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 GMX_LIBGROMACS_GPU_IMPL_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 configure_file(version.h.cmakein version.h)
146 if(GMX_INSTALL_LEGACY_API)
148 ${CMAKE_CURRENT_BINARY_DIR}/version.h
153 DESTINATION include/gromacs)
156 # This code is here instead of utility/CMakeLists.txt, because CMake
157 # custom commands and source file properties can only be set in the directory
158 # that contains the target that uses them.
159 # TODO: Generate a header instead that can be included from baseversion.cpp.
160 # That probably simplifies things somewhat.
161 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
162 gmx_configure_version_file(
163 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
170 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
172 # Mark some shared GPU implementation files to compile with CUDA if needed
174 get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
175 set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
178 # set up CUDA compilation with clang
180 foreach (_file ${LIBGROMACS_SOURCES})
181 get_filename_component(_ext ${_file} EXT)
182 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
183 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
184 gmx_compile_cuda_file_with_clang(${_file})
190 # Work around FindCUDA that prevents using target_link_libraries()
191 # with keywords otherwise...
192 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
193 if (NOT GMX_CLANG_CUDA)
194 gmx_cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
196 add_library(libgromacs ${LIBGROMACS_SOURCES})
198 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
200 add_library(libgromacs ${LIBGROMACS_SOURCES})
203 # Add these contents first because linking their tests can take a lot
204 # of time, so we want lots of parallel work still available after
206 add_subdirectory(fileio)
207 add_subdirectory(selection)
209 # Suppress a warning about our abuse of t_inputrec
210 gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
212 # Handle the object libraries that contain the source file
213 # dependencies that need special handling because they are generated
215 foreach(object_library ${libgromacs_object_library_dependencies})
216 if (BUILD_SHARED_LIBS)
217 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
219 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
221 # Add the sources from the object libraries to the main library.
222 target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
224 gmx_target_compile_options(libgromacs)
225 target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
226 target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
229 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
230 mark_as_advanced(GMX_EXTERNAL_CLFFT)
232 # Default to using clFFT found on the system
233 # switch to quiet at the second run.
234 if (DEFINED clFFT_LIBRARY)
235 set (clFFT_FIND_QUIETLY TRUE)
239 if (GMX_EXTERNAL_CLFFT)
240 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
245 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
246 requires clFFT, which was not found on your system. GROMACS does bundle
247 clFFT to help with building for OpenCL, but that clFFT has not yet been
248 ported to the more recent versions of that compiler that GROMACS itself
249 requires. Thus for now, OpenCL is not available with MSVC and the internal
250 build of clFFT in GROMACS 2019. Either change compiler, try installing
251 a clFFT package, or use the latest GROMACS 2018 point release.")
254 # Fall back on the internal version
255 set (_clFFT_dir ../external/clFFT/src)
256 add_subdirectory(${_clFFT_dir} clFFT-build)
257 target_sources(libgromacs PRIVATE
258 $<TARGET_OBJECTS:clFFT>
260 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
261 # Use the magic variable for how to link any library needed for
262 # dlopen, etc. which is -ldl where needed, and empty otherwise
263 # (e.g. Windows, BSD, Mac).
264 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
266 target_link_libraries(libgromacs PRIVATE clFFT)
270 # Permit GROMACS code to include externally developed headers, such as
271 # the functionality from the nonstd project that we use for
272 # gmx::compat::optional. These are included as system headers so that
273 # no warnings are issued from them.
275 # TODO Perhaps generalize this for all headers from src/external
276 target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
278 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
279 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
280 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
281 # with the SIMD_AVX_512_CXX_FLAGS flags.
282 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
285 # Do any special handling needed for .cpp files that use
286 # CUDA runtime headers
287 if (GMX_GPU_CUDA AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
288 # CUDA header cuda_runtime_api.h in at least CUDA 10.1 uses 0
289 # where nullptr would be preferable. GROMACS can't fix these, so
290 # must suppress them.
291 GMX_TEST_CXXFLAG(CXXFLAGS_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
293 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
294 foreach(_compile_flag ${NVCC_CLANG_SUPPRESSIONS_CXXFLAGS})
295 set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS ${_compile_flag})
299 # Only add the -fsycl flag to sources that really need it
301 get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
302 set_source_files_properties(${SYCL_SOURCES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
305 gmx_setup_tng_for_libgromacs()
307 # We apply the SYCL flag explicitly just for libgromacs, since bugs in the beta versions of
308 # icpx/dpcpp leads to crashes if we try to link an library without any SYCL code with the
309 # -fsycl flag enabled. Once that bug is fixed, we should change it to simply add
310 # SYCL_CXX_FLAGS to GMX_SHARED_LINKER_FLAGS.
311 target_link_libraries(libgromacs
314 ${GMX_EXTRA_LIBRARIES}
315 ${GMX_COMMON_LIBRARIES}
316 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
317 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
320 $<$<PLATFORM_ID:SunOS>:socket>
322 ${GMX_PUBLIC_LIBRARIES}
325 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
327 set_target_properties(libgromacs PROPERTIES
328 OUTPUT_NAME "gromacs${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 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
384 install(TARGETS libgromacs
387 DESTINATION ${CMAKE_INSTALL_LIBDIR}
390 DESTINATION ${CMAKE_INSTALL_BINDIR}
393 DESTINATION ${CMAKE_INSTALL_LIBDIR}
395 INCLUDES DESTINATION include)
396 target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
397 # legacy headers use c++17 features, so consumer codes need to use that standard, too
398 if(GMX_INSTALL_LEGACY_API)
399 target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
401 add_library(Gromacs::libgromacs ALIAS libgromacs)
404 if (NOT GMX_BUILD_MDRUN_ONLY)
405 include(InstallLibInfo.cmake)
408 # Technically, the user could want to do this for an OpenCL build
409 # using the CUDA runtime, but currently there's no reason to want to
411 if (INSTALL_CUDART_LIB) #can be set manual by user
413 foreach(CUDA_LIB ${CUDA_LIBRARIES})
414 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
415 if(IS_CUDART) #libcuda should not be installed
416 #install also name-links (linker uses those)
417 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
418 install(FILES ${CUDA_LIBS} DESTINATION
419 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
423 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
428 # Install the utility headers
429 file(GLOB OPENCL_INSTALLED_FILES
430 gpu_utils/vectype_ops.clh
431 gpu_utils/device_utils.clh
433 install(FILES ${OPENCL_INSTALLED_FILES}
434 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
436 file(GLOB OPENCL_INSTALLED_FILES
439 install(FILES ${OPENCL_INSTALLED_FILES}
440 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
443 # Install the NBNXM source and headers
444 file(GLOB OPENCL_INSTALLED_FILES
447 install(FILES ${OPENCL_INSTALLED_FILES}
448 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
450 file(GLOB OPENCL_INSTALLED_FILES
451 nbnxm/opencl/nbnxm_ocl_kernels.cl
452 nbnxm/opencl/nbnxm_ocl_kernel.clh
453 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
454 nbnxm/opencl/nbnxm_ocl_kernels.clh
455 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
456 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
457 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
458 nbnxm/opencl/nbnxm_ocl_consts.h
460 install(FILES ${OPENCL_INSTALLED_FILES}
461 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
464 # Install the PME source and headers
465 file(GLOB OPENCL_INSTALLED_FILES
469 ewald/pme_gpu_calculate_splines.clh
471 ewald/pme_gpu_types.h
473 install(FILES ${OPENCL_INSTALLED_FILES}
474 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald