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 add_subdirectory(gmxana)
112 add_subdirectory(gmxpreprocess)
113 add_subdirectory(correlationfunctions)
114 add_subdirectory(statistics)
115 add_subdirectory(analysisdata)
116 add_subdirectory(coordinateio)
117 add_subdirectory(trajectoryanalysis)
118 add_subdirectory(energyanalysis)
119 add_subdirectory(tools)
121 get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
122 list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
124 # This would be the standard way to include thread_mpi, but
125 # we want libgromacs to link the functions directly
127 # add_subdirectory(thread_mpi)
129 #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
130 tmpi_get_source_list(THREAD_MPI_SOURCES ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/src)
131 add_library(thread_mpi OBJECT ${THREAD_MPI_SOURCES})
132 target_compile_definitions(thread_mpi PRIVATE HAVE_CONFIG_H)
134 # Needs POSIX-isms for strdup, not just std-isms
135 target_compile_definitions(thread_mpi PRIVATE _POSIX_C_SOURCE=200809L)
137 gmx_target_compile_options(thread_mpi)
139 gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
141 list(APPEND libgromacs_object_library_dependencies thread_mpi)
143 if(GMX_INSTALL_LEGACY_API)
149 DESTINATION include/gromacs)
152 # This code is here instead of utility/CMakeLists.txt, because CMake
153 # custom commands and source file properties can only be set in the directory
154 # that contains the target that uses them.
155 # TODO: Generate a header instead that can be included from baseversion.cpp.
156 # That probably simplifies things somewhat.
157 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
158 gmx_configure_version_file(
159 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
166 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
168 # Mark some shared GPU implementation files to compile with CUDA if needed
170 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
171 set_source_files_properties(${CUDA_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
175 # Work around FindCUDA that prevents using target_link_libraries()
176 # with keywords otherwise...
177 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
178 if (NOT GMX_CLANG_CUDA)
179 gmx_cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
181 add_library(libgromacs ${LIBGROMACS_SOURCES})
183 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
185 add_library(libgromacs ${LIBGROMACS_SOURCES})
187 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:common>)
188 # As long as the libgromacs target has source files that reference headers from
189 # modules that don't provide CMake targets, libgromacs needs to use `src/`
190 # amongst its include directories (to support `#include "gromacs/module/header.h"`).
191 add_library(legacy_modules INTERFACE)
192 target_include_directories(legacy_modules INTERFACE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
193 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:legacy_modules>)
195 # Add these contents first because linking their tests can take a lot
196 # of time, so we want lots of parallel work still available after
198 add_subdirectory(fileio)
199 add_subdirectory(selection)
201 # Suppress a warning about our abuse of t_inputrec
202 gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
204 # Handle the object libraries that contain the source file
205 # dependencies that need special handling because they are generated
207 foreach(object_library ${libgromacs_object_library_dependencies})
208 if (BUILD_SHARED_LIBS)
209 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
211 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
212 target_link_libraries(${object_library} PRIVATE common)
214 # Add the sources from the object libraries to the main library.
215 target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
217 gmx_target_compile_options(libgromacs)
218 target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
219 target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
222 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
223 mark_as_advanced(GMX_EXTERNAL_CLFFT)
225 # Default to using clFFT found on the system
226 # switch to quiet at the second run.
227 if (DEFINED clFFT_LIBRARY)
228 set (clFFT_FIND_QUIETLY TRUE)
232 if (GMX_EXTERNAL_CLFFT)
233 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
238 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
239 requires clFFT, which was not found on your system. GROMACS does bundle
240 clFFT to help with building for OpenCL, but that clFFT has not yet been
241 ported to the more recent versions of that compiler that GROMACS itself
242 requires. Thus for now, OpenCL is not available with MSVC and the internal
243 build of clFFT in GROMACS 2019. Either change compiler, try installing
244 a clFFT package, or use the latest GROMACS 2018 point release.")
247 # Fall back on the internal version
248 set (_clFFT_dir ../external/clFFT/src)
249 add_subdirectory(${_clFFT_dir} clFFT-build)
250 target_sources(libgromacs PRIVATE
251 $<TARGET_OBJECTS:clFFT>
253 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
254 # Use the magic variable for how to link any library needed for
255 # dlopen, etc. which is -ldl where needed, and empty otherwise
256 # (e.g. Windows, BSD, Mac).
257 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
259 target_link_libraries(libgromacs PRIVATE clFFT)
263 # Permit GROMACS code to include externally developed headers, such as
264 # the functionality from the nonstd project that we use for
265 # gmx::compat::optional. These are included as system headers so that
266 # no warnings are issued from them.
268 # TODO Perhaps generalize this for all headers from src/external
269 target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
271 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
272 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
273 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
274 # with the SIMD_AVX_512_CXX_FLAGS flags.
275 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
278 # Do any special handling needed for .cpp files that use
279 # CUDA runtime headers
280 if (GMX_GPU_CUDA AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
281 # CUDA header cuda_runtime_api.h in at least CUDA 10.1 uses 0
282 # where nullptr would be preferable. GROMACS can't fix these, so
283 # must suppress them.
284 GMX_TEST_CXXFLAG(CXXFLAGS_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
286 foreach(_compile_flag ${NVCC_CLANG_SUPPRESSIONS_CXXFLAGS})
287 set(GMX_CUDA_CLANG_FLAGS "${GMX_CUDA_CLANG_FLAGS} ${_compile_flag}")
290 foreach (_file ${LIBGROMACS_SOURCES})
291 get_filename_component(_ext ${_file} EXT)
292 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
293 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
294 gmx_compile_cuda_file_with_clang(${_file})
298 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
299 set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS ${GMX_CUDA_CLANG_FLAGS})
303 # Only add the -fsycl flag to sources that really need it
305 get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
306 set_source_files_properties(${SYCL_SOURCES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
309 gmx_setup_tng_for_libgromacs()
311 # We apply the SYCL flag explicitly just for libgromacs, since bugs in the beta versions of
312 # icpx/dpcpp leads to crashes if we try to link an library without any SYCL code with the
313 # -fsycl flag enabled. Once that bug is fixed, we should change it to simply add
314 # SYCL_CXX_FLAGS to GMX_SHARED_LINKER_FLAGS.
315 target_link_libraries(libgromacs
318 ${GMX_EXTRA_LIBRARIES}
319 ${GMX_COMMON_LIBRARIES}
320 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
321 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
324 $<$<PLATFORM_ID:SunOS>:socket>
326 ${GMX_PUBLIC_LIBRARIES}
328 target_link_libraries(libgromacs PUBLIC legacy_api)
329 # Dependencies from libgromacs to the modules are set up here, but
330 # once the add_subdirectory() commands are re-ordered then
331 # responsibility for setting this up will move to the respective
333 target_link_libraries(libgromacs PRIVATE
334 $<BUILD_INTERFACE:analysisdata>
335 $<BUILD_INTERFACE:applied_forces>
336 $<BUILD_INTERFACE:commandline>
337 $<BUILD_INTERFACE:compat>
338 $<BUILD_INTERFACE:coordinateio>
339 $<BUILD_INTERFACE:correlationfunctions>
340 $<BUILD_INTERFACE:domdec>
341 # $<BUILD_INTERFACE:energyanalysis>
342 $<BUILD_INTERFACE:essentialdynamics>
343 $<BUILD_INTERFACE:ewald>
344 $<BUILD_INTERFACE:fft>
345 $<BUILD_INTERFACE:fileio>
346 $<BUILD_INTERFACE:gmxana>
347 $<BUILD_INTERFACE:gmxlib>
348 $<BUILD_INTERFACE:gmxpreprocess>
349 $<BUILD_INTERFACE:gpu_utils>
350 $<BUILD_INTERFACE:hardware>
351 $<BUILD_INTERFACE:imd>
352 $<BUILD_INTERFACE:linearalgebra>
353 $<BUILD_INTERFACE:listed_forces>
354 $<BUILD_INTERFACE:math>
355 $<BUILD_INTERFACE:mdlib>
356 $<BUILD_INTERFACE:mdrun>
357 $<BUILD_INTERFACE:mdrunutility>
358 $<BUILD_INTERFACE:mdspan>
359 $<BUILD_INTERFACE:mdtypes>
360 $<BUILD_INTERFACE:mimic>
361 $<BUILD_INTERFACE:modularsimulator>
362 $<BUILD_INTERFACE:nbnxm>
363 $<BUILD_INTERFACE:onlinehelp>
364 $<BUILD_INTERFACE:options>
365 $<BUILD_INTERFACE:pbcutil>
366 $<BUILD_INTERFACE:pulling>
367 $<BUILD_INTERFACE:random>
368 $<BUILD_INTERFACE:restraint>
369 $<BUILD_INTERFACE:selection>
370 $<BUILD_INTERFACE:simd>
371 $<BUILD_INTERFACE:statistics>
372 $<BUILD_INTERFACE:swap>
373 $<BUILD_INTERFACE:tables>
374 $<BUILD_INTERFACE:taskassignment>
375 $<BUILD_INTERFACE:timing>
376 $<BUILD_INTERFACE:tools>
377 $<BUILD_INTERFACE:topology>
378 $<BUILD_INTERFACE:trajectory>
379 $<BUILD_INTERFACE:trajectoryanalysis>
380 $<BUILD_INTERFACE:utility>
383 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
385 set_target_properties(libgromacs PROPERTIES
386 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
387 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
388 VERSION ${LIBRARY_VERSION}
392 target_link_libraries(libgromacs PRIVATE lmfit)
394 # Make sure we fix "everything" found by more recent versions of clang.
395 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "7")
396 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
398 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
399 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
400 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
401 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
402 /wd6001 #unitialized memory
403 /wd6011 #derefencing NULL
404 /wd6053 #prior call not zero-terminate
405 /wd6054 #might not be zero-terminated
406 /wd6385 #reading invalid data
407 /wd6386 #buffer overrun
408 /wd6387 #could be '0'
409 /wd28199 #uninitialized memory
410 # For compile time constant (e.g. templates) the following warnings have flase postives
411 /wd6239 #(<non-zero> && <expr>)
412 /wd6240 #(<expr> && <non-zero>)
413 /wd6294 #Ill-defined for-loop
414 /wd6326 #comparison of constant with other constant
415 /wd28020 #expression involving paramter is not true
417 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
418 /wd6993 #OpenMP ignored
420 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
421 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
422 /wd6246 #hides declaration
428 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
429 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
432 # clang-3.6 warns about a number of issues that are not reported by more modern compilers
433 # and we know they are not real issues. So we only check that it can compile without error
434 # but ignore all warnings.
435 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
436 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
439 # TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
440 if (BUILD_SHARED_LIBS)
441 install(TARGETS libgromacs
444 DESTINATION ${CMAKE_INSTALL_LIBDIR}
447 DESTINATION ${CMAKE_INSTALL_BINDIR}
450 DESTINATION ${CMAKE_INSTALL_LIBDIR}
452 INCLUDES DESTINATION include)
453 target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
454 # legacy headers use c++17 features, so consumer codes need to use that standard, too
455 if(GMX_INSTALL_LEGACY_API)
456 target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
459 add_library(Gromacs::libgromacs ALIAS libgromacs)
461 include(InstallLibInfo.cmake)
463 # Technically, the user could want to do this for an OpenCL build
464 # using the CUDA runtime, but currently there's no reason to want to
466 if (INSTALL_CUDART_LIB) #can be set manual by user
468 foreach(CUDA_LIB ${CUDA_LIBRARIES})
469 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
470 if(IS_CUDART) #libcuda should not be installed
471 #install also name-links (linker uses those)
472 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
473 install(FILES ${CUDA_LIBS} DESTINATION
474 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
478 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
483 # Install the utility headers
484 file(GLOB OPENCL_INSTALLED_FILES
485 gpu_utils/vectype_ops.clh
486 gpu_utils/device_utils.clh
488 install(FILES ${OPENCL_INSTALLED_FILES}
489 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
491 file(GLOB OPENCL_INSTALLED_FILES
494 install(FILES ${OPENCL_INSTALLED_FILES}
495 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
498 # Install the NBNXM source and headers
499 file(GLOB OPENCL_INSTALLED_FILES
502 install(FILES ${OPENCL_INSTALLED_FILES}
503 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
505 file(GLOB OPENCL_INSTALLED_FILES
506 nbnxm/opencl/nbnxm_ocl_kernels.cl
507 nbnxm/opencl/nbnxm_ocl_kernel.clh
508 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
509 nbnxm/opencl/nbnxm_ocl_kernels.clh
510 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
511 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
512 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
513 nbnxm/opencl/nbnxm_ocl_consts.h
515 install(FILES ${OPENCL_INSTALLED_FILES}
516 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
519 # Install the PME source and headers
520 file(GLOB OPENCL_INSTALLED_FILES
524 ewald/pme_gpu_calculate_splines.clh
526 ewald/pme_gpu_types.h
528 install(FILES ${OPENCL_INSTALLED_FILES}
529 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald