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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 (GMX_SYCL_HIPSYCL)
190 target_link_libraries(libgromacs PUBLIC roc::rocfft)
193 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:common>)
194 # As long as the libgromacs target has source files that reference headers from
195 # modules that don't provide CMake targets, libgromacs needs to use `src/`
196 # amongst its include directories (to support `#include "gromacs/module/header.h"`).
197 add_library(legacy_modules INTERFACE)
198 target_include_directories(legacy_modules INTERFACE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
199 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:legacy_modules>)
201 # Add these contents first because linking their tests can take a lot
202 # of time, so we want lots of parallel work still available after
204 add_subdirectory(fileio)
205 add_subdirectory(selection)
207 # Suppress a warning about our abuse of t_inputrec
208 gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
210 # Handle the object libraries that contain the source file
211 # dependencies that need special handling because they are generated
213 foreach(object_library ${libgromacs_object_library_dependencies})
214 if (BUILD_SHARED_LIBS)
215 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
217 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
218 target_link_libraries(${object_library} PRIVATE common)
220 # Add the sources from the object libraries to the main library.
221 target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
223 gmx_target_compile_options(libgromacs)
224 target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
225 target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
228 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
229 mark_as_advanced(GMX_EXTERNAL_CLFFT)
231 # Default to using clFFT found on the system
232 # switch to quiet at the second run.
233 if (DEFINED clFFT_LIBRARY)
234 set (clFFT_FIND_QUIETLY TRUE)
238 if (GMX_EXTERNAL_CLFFT)
239 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
244 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
245 requires clFFT, which was not found on your system. GROMACS does bundle
246 clFFT to help with building for OpenCL, but that clFFT has not yet been
247 ported to the more recent versions of that compiler that GROMACS itself
248 requires. Thus for now, OpenCL is not available with MSVC and the internal
249 build of clFFT in GROMACS 2019. Either change compiler, try installing
250 a clFFT package, or use the latest GROMACS 2018 point release.")
253 # Fall back on the internal version
254 set (_clFFT_dir ../external/clFFT/src)
255 add_subdirectory(${_clFFT_dir} clFFT-build)
256 target_sources(libgromacs PRIVATE
257 $<TARGET_OBJECTS:clFFT>
259 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
260 # Use the magic variable for how to link any library needed for
261 # dlopen, etc. which is -ldl where needed, and empty otherwise
262 # (e.g. Windows, BSD, Mac).
263 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
265 target_link_libraries(libgromacs PRIVATE clFFT)
269 # Permit GROMACS code to include externally developed headers, such as
270 # the functionality from the nonstd project that we use for
271 # gmx::compat::optional. These are included as system headers so that
272 # no warnings are issued from them.
274 # TODO Perhaps generalize this for all headers from src/external
275 target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
277 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
278 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
279 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
280 # with the SIMD_AVX_512_CXX_FLAGS flags.
281 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
284 # Do any special handling needed for .cpp files that use
285 # CUDA runtime headers
286 if (GMX_GPU_CUDA AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
287 foreach(_compile_flag ${NVCC_CLANG_SUPPRESSIONS_CXXFLAGS})
288 set(GMX_CUDA_CLANG_FLAGS "${GMX_CUDA_CLANG_FLAGS} ${_compile_flag}")
291 foreach (_file ${LIBGROMACS_SOURCES})
292 get_filename_component(_ext ${_file} EXT)
293 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
294 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
295 gmx_compile_cuda_file_with_clang(${_file})
299 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
300 set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS ${GMX_CUDA_CLANG_FLAGS})
304 # Only add the -fsycl flag to sources that really need it
306 get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
307 add_sycl_to_target(TARGET libgromacs SOURCES ${SYCL_SOURCES})
310 gmx_setup_tng_for_libgromacs()
312 # We apply the SYCL flag explicitly just for libgromacs, since bugs in the beta versions of
313 # icpx/dpcpp leads to crashes if we try to link an library without any SYCL code with the
314 # -fsycl flag enabled. Once that bug is fixed, we should change it to simply add
315 # SYCL_CXX_FLAGS to GMX_SHARED_LINKER_FLAGS.
316 target_link_libraries(libgromacs
319 ${GMX_EXTRA_LIBRARIES}
320 ${GMX_COMMON_LIBRARIES}
321 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
322 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
325 $<$<PLATFORM_ID:SunOS>:socket>
327 ${GMX_PUBLIC_LIBRARIES}
329 target_link_libraries(libgromacs PUBLIC legacy_api)
330 # Dependencies from libgromacs to the modules are set up here, but
331 # once the add_subdirectory() commands are re-ordered then
332 # responsibility for setting this up will move to the respective
334 target_link_libraries(libgromacs PRIVATE
335 $<BUILD_INTERFACE:analysisdata>
336 $<BUILD_INTERFACE:applied_forces>
337 $<BUILD_INTERFACE:commandline>
338 $<BUILD_INTERFACE:compat>
339 $<BUILD_INTERFACE:coordinateio>
340 $<BUILD_INTERFACE:correlationfunctions>
341 $<BUILD_INTERFACE:domdec>
342 # $<BUILD_INTERFACE:energyanalysis>
343 $<BUILD_INTERFACE:essentialdynamics>
344 $<BUILD_INTERFACE:ewald>
345 $<BUILD_INTERFACE:fft>
346 $<BUILD_INTERFACE:fileio>
347 $<BUILD_INTERFACE:gmxana>
348 $<BUILD_INTERFACE:gmxlib>
349 $<BUILD_INTERFACE:gmxpreprocess>
350 $<BUILD_INTERFACE:gpu_utils>
351 $<BUILD_INTERFACE:hardware>
352 $<BUILD_INTERFACE:imd>
353 $<BUILD_INTERFACE:linearalgebra>
354 $<BUILD_INTERFACE:listed_forces>
355 $<BUILD_INTERFACE:math>
356 $<BUILD_INTERFACE:mdlib>
357 $<BUILD_INTERFACE:mdrun>
358 $<BUILD_INTERFACE:mdrunutility>
359 $<BUILD_INTERFACE:mdspan>
360 $<BUILD_INTERFACE:mdtypes>
361 $<BUILD_INTERFACE:mimic>
362 $<BUILD_INTERFACE:modularsimulator>
363 $<BUILD_INTERFACE:nbnxm>
364 $<BUILD_INTERFACE:onlinehelp>
365 $<BUILD_INTERFACE:options>
366 $<BUILD_INTERFACE:pbcutil>
367 $<BUILD_INTERFACE:pulling>
368 $<BUILD_INTERFACE:random>
369 $<BUILD_INTERFACE:restraint>
370 $<BUILD_INTERFACE:selection>
371 $<BUILD_INTERFACE:simd>
372 $<BUILD_INTERFACE:statistics>
373 $<BUILD_INTERFACE:swap>
374 $<BUILD_INTERFACE:tables>
375 $<BUILD_INTERFACE:taskassignment>
376 $<BUILD_INTERFACE:timing>
377 $<BUILD_INTERFACE:tools>
378 $<BUILD_INTERFACE:topology>
379 $<BUILD_INTERFACE:trajectory>
380 $<BUILD_INTERFACE:trajectoryanalysis>
381 $<BUILD_INTERFACE:utility>
384 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
386 set_target_properties(libgromacs PROPERTIES
387 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
388 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
389 VERSION ${LIBRARY_VERSION}
393 target_link_libraries(libgromacs PRIVATE lmfit)
395 # Make sure we fix "everything" found by compilers that support that
396 gmx_warn_on_everything(libgromacs)
397 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
398 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
399 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
400 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
401 /wd6001 #unitialized memory
402 /wd6011 #derefencing NULL
403 /wd6053 #prior call not zero-terminate
404 /wd6054 #might not be zero-terminated
405 /wd6385 #reading invalid data
406 /wd6386 #buffer overrun
407 /wd6387 #could be '0'
408 /wd28199 #uninitialized memory
409 # For compile time constant (e.g. templates) the following warnings have flase postives
410 /wd6239 #(<non-zero> && <expr>)
411 /wd6240 #(<expr> && <non-zero>)
412 /wd6294 #Ill-defined for-loop
413 /wd6326 #comparison of constant with other constant
414 /wd28020 #expression involving paramter is not true
416 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
417 /wd6993 #OpenMP ignored
419 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
420 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
421 /wd6246 #hides declaration
427 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
428 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
431 # clang-3.6 warns about a number of issues that are not reported by more modern compilers
432 # and we know they are not real issues. So we only check that it can compile without error
433 # but ignore all warnings.
434 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
435 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
438 # TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
439 if (BUILD_SHARED_LIBS)
440 install(TARGETS libgromacs
443 DESTINATION ${CMAKE_INSTALL_LIBDIR}
446 DESTINATION ${CMAKE_INSTALL_BINDIR}
449 DESTINATION ${CMAKE_INSTALL_LIBDIR}
451 INCLUDES DESTINATION include)
452 target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
453 # legacy headers use c++17 features, so consumer codes need to use that standard, too
454 if(GMX_INSTALL_LEGACY_API)
455 target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
458 add_library(Gromacs::libgromacs ALIAS libgromacs)
460 include(InstallLibInfo.cmake)
462 # Technically, the user could want to do this for an OpenCL build
463 # using the CUDA runtime, but currently there's no reason to want to
465 if (INSTALL_CUDART_LIB) #can be set manual by user
467 foreach(CUDA_LIB ${CUDA_LIBRARIES})
468 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
469 if(IS_CUDART) #libcuda should not be installed
470 #install also name-links (linker uses those)
471 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
472 install(FILES ${CUDA_LIBS} DESTINATION
473 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
477 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
482 # Install the utility headers
483 file(GLOB OPENCL_INSTALLED_FILES
484 gpu_utils/vectype_ops.clh
485 gpu_utils/device_utils.clh
487 install(FILES ${OPENCL_INSTALLED_FILES}
488 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
490 file(GLOB OPENCL_INSTALLED_FILES
493 install(FILES ${OPENCL_INSTALLED_FILES}
494 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
497 # Install the NBNXM source and headers
498 file(GLOB OPENCL_INSTALLED_FILES
501 install(FILES ${OPENCL_INSTALLED_FILES}
502 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
504 file(GLOB OPENCL_INSTALLED_FILES
505 nbnxm/opencl/nbnxm_ocl_kernels.cl
506 nbnxm/opencl/nbnxm_ocl_kernel.clh
507 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
508 nbnxm/opencl/nbnxm_ocl_kernels.clh
509 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
510 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
511 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
512 nbnxm/opencl/nbnxm_ocl_consts.h
514 install(FILES ${OPENCL_INSTALLED_FILES}
515 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
518 # Install the PME source and headers
519 file(GLOB OPENCL_INSTALLED_FILES
523 ewald/pme_gpu_calculate_splines.clh
525 ewald/pme_gpu_types.h
527 install(FILES ${OPENCL_INSTALLED_FILES}
528 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald