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37 set(LIBGROMACS_SOURCES)
40 include(gmxClangCudaUtils)
43 set_property(GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
44 set_property(GLOBAL PROPERTY CUDA_SOURCES)
45 set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
46 set_property(GLOBAL PROPERTY GMX_AVX_512_SOURCE)
48 set(libgromacs_object_library_dependencies "")
49 function (_gmx_add_files_to_property PROPERTY)
50 foreach (_file ${ARGN})
51 if (IS_ABSOLUTE "${_file}")
52 set_property(GLOBAL APPEND PROPERTY ${PROPERTY} ${_file})
54 set_property(GLOBAL APPEND PROPERTY ${PROPERTY}
55 ${CMAKE_CURRENT_LIST_DIR}/${_file})
60 function (gmx_add_libgromacs_sources)
61 _gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
64 # Permit the configuration to disable compiling the many nbnxm kernels
65 # and others involved in force calculations. Currently only
66 # short-ranged and bonded kernels are disabled this way, but in future
67 # others may be appropriate. Thus the cmake option is not specific to
69 option(GMX_USE_SIMD_KERNELS "Whether to compile NBNXM and other SIMD kernels" ON)
70 mark_as_advanced(GMX_USE_SIMD_KERNELS)
72 # Add these contents first because linking their tests can take a lot
73 # of time, so we want lots of parallel work still available after
75 add_subdirectory(utility)
77 add_subdirectory(gmxlib)
78 add_subdirectory(mdlib)
79 add_subdirectory(applied_forces)
80 add_subdirectory(listed_forces)
81 add_subdirectory(nbnxm)
82 add_subdirectory(commandline)
83 add_subdirectory(domdec)
84 add_subdirectory(ewald)
86 add_subdirectory(gpu_utils)
87 add_subdirectory(hardware)
88 add_subdirectory(linearalgebra)
89 add_subdirectory(math)
90 add_subdirectory(mdrun)
91 add_subdirectory(mdrunutility)
92 add_subdirectory(mdspan)
93 add_subdirectory(mdtypes)
94 add_subdirectory(onlinehelp)
95 add_subdirectory(options)
96 add_subdirectory(pbcutil)
97 add_subdirectory(random)
98 add_subdirectory(restraint)
99 add_subdirectory(tables)
100 add_subdirectory(taskassignment)
101 add_subdirectory(timing)
102 add_subdirectory(topology)
103 add_subdirectory(trajectory)
104 add_subdirectory(swap)
105 add_subdirectory(essentialdynamics)
106 add_subdirectory(pulling)
107 add_subdirectory(simd)
108 add_subdirectory(imd)
109 add_subdirectory(compat)
110 add_subdirectory(mimic)
111 add_subdirectory(modularsimulator)
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)
122 get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
123 list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
125 # This would be the standard way to include thread_mpi, but
126 # we want libgromacs to link the functions directly
128 # add_subdirectory(thread_mpi)
130 #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
131 tmpi_get_source_list(THREAD_MPI_SOURCES ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/src)
132 add_library(thread_mpi OBJECT ${THREAD_MPI_SOURCES})
133 target_compile_definitions(thread_mpi PRIVATE HAVE_CONFIG_H)
135 # Needs POSIX-isms for strdup, not just std-isms
136 target_compile_definitions(thread_mpi PRIVATE _POSIX_C_SOURCE=200809L)
138 gmx_target_compile_options(thread_mpi)
140 gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
142 list(APPEND libgromacs_object_library_dependencies thread_mpi)
144 if(GMX_INSTALL_LEGACY_API)
150 DESTINATION include/gromacs)
153 # This code is here instead of utility/CMakeLists.txt, because CMake
154 # custom commands and source file properties can only be set in the directory
155 # that contains the target that uses them.
156 # TODO: Generate a header instead that can be included from baseversion.cpp.
157 # That probably simplifies things somewhat.
158 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
159 gmx_configure_version_file(
160 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
167 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
169 # Mark some shared GPU implementation files to compile with CUDA if needed
171 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
172 set_source_files_properties(${CUDA_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
176 # Work around FindCUDA that prevents using target_link_libraries()
177 # with keywords otherwise...
178 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
179 if (NOT GMX_CLANG_CUDA)
180 gmx_cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
182 add_library(libgromacs ${LIBGROMACS_SOURCES})
184 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
186 add_library(libgromacs ${LIBGROMACS_SOURCES})
189 if (TARGET Heffte::Heffte)
190 target_link_libraries(libgromacs PRIVATE Heffte::Heffte)
193 if (GMX_SYCL_HIPSYCL)
194 target_link_libraries(libgromacs PUBLIC roc::rocfft)
197 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:common>)
198 # As long as the libgromacs target has source files that reference headers from
199 # modules that don't provide CMake targets, libgromacs needs to use `src/`
200 # amongst its include directories (to support `#include "gromacs/module/header.h"`).
201 add_library(legacy_modules INTERFACE)
202 target_include_directories(legacy_modules INTERFACE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
203 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:legacy_modules>)
205 # Add these contents first because linking their tests can take a lot
206 # of time, so we want lots of parallel work still available after
208 add_subdirectory(fileio)
209 add_subdirectory(selection)
211 # Handle the object libraries that contain the source file
212 # dependencies that need special handling because they are generated
214 foreach(object_library ${libgromacs_object_library_dependencies})
215 if (BUILD_SHARED_LIBS)
216 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
218 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
219 target_link_libraries(${object_library} PRIVATE common)
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 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 add_sycl_to_target(TARGET libgromacs SOURCES ${SYCL_SOURCES})
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)
331 # Dependencies from libgromacs to the modules are set up here, but
332 # once the add_subdirectory() commands are re-ordered then
333 # responsibility for setting this up will move to the respective
335 target_link_libraries(libgromacs PRIVATE
336 $<BUILD_INTERFACE:analysisdata>
337 $<BUILD_INTERFACE:applied_forces>
338 $<BUILD_INTERFACE:commandline>
339 $<BUILD_INTERFACE:compat>
340 $<BUILD_INTERFACE:coordinateio>
341 $<BUILD_INTERFACE:correlationfunctions>
342 $<BUILD_INTERFACE:domdec>
343 # $<BUILD_INTERFACE:energyanalysis>
344 $<BUILD_INTERFACE:essentialdynamics>
345 $<BUILD_INTERFACE:ewald>
346 $<BUILD_INTERFACE:fft>
347 $<BUILD_INTERFACE:fileio>
348 $<BUILD_INTERFACE:gmxana>
349 $<BUILD_INTERFACE:gmxlib>
350 $<BUILD_INTERFACE:gmxpreprocess>
351 $<BUILD_INTERFACE:gpu_utils>
352 $<BUILD_INTERFACE:hardware>
353 $<BUILD_INTERFACE:imd>
354 $<BUILD_INTERFACE:linearalgebra>
355 $<BUILD_INTERFACE:listed_forces>
356 $<BUILD_INTERFACE:math>
357 $<BUILD_INTERFACE:mdlib>
358 $<BUILD_INTERFACE:mdrun>
359 $<BUILD_INTERFACE:mdrunutility>
360 $<BUILD_INTERFACE:mdspan>
361 $<BUILD_INTERFACE:mdtypes>
362 $<BUILD_INTERFACE:mimic>
363 $<BUILD_INTERFACE:modularsimulator>
364 $<BUILD_INTERFACE:nbnxm>
365 $<BUILD_INTERFACE:onlinehelp>
366 $<BUILD_INTERFACE:options>
367 $<BUILD_INTERFACE:pbcutil>
368 $<BUILD_INTERFACE:pulling>
369 $<BUILD_INTERFACE:random>
370 $<BUILD_INTERFACE:restraint>
371 $<BUILD_INTERFACE:selection>
372 $<BUILD_INTERFACE:simd>
373 $<BUILD_INTERFACE:statistics>
374 $<BUILD_INTERFACE:swap>
375 $<BUILD_INTERFACE:tables>
376 $<BUILD_INTERFACE:taskassignment>
377 $<BUILD_INTERFACE:timing>
378 $<BUILD_INTERFACE:tools>
379 $<BUILD_INTERFACE:topology>
380 $<BUILD_INTERFACE:trajectory>
381 $<BUILD_INTERFACE:trajectoryanalysis>
382 $<BUILD_INTERFACE:utility>
385 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
387 set_target_properties(libgromacs PROPERTIES
388 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
389 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
390 VERSION ${LIBRARY_VERSION}
394 target_link_libraries(libgromacs PRIVATE lmfit)
395 gmx_manage_muparser()
396 target_link_libraries(libgromacs PRIVATE muparser)
398 # Make sure we fix "everything" found by compilers that support that
399 gmx_warn_on_everything(libgromacs)
400 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
401 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
402 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
403 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
404 /wd6001 #unitialized memory
405 /wd6011 #derefencing NULL
406 /wd6053 #prior call not zero-terminate
407 /wd6054 #might not be zero-terminated
408 /wd6385 #reading invalid data
409 /wd6386 #buffer overrun
410 /wd6387 #could be '0'
411 /wd28199 #uninitialized memory
412 # For compile time constant (e.g. templates) the following warnings have flase postives
413 /wd6239 #(<non-zero> && <expr>)
414 /wd6240 #(<expr> && <non-zero>)
415 /wd6294 #Ill-defined for-loop
416 /wd6326 #comparison of constant with other constant
417 /wd28020 #expression involving paramter is not true
419 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
420 /wd6993 #OpenMP ignored
422 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
423 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
424 /wd6246 #hides declaration
430 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
431 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
434 # clang-3.6 warns about a number of issues that are not reported by more modern compilers
435 # and we know they are not real issues. So we only check that it can compile without error
436 # but ignore all warnings.
437 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
438 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
441 # TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
442 if (BUILD_SHARED_LIBS)
443 install(TARGETS libgromacs
446 DESTINATION ${CMAKE_INSTALL_LIBDIR}
449 DESTINATION ${CMAKE_INSTALL_BINDIR}
452 DESTINATION ${CMAKE_INSTALL_LIBDIR}
454 INCLUDES DESTINATION include)
455 target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
456 # legacy headers use c++17 features, so consumer codes need to use that standard, too
457 if(GMX_INSTALL_LEGACY_API)
458 target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
461 add_library(Gromacs::libgromacs ALIAS libgromacs)
463 include(InstallLibInfo.cmake)
465 # Technically, the user could want to do this for an OpenCL build
466 # using the CUDA runtime, but currently there's no reason to want to
468 if (INSTALL_CUDART_LIB) #can be set manual by user
470 foreach(CUDA_LIB ${CUDA_LIBRARIES})
471 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
472 if(IS_CUDART) #libcuda should not be installed
473 #install also name-links (linker uses those)
474 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
475 install(FILES ${CUDA_LIBS} DESTINATION
476 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
480 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
485 # Install the utility headers
486 file(GLOB OPENCL_INSTALLED_FILES
487 gpu_utils/vectype_ops.clh
488 gpu_utils/device_utils.clh
490 install(FILES ${OPENCL_INSTALLED_FILES}
491 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
493 file(GLOB OPENCL_INSTALLED_FILES
496 install(FILES ${OPENCL_INSTALLED_FILES}
497 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
500 # Install the NBNXM source and headers
501 file(GLOB OPENCL_INSTALLED_FILES
504 install(FILES ${OPENCL_INSTALLED_FILES}
505 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
507 file(GLOB OPENCL_INSTALLED_FILES
508 nbnxm/opencl/nbnxm_ocl_kernels.cl
509 nbnxm/opencl/nbnxm_ocl_kernel.clh
510 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
511 nbnxm/opencl/nbnxm_ocl_kernels.clh
512 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
513 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
514 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
515 nbnxm/opencl/nbnxm_ocl_consts.h
517 install(FILES ${OPENCL_INSTALLED_FILES}
518 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
521 # Install the PME source and headers
522 file(GLOB OPENCL_INSTALLED_FILES
526 ewald/pme_gpu_calculate_splines.clh
528 ewald/pme_gpu_types.h
530 install(FILES ${OPENCL_INSTALLED_FILES}
531 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald