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})
190 # Add these contents first because linking their tests can take a lot
191 # of time, so we want lots of parallel work still available after
193 add_subdirectory(fileio)
194 add_subdirectory(selection)
196 # Suppress a warning about our abuse of t_inputrec
197 gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
199 # Handle the object libraries that contain the source file
200 # dependencies that need special handling because they are generated
202 foreach(object_library ${libgromacs_object_library_dependencies})
203 if (BUILD_SHARED_LIBS)
204 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
206 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
208 # Add the sources from the object libraries to the main library.
209 target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
211 gmx_target_compile_options(libgromacs)
212 target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
213 target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
216 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
217 mark_as_advanced(GMX_EXTERNAL_CLFFT)
219 # Default to using clFFT found on the system
220 # switch to quiet at the second run.
221 if (DEFINED clFFT_LIBRARY)
222 set (clFFT_FIND_QUIETLY TRUE)
226 if (GMX_EXTERNAL_CLFFT)
227 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
232 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
233 requires clFFT, which was not found on your system. GROMACS does bundle
234 clFFT to help with building for OpenCL, but that clFFT has not yet been
235 ported to the more recent versions of that compiler that GROMACS itself
236 requires. Thus for now, OpenCL is not available with MSVC and the internal
237 build of clFFT in GROMACS 2019. Either change compiler, try installing
238 a clFFT package, or use the latest GROMACS 2018 point release.")
241 # Fall back on the internal version
242 set (_clFFT_dir ../external/clFFT/src)
243 add_subdirectory(${_clFFT_dir} clFFT-build)
244 target_sources(libgromacs PRIVATE
245 $<TARGET_OBJECTS:clFFT>
247 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
248 # Use the magic variable for how to link any library needed for
249 # dlopen, etc. which is -ldl where needed, and empty otherwise
250 # (e.g. Windows, BSD, Mac).
251 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
253 target_link_libraries(libgromacs PRIVATE clFFT)
257 # Permit GROMACS code to include externally developed headers, such as
258 # the functionality from the nonstd project that we use for
259 # gmx::compat::optional. These are included as system headers so that
260 # no warnings are issued from them.
262 # TODO Perhaps generalize this for all headers from src/external
263 target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
265 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
266 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
267 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
268 # with the SIMD_AVX_512_CXX_FLAGS flags.
269 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
272 # Do any special handling needed for .cpp files that use
273 # CUDA runtime headers
274 if (GMX_GPU_CUDA AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
275 # CUDA header cuda_runtime_api.h in at least CUDA 10.1 uses 0
276 # where nullptr would be preferable. GROMACS can't fix these, so
277 # must suppress them.
278 GMX_TEST_CXXFLAG(CXXFLAGS_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
280 foreach(_compile_flag ${NVCC_CLANG_SUPPRESSIONS_CXXFLAGS})
281 set(GMX_CUDA_CLANG_FLAGS "${GMX_CUDA_CLANG_FLAGS} ${_compile_flag}")
284 foreach (_file ${LIBGROMACS_SOURCES})
285 get_filename_component(_ext ${_file} EXT)
286 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
287 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
288 gmx_compile_cuda_file_with_clang(${_file})
292 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
293 set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS ${GMX_CUDA_CLANG_FLAGS})
297 # Only add the -fsycl flag to sources that really need it
299 get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
300 set_source_files_properties(${SYCL_SOURCES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
303 gmx_setup_tng_for_libgromacs()
305 # We apply the SYCL flag explicitly just for libgromacs, since bugs in the beta versions of
306 # icpx/dpcpp leads to crashes if we try to link an library without any SYCL code with the
307 # -fsycl flag enabled. Once that bug is fixed, we should change it to simply add
308 # SYCL_CXX_FLAGS to GMX_SHARED_LINKER_FLAGS.
309 target_link_libraries(libgromacs
312 ${GMX_EXTRA_LIBRARIES}
313 ${GMX_COMMON_LIBRARIES}
314 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
315 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
318 $<$<PLATFORM_ID:SunOS>:socket>
320 ${GMX_PUBLIC_LIBRARIES}
322 target_link_libraries(libgromacs PUBLIC legacy_api)
325 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
327 set_target_properties(libgromacs PROPERTIES
328 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
329 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
330 VERSION ${LIBRARY_VERSION}
334 target_link_libraries(libgromacs PRIVATE lmfit)
336 # Make sure we fix "everything" found by more recent versions of clang.
337 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "7")
338 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
340 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
341 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
342 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
343 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
344 /wd6001 #unitialized memory
345 /wd6011 #derefencing NULL
346 /wd6053 #prior call not zero-terminate
347 /wd6054 #might not be zero-terminated
348 /wd6385 #reading invalid data
349 /wd6386 #buffer overrun
350 /wd6387 #could be '0'
351 /wd28199 #uninitialized memory
352 # For compile time constant (e.g. templates) the following warnings have flase postives
353 /wd6239 #(<non-zero> && <expr>)
354 /wd6240 #(<expr> && <non-zero>)
355 /wd6294 #Ill-defined for-loop
356 /wd6326 #comparison of constant with other constant
357 /wd28020 #expression involving paramter is not true
359 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
360 /wd6993 #OpenMP ignored
362 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
363 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
364 /wd6246 #hides declaration
370 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
371 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
374 # clang-3.6 warns about a number of issues that are not reported by more modern compilers
375 # and we know they are not real issues. So we only check that it can compile without error
376 # but ignore all warnings.
377 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
378 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
381 # Only install the library in mdrun-only mode if it is actually necessary
383 # TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
384 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
385 install(TARGETS libgromacs
388 DESTINATION ${CMAKE_INSTALL_LIBDIR}
391 DESTINATION ${CMAKE_INSTALL_BINDIR}
394 DESTINATION ${CMAKE_INSTALL_LIBDIR}
396 INCLUDES DESTINATION include)
397 target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
398 # legacy headers use c++17 features, so consumer codes need to use that standard, too
399 if(GMX_INSTALL_LEGACY_API)
400 target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
403 add_library(Gromacs::libgromacs ALIAS libgromacs)
405 if (NOT GMX_BUILD_MDRUN_ONLY)
406 include(InstallLibInfo.cmake)
409 # Technically, the user could want to do this for an OpenCL build
410 # using the CUDA runtime, but currently there's no reason to want to
412 if (INSTALL_CUDART_LIB) #can be set manual by user
414 foreach(CUDA_LIB ${CUDA_LIBRARIES})
415 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
416 if(IS_CUDART) #libcuda should not be installed
417 #install also name-links (linker uses those)
418 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
419 install(FILES ${CUDA_LIBS} DESTINATION
420 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
424 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
429 # Install the utility headers
430 file(GLOB OPENCL_INSTALLED_FILES
431 gpu_utils/vectype_ops.clh
432 gpu_utils/device_utils.clh
434 install(FILES ${OPENCL_INSTALLED_FILES}
435 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
437 file(GLOB OPENCL_INSTALLED_FILES
440 install(FILES ${OPENCL_INSTALLED_FILES}
441 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
444 # Install the NBNXM source and headers
445 file(GLOB OPENCL_INSTALLED_FILES
448 install(FILES ${OPENCL_INSTALLED_FILES}
449 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
451 file(GLOB OPENCL_INSTALLED_FILES
452 nbnxm/opencl/nbnxm_ocl_kernels.cl
453 nbnxm/opencl/nbnxm_ocl_kernel.clh
454 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
455 nbnxm/opencl/nbnxm_ocl_kernels.clh
456 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
457 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
458 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
459 nbnxm/opencl/nbnxm_ocl_consts.h
461 install(FILES ${OPENCL_INSTALLED_FILES}
462 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
465 # Install the PME source and headers
466 file(GLOB OPENCL_INSTALLED_FILES
470 ewald/pme_gpu_calculate_splines.clh
472 ewald/pme_gpu_types.h
474 install(FILES ${OPENCL_INSTALLED_FILES}
475 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald