently there's no reason to want to
420 if (INSTALL_CUDART_LIB) #can be set manual by user
422 foreach(CUDA_LIB ${CUDA_LIBRARIES})
423 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
424 if(IS_CUDART) #libcuda should not be installed
425 #install also name-links (linker uses those)
426 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
427 install(FILES ${CUDA_LIBS} DESTINATION
428 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
432 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
437 # Install the utility headers
438 file(GLOB OPENCL_INSTALLED_FILES
439 gpu_utils/vectype_ops.clh
440 gpu_utils/device_utils.clh
442 install(FILES ${OPENCL_INSTALLED_FILES}
443 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
445 file(GLOB OPENCL_INSTALLED_FILES
448 install(FILES ${OPENCL_INSTALLED_FILES}
449 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
452 # Install the NBNXM source and headers
453 file(GLOB OPENCL_INSTALLED_FILES
456 install(FILES ${OPENCL_INSTALLED_FILES}
457 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
459 file(GLOB OPENCL_INSTALLED_FILES
460 nbnxm/opencl/nbnxm_ocl_kernels.cl
461 nbnxm/opencl/nbnxm_ocl_kernel.clh
462 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
463 nbnxm/opencl/nbnxm_ocl_kernels.clh
464 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
465 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
466 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
467 nbnxm/opencl/nbnxm_ocl_consts.h
469 install(FILES ${OPENCL_INSTALLED_FILES}
470 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
473 # Install the PME source and headers
474 file(GLOB OPENCL_INSTALLED_FILES
478 ewald/pme_gpu_calculate_splines.clh
480 ewald/pme_gpu_types.h
482 install(FILES ${OPENCL_INSTALLED_FILES}
483 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald