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 # Note that this subset should match the subset of module
112 # BUILD_INTERFACEs added to libgromacs below.
113 if (NOT GMX_BUILD_MDRUN_ONLY)
114 add_subdirectory(gmxana)
115 add_subdirectory(gmxpreprocess)
116 add_subdirectory(correlationfunctions)
117 add_subdirectory(statistics)
118 add_subdirectory(analysisdata)
119 add_subdirectory(coordinateio)
120 add_subdirectory(trajectoryanalysis)
121 add_subdirectory(energyanalysis)
122 add_subdirectory(tools)
125 get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
126 list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
128 # This would be the standard way to include thread_mpi, but
129 # we want libgromacs to link the functions directly
131 # add_subdirectory(thread_mpi)
133 #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
134 tmpi_get_source_list(THREAD_MPI_SOURCES ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/src)
135 add_library(thread_mpi OBJECT ${THREAD_MPI_SOURCES})
136 target_compile_definitions(thread_mpi PRIVATE HAVE_CONFIG_H)
138 # Needs POSIX-isms for strdup, not just std-isms
139 target_compile_definitions(thread_mpi PRIVATE _POSIX_C_SOURCE=200809L)
141 gmx_target_compile_options(thread_mpi)
143 gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
145 list(APPEND libgromacs_object_library_dependencies thread_mpi)
147 if(GMX_INSTALL_LEGACY_API)
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 ${GENERATED_VERSION_FILE})
172 # Mark some shared GPU implementation files to compile with CUDA if needed
174 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
175 set_source_files_properties(${CUDA_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
179 # Work around FindCUDA that prevents using target_link_libraries()
180 # with keywords otherwise...
181 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
182 if (NOT GMX_CLANG_CUDA)
183 gmx_cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
185 add_library(libgromacs ${LIBGROMACS_SOURCES})
187 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
189 add_library(libgromacs ${LIBGROMACS_SOURCES})
191 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:common>)
192 # As long as the libgromacs target has source files that reference headers from
193 # modules that don't provide CMake targets, libgromacs needs to use `src/`
194 # amongst its include directories (to support `#include "gromacs/module/header.h"`).
195 add_library(legacy_modules INTERFACE)
196 target_include_directories(legacy_modules INTERFACE $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/src>)
197 target_link_libraries(libgromacs PRIVATE $<BUILD_INTERFACE:legacy_modules>)
199 # Add these contents first because linking their tests can take a lot
200 # of time, so we want lots of parallel work still available after
202 add_subdirectory(fileio)
203 add_subdirectory(selection)
205 # Suppress a warning about our abuse of t_inputrec
206 gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
208 # Handle the object libraries that contain the source file
209 # dependencies that need special handling because they are generated
211 foreach(object_library ${libgromacs_object_library_dependencies})
212 if (BUILD_SHARED_LIBS)
213 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
215 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
216 target_link_libraries(${object_library} PRIVATE common)
218 # Add the sources from the object libraries to the main library.
219 target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
221 gmx_target_compile_options(libgromacs)
222 target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
223 target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
226 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
227 mark_as_advanced(GMX_EXTERNAL_CLFFT)
229 # Default to using clFFT found on the system
230 # switch to quiet at the second run.
231 if (DEFINED clFFT_LIBRARY)
232 set (clFFT_FIND_QUIETLY TRUE)
236 if (GMX_EXTERNAL_CLFFT)
237 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
242 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
243 requires clFFT, which was not found on your system. GROMACS does bundle
244 clFFT to help with building for OpenCL, but that clFFT has not yet been
245 ported to the more recent versions of that compiler that GROMACS itself
246 requires. Thus for now, OpenCL is not available with MSVC and the internal
247 build of clFFT in GROMACS 2019. Either change compiler, try installing
248 a clFFT package, or use the latest GROMACS 2018 point release.")
251 # Fall back on the internal version
252 set (_clFFT_dir ../external/clFFT/src)
253 add_subdirectory(${_clFFT_dir} clFFT-build)
254 target_sources(libgromacs PRIVATE
255 $<TARGET_OBJECTS:clFFT>
257 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
258 # Use the magic variable for how to link any library needed for
259 # dlopen, etc. which is -ldl where needed, and empty otherwise
260 # (e.g. Windows, BSD, Mac).
261 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
263 target_link_libraries(libgromacs PRIVATE clFFT)
267 # Permit GROMACS code to include externally developed headers, such as
268 # the functionality from the nonstd project that we use for
269 # gmx::compat::optional. These are included as system headers so that
270 # no warnings are issued from them.
272 # TODO Perhaps generalize this for all headers from src/external
273 target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
275 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
276 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
277 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
278 # with the SIMD_AVX_512_CXX_FLAGS flags.
279 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
282 # Do any special handling needed for .cpp files that use
283 # CUDA runtime headers
284 if (GMX_GPU_CUDA AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
285 # CUDA header cuda_runtime_api.h in at least CUDA 10.1 uses 0
286 # where nullptr would be preferable. GROMACS can't fix these, so
287 # must suppress them.
288 GMX_TEST_CXXFLAG(CXXFLAGS_NO_ZERO_AS_NULL_POINTER_CONSTANT "-Wno-zero-as-null-pointer-constant" NVCC_CLANG_SUPPRESSIONS_CXXFLAGS)
290 foreach(_compile_flag ${NVCC_CLANG_SUPPRESSIONS_CXXFLAGS})
291 set(GMX_CUDA_CLANG_FLAGS "${GMX_CUDA_CLANG_FLAGS} ${_compile_flag}")
294 foreach (_file ${LIBGROMACS_SOURCES})
295 get_filename_component(_ext ${_file} EXT)
296 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
297 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
298 gmx_compile_cuda_file_with_clang(${_file})
302 get_property(CUDA_SOURCES GLOBAL PROPERTY CUDA_SOURCES)
303 set_source_files_properties(${CUDA_SOURCES} PROPERTIES COMPILE_FLAGS ${GMX_CUDA_CLANG_FLAGS})
307 # Only add the -fsycl flag to sources that really need it
309 get_property(SYCL_SOURCES GLOBAL PROPERTY SYCL_SOURCES)
310 set_source_files_properties(${SYCL_SOURCES} PROPERTIES COMPILE_FLAGS "${SYCL_CXX_FLAGS}")
313 gmx_setup_tng_for_libgromacs()
315 # We apply the SYCL flag explicitly just for libgromacs, since bugs in the beta versions of
316 # icpx/dpcpp leads to crashes if we try to link an library without any SYCL code with the
317 # -fsycl flag enabled. Once that bug is fixed, we should change it to simply add
318 # SYCL_CXX_FLAGS to GMX_SHARED_LINKER_FLAGS.
319 target_link_libraries(libgromacs
322 ${GMX_EXTRA_LIBRARIES}
323 ${GMX_COMMON_LIBRARIES}
324 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
325 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
328 $<$<PLATFORM_ID:SunOS>:socket>
330 ${GMX_PUBLIC_LIBRARIES}
332 target_link_libraries(libgromacs PUBLIC legacy_api)
333 # Dependencies from libgromacs to the modules are set up here, but
334 # once the add_subdirectory() commands are re-ordered then
335 # responsibility for setting this up will move to the respective
337 target_link_libraries(libgromacs PRIVATE
338 $<BUILD_INTERFACE:applied_forces>
339 $<BUILD_INTERFACE:commandline>
340 $<BUILD_INTERFACE:compat>
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:gmxlib>
348 $<BUILD_INTERFACE:gpu_utils>
349 $<BUILD_INTERFACE:hardware>
350 $<BUILD_INTERFACE:imd>
351 $<BUILD_INTERFACE:linearalgebra>
352 $<BUILD_INTERFACE:listed_forces>
353 $<BUILD_INTERFACE:math>
354 $<BUILD_INTERFACE:mdlib>
355 $<BUILD_INTERFACE:mdrun>
356 $<BUILD_INTERFACE:mdrunutility>
357 $<BUILD_INTERFACE:mdspan>
358 $<BUILD_INTERFACE:mdtypes>
359 $<BUILD_INTERFACE:mimic>
360 $<BUILD_INTERFACE:modularsimulator>
361 $<BUILD_INTERFACE:nbnxm>
362 $<BUILD_INTERFACE:onlinehelp>
363 $<BUILD_INTERFACE:options>
364 $<BUILD_INTERFACE:pbcutil>
365 $<BUILD_INTERFACE:pulling>
366 $<BUILD_INTERFACE:random>
367 $<BUILD_INTERFACE:restraint>
368 $<BUILD_INTERFACE:selection>
369 $<BUILD_INTERFACE:simd>
370 $<BUILD_INTERFACE:swap>
371 $<BUILD_INTERFACE:tables>
372 $<BUILD_INTERFACE:taskassignment>
373 $<BUILD_INTERFACE:timing>
374 $<BUILD_INTERFACE:topology>
375 $<BUILD_INTERFACE:trajectory>
376 $<BUILD_INTERFACE:utility>
378 # Note that this subset should match the subset of module
379 # subdirectories added above.
380 if (NOT GMX_BUILD_MDRUN_ONLY)
381 target_link_libraries(libgromacs PRIVATE
382 $<BUILD_INTERFACE:analysisdata>
383 $<BUILD_INTERFACE:coordinateio>
384 $<BUILD_INTERFACE:correlationfunctions>
385 $<BUILD_INTERFACE:gmxana>
386 $<BUILD_INTERFACE:gmxpreprocess>
387 $<BUILD_INTERFACE:statistics>
388 $<BUILD_INTERFACE:tools>
389 $<BUILD_INTERFACE:trajectoryanalysis>
393 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
395 set_target_properties(libgromacs PROPERTIES
396 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
397 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
398 VERSION ${LIBRARY_VERSION}
402 target_link_libraries(libgromacs PRIVATE lmfit)
404 # Make sure we fix "everything" found by more recent versions of clang.
405 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "7")
406 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
408 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
409 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
410 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
411 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
412 /wd6001 #unitialized memory
413 /wd6011 #derefencing NULL
414 /wd6053 #prior call not zero-terminate
415 /wd6054 #might not be zero-terminated
416 /wd6385 #reading invalid data
417 /wd6386 #buffer overrun
418 /wd6387 #could be '0'
419 /wd28199 #uninitialized memory
420 # For compile time constant (e.g. templates) the following warnings have flase postives
421 /wd6239 #(<non-zero> && <expr>)
422 /wd6240 #(<expr> && <non-zero>)
423 /wd6294 #Ill-defined for-loop
424 /wd6326 #comparison of constant with other constant
425 /wd28020 #expression involving paramter is not true
427 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
428 /wd6993 #OpenMP ignored
430 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
431 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
432 /wd6246 #hides declaration
438 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
439 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
442 # clang-3.6 warns about a number of issues that are not reported by more modern compilers
443 # and we know they are not real issues. So we only check that it can compile without error
444 # but ignore all warnings.
445 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
446 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
449 # Only install the library in mdrun-only mode if it is actually necessary
451 # TODO: Stop installing libgromacs. Possibly allow installation during deprecation period with GMX_INSTALL_LEGACY_API.
452 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
453 install(TARGETS libgromacs
456 DESTINATION ${CMAKE_INSTALL_LIBDIR}
459 DESTINATION ${CMAKE_INSTALL_BINDIR}
462 DESTINATION ${CMAKE_INSTALL_LIBDIR}
464 INCLUDES DESTINATION include)
465 target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
466 # legacy headers use c++17 features, so consumer codes need to use that standard, too
467 if(GMX_INSTALL_LEGACY_API)
468 target_compile_features(libgromacs INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
471 add_library(Gromacs::libgromacs ALIAS libgromacs)
473 if (NOT GMX_BUILD_MDRUN_ONLY)
474 include(InstallLibInfo.cmake)
477 # Technically, the user could want to do this for an OpenCL build
478 # using the CUDA runtime, but currently there's no reason to want to
480 if (INSTALL_CUDART_LIB) #can be set manual by user
482 foreach(CUDA_LIB ${CUDA_LIBRARIES})
483 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
484 if(IS_CUDART) #libcuda should not be installed
485 #install also name-links (linker uses those)
486 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
487 install(FILES ${CUDA_LIBS} DESTINATION
488 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
492 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
497 # Install the utility headers
498 file(GLOB OPENCL_INSTALLED_FILES
499 gpu_utils/vectype_ops.clh
500 gpu_utils/device_utils.clh
502 install(FILES ${OPENCL_INSTALLED_FILES}
503 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
505 file(GLOB OPENCL_INSTALLED_FILES
508 install(FILES ${OPENCL_INSTALLED_FILES}
509 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
512 # Install the NBNXM source and headers
513 file(GLOB OPENCL_INSTALLED_FILES
516 install(FILES ${OPENCL_INSTALLED_FILES}
517 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
519 file(GLOB OPENCL_INSTALLED_FILES
520 nbnxm/opencl/nbnxm_ocl_kernels.cl
521 nbnxm/opencl/nbnxm_ocl_kernel.clh
522 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
523 nbnxm/opencl/nbnxm_ocl_kernels.clh
524 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
525 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
526 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
527 nbnxm/opencl/nbnxm_ocl_consts.h
529 install(FILES ${OPENCL_INSTALLED_FILES}
530 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
533 # Install the PME source and headers
534 file(GLOB OPENCL_INSTALLED_FILES
538 ewald/pme_gpu_calculate_splines.clh
540 ewald/pme_gpu_types.h
542 install(FILES ${OPENCL_INSTALLED_FILES}
543 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald