2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2010,2011,2012,2013,2014 by the GROMACS development team.
5 # Copyright (c) 2015,2016,2017,2018,2019,2020, by the GROMACS development team, led by
6 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
7 # and including many others, as listed in the AUTHORS file in the
8 # top-level source directory and at http://www.gromacs.org.
10 # GROMACS is free software; you can redistribute it and/or
11 # modify it under the terms of the GNU Lesser General Public License
12 # as published by the Free Software Foundation; either version 2.1
13 # of the License, or (at your option) any later version.
15 # GROMACS is distributed in the hope that it will be useful,
16 # but WITHOUT ANY WARRANTY; without even the implied warranty of
17 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 # Lesser General Public License for more details.
20 # You should have received a copy of the GNU Lesser General Public
21 # License along with GROMACS; if not, see
22 # http://www.gnu.org/licenses, or write to the Free Software Foundation,
23 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
25 # If you want to redistribute modifications to GROMACS, please
26 # consider that scientific software is very special. Version
27 # control is crucial - bugs must be traceable. We will be happy to
28 # consider code for inclusion in the official distribution, but
29 # derived work must not be called official GROMACS. Details are found
30 # in the README & COPYING files - if they are missing, get the
31 # official version at http://www.gromacs.org.
33 # To help us fund GROMACS development, we humbly ask that you cite
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 # TODO Reconsider this, as the CUDA driver API is probably a simpler
64 # approach, at least for the build system. See Issue #2530
65 function (gmx_compile_cpp_as_cuda)
66 _gmx_add_files_to_property(GMX_LIBGROMACS_GPU_IMPL_SOURCES ${ARGN})
69 # Permit the configuration to disable compiling the many nbnxm kernels
70 # and others involved in force calculations. Currently only
71 # short-ranged and bonded kernels are disabled this way, but in future
72 # others may be appropriate. Thus the cmake option is not specific to
74 option(GMX_USE_SIMD_KERNELS "Whether to compile NBNXM and other SIMD kernels" ON)
75 mark_as_advanced(GMX_USE_SIMD_KERNELS)
77 # Add these contents first because linking their tests can take a lot
78 # of time, so we want lots of parallel work still available after
80 add_subdirectory(utility)
82 add_subdirectory(gmxlib)
83 add_subdirectory(mdlib)
84 add_subdirectory(applied_forces)
85 add_subdirectory(listed_forces)
86 add_subdirectory(nbnxm)
87 add_subdirectory(commandline)
88 add_subdirectory(domdec)
89 add_subdirectory(ewald)
91 add_subdirectory(gpu_utils)
92 add_subdirectory(hardware)
93 add_subdirectory(linearalgebra)
94 add_subdirectory(math)
95 add_subdirectory(mdrun)
96 add_subdirectory(mdrunutility)
97 add_subdirectory(mdspan)
98 add_subdirectory(mdtypes)
99 add_subdirectory(onlinehelp)
100 add_subdirectory(options)
101 add_subdirectory(pbcutil)
102 add_subdirectory(random)
103 add_subdirectory(restraint)
104 add_subdirectory(tables)
105 add_subdirectory(taskassignment)
106 add_subdirectory(timing)
107 add_subdirectory(topology)
108 add_subdirectory(trajectory)
109 add_subdirectory(swap)
110 add_subdirectory(essentialdynamics)
111 add_subdirectory(pulling)
112 add_subdirectory(awh)
113 add_subdirectory(simd)
114 add_subdirectory(imd)
115 add_subdirectory(compat)
116 add_subdirectory(mimic)
117 add_subdirectory(modularsimulator)
118 if (NOT GMX_BUILD_MDRUN_ONLY)
119 add_subdirectory(gmxana)
120 add_subdirectory(gmxpreprocess)
121 add_subdirectory(correlationfunctions)
122 add_subdirectory(statistics)
123 add_subdirectory(analysisdata)
124 add_subdirectory(coordinateio)
125 add_subdirectory(trajectoryanalysis)
126 add_subdirectory(energyanalysis)
127 add_subdirectory(tools)
130 get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
131 list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
133 # This would be the standard way to include thread_mpi, but
134 # we want libgromacs to link the functions directly
136 # add_subdirectory(thread_mpi)
138 #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
139 tmpi_get_source_list(THREAD_MPI_SOURCES ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/src)
140 add_library(thread_mpi OBJECT ${THREAD_MPI_SOURCES})
141 target_compile_definitions(thread_mpi PRIVATE HAVE_CONFIG_H)
143 # Needs POSIX-isms for strdup, not just std-isms
144 target_compile_definitions(thread_mpi PRIVATE _POSIX_C_SOURCE=200809L)
146 gmx_target_compile_options(thread_mpi)
148 gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
150 list(APPEND libgromacs_object_library_dependencies thread_mpi)
152 configure_file(version.h.cmakein version.h)
153 if(GMX_INSTALL_LEGACY_API)
155 ${CMAKE_CURRENT_BINARY_DIR}/version.h
156 DESTINATION include/gromacs)
159 # This code is here instead of utility/CMakeLists.txt, because CMake
160 # custom commands and source file properties can only be set in the directory
161 # that contains the target that uses them.
162 # TODO: Generate a header instead that can be included from baseversion.cpp.
163 # That probably simplifies things somewhat.
164 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
165 gmx_configure_version_file(
166 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
173 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
175 # Mark some shared GPU implementation files to compile with CUDA if needed
177 get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
178 set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
181 # set up CUDA compilation with clang
183 foreach (_file ${LIBGROMACS_SOURCES})
184 get_filename_component(_ext ${_file} EXT)
185 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
186 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
187 gmx_compile_cuda_file_with_clang(${_file})
193 # Work around FindCUDA that prevents using target_link_libraries()
194 # with keywords otherwise...
195 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
196 if (NOT GMX_CLANG_CUDA)
197 gmx_cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
199 add_library(libgromacs ${LIBGROMACS_SOURCES})
201 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
203 add_library(libgromacs ${LIBGROMACS_SOURCES})
206 # Add these contents first because linking their tests can take a lot
207 # of time, so we want lots of parallel work still available after
209 add_subdirectory(fileio)
210 add_subdirectory(selection)
212 # Suppress a warning about our abuse of t_inputrec
213 gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
215 # Handle the object libraries that contain the source file
216 # dependencies that need special handling because they are generated
218 foreach(object_library ${libgromacs_object_library_dependencies})
219 if (BUILD_SHARED_LIBS)
220 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
222 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
224 # Add the sources from the object libraries to the main library.
225 target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
227 gmx_target_compile_options(libgromacs)
228 target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
229 target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
232 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
233 mark_as_advanced(GMX_EXTERNAL_CLFFT)
235 # Default to using clFFT found on the system
236 # switch to quiet at the second run.
237 if (DEFINED clFFT_LIBRARY)
238 set (clFFT_FIND_QUIETLY TRUE)
242 if (GMX_EXTERNAL_CLFFT)
243 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
248 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
249 requires clFFT, which was not found on your system. GROMACS does bundle
250 clFFT to help with building for OpenCL, but that clFFT has not yet been
251 ported to the more recent versions of that compiler that GROMACS itself
252 requires. Thus for now, OpenCL is not available with MSVC and the internal
253 build of clFFT in GROMACS 2019. Either change compiler, try installing
254 a clFFT package, or use the latest GROMACS 2018 point release.")
257 # Fall back on the internal version
258 set (_clFFT_dir ../external/clFFT/src)
259 add_subdirectory(${_clFFT_dir} clFFT-build)
260 target_sources(libgromacs PRIVATE
261 $<TARGET_OBJECTS:clFFT>
263 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
264 # Use the magic variable for how to link any library needed for
265 # dlopen, etc. which is -ldl where needed, and empty otherwise
266 # (e.g. Windows, BSD, Mac).
267 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
269 target_link_libraries(libgromacs PRIVATE clFFT)
273 # Permit GROMACS code to include externally developed headers, such as
274 # the functionality from the nonstd project that we use for
275 # gmx::compat::optional. These are included as system headers so that
276 # no warnings are issued from them.
278 # TODO Perhaps generalize this for all headers from src/external
279 target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
281 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
282 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
283 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
284 # with the SIMD_AVX_512_CXX_FLAGS flags.
285 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
288 gmx_setup_tng_for_libgromacs()
290 target_link_libraries(libgromacs
293 ${GMX_EXTRA_LIBRARIES}
294 ${GMX_COMMON_LIBRARIES}
295 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
296 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
298 $<$<PLATFORM_ID:SunOS>:socket>
300 ${GMX_PUBLIC_LIBRARIES}
303 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
305 set_target_properties(libgromacs PROPERTIES
306 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
307 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
308 VERSION ${LIBRARY_VERSION}
312 target_link_libraries(libgromacs PRIVATE lmfit)
314 # Make sure we fix "everything" found by more recent versions of clang.
315 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER "7")
316 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
318 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
319 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
320 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
321 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
322 /wd6001 #unitialized memory
323 /wd6011 #derefencing NULL
324 /wd6053 #prior call not zero-terminate
325 /wd6054 #might not be zero-terminated
326 /wd6385 #reading invalid data
327 /wd6386 #buffer overrun
328 /wd6387 #could be '0'
329 /wd28199 #uninitialized memory
330 # For compile time constant (e.g. templates) the following warnings have flase postives
331 /wd6239 #(<non-zero> && <expr>)
332 /wd6240 #(<expr> && <non-zero>)
333 /wd6294 #Ill-defined for-loop
334 /wd6326 #comparison of constant with other constant
335 /wd28020 #expression involving paramter is not true
337 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
338 /wd6993 #OpenMP ignored
340 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
341 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
342 /wd6246 #hides declaration
348 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
349 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
352 # clang-3.6 warns about a number of issues that are not reported by more modern compilers
353 # and we know they are not real issues. So we only check that it can compile without error
354 # but ignore all warnings.
355 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^3\.6")
356 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-w>)
359 # Only install the library in mdrun-only mode if it is actually necessary
361 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
362 install(TARGETS libgromacs
365 LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
366 RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
367 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
368 INCLUDES DESTINATION include)
369 target_compile_definitions(libgromacs PUBLIC $<INSTALL_INTERFACE:GMX_DOUBLE=${GMX_DOUBLE_VALUE}>)
370 add_library(Gromacs::libgromacs ALIAS libgromacs)
373 if (NOT GMX_BUILD_MDRUN_ONLY)
374 include(InstallLibInfo.cmake)
377 # Technically, the user could want to do this for an OpenCL build
378 # using the CUDA runtime, but currently there's no reason to want to
380 if (INSTALL_CUDART_LIB) #can be set manual by user
382 foreach(CUDA_LIB ${CUDA_LIBRARIES})
383 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
384 if(IS_CUDART) #libcuda should not be installed
385 #install also name-links (linker uses those)
386 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
387 install(FILES ${CUDA_LIBS} DESTINATION
388 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
392 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
397 # Install the utility headers
398 file(GLOB OPENCL_INSTALLED_FILES
399 gpu_utils/vectype_ops.clh
400 gpu_utils/device_utils.clh
402 install(FILES ${OPENCL_INSTALLED_FILES}
403 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
405 file(GLOB OPENCL_INSTALLED_FILES
408 install(FILES ${OPENCL_INSTALLED_FILES}
409 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
412 # Install the NBNXM source and headers
413 file(GLOB OPENCL_INSTALLED_FILES
416 install(FILES ${OPENCL_INSTALLED_FILES}
417 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
419 file(GLOB OPENCL_INSTALLED_FILES
420 nbnxm/opencl/nbnxm_ocl_kernels.cl
421 nbnxm/opencl/nbnxm_ocl_kernel.clh
422 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
423 nbnxm/opencl/nbnxm_ocl_kernels.clh
424 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
425 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
426 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
427 nbnxm/opencl/nbnxm_ocl_consts.h
429 install(FILES ${OPENCL_INSTALLED_FILES}
430 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
433 # Install the PME source and headers
434 file(GLOB OPENCL_INSTALLED_FILES
438 ewald/pme_gpu_utils.clh
440 ewald/pme_gpu_types.h
442 install(FILES ${OPENCL_INSTALLED_FILES}
443 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald