2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
5 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 # and including many others, as listed in the AUTHORS file in the
7 # top-level source directory and at http://www.gromacs.org.
9 # GROMACS is free software; you can redistribute it and/or
10 # modify it under the terms of the GNU Lesser General Public License
11 # as published by the Free Software Foundation; either version 2.1
12 # of the License, or (at your option) any later version.
14 # GROMACS is distributed in the hope that it will be useful,
15 # but WITHOUT ANY WARRANTY; without even the implied warranty of
16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 # Lesser General Public License for more details.
19 # You should have received a copy of the GNU Lesser General Public
20 # License along with GROMACS; if not, see
21 # http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 # If you want to redistribute modifications to GROMACS, please
25 # consider that scientific software is very special. Version
26 # control is crucial - bugs must be traceable. We will be happy to
27 # consider code for inclusion in the official distribution, but
28 # derived work must not be called official GROMACS. Details are found
29 # in the README & COPYING files - if they are missing, get the
30 # official version at http://www.gromacs.org.
32 # To help us fund GROMACS development, we humbly ask that you cite
33 # the research papers on the package. Check out http://www.gromacs.org.
35 set(LIBGROMACS_SOURCES)
38 include(gmxClangCudaUtils)
41 set_property(GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
42 set_property(GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
43 set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
44 set_property(GLOBAL PROPERTY GMX_AVX_512_SOURCE)
46 set(libgromacs_object_library_dependencies "")
47 function (_gmx_add_files_to_property PROPERTY)
48 foreach (_file ${ARGN})
49 if (IS_ABSOLUTE "${_file}")
50 set_property(GLOBAL APPEND PROPERTY ${PROPERTY} ${_file})
52 set_property(GLOBAL APPEND PROPERTY ${PROPERTY}
53 ${CMAKE_CURRENT_LIST_DIR}/${_file})
58 function (gmx_add_libgromacs_sources)
59 _gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
62 # TODO Reconsider this, as the CUDA driver API is probably a simpler
63 # approach, at least for the build system. See Redmine #2530
64 function (gmx_compile_cpp_as_cuda)
65 _gmx_add_files_to_property(GMX_LIBGROMACS_GPU_IMPL_SOURCES ${ARGN})
68 # Add these contents first because linking their tests can take a lot
69 # of time, so we want lots of parallel work still available after
71 add_subdirectory(utility)
73 add_subdirectory(gmxlib)
74 add_subdirectory(mdlib)
75 add_subdirectory(applied_forces)
76 add_subdirectory(listed_forces)
77 add_subdirectory(nbnxm)
78 add_subdirectory(commandline)
79 add_subdirectory(domdec)
80 add_subdirectory(ewald)
82 add_subdirectory(gpu_utils)
83 add_subdirectory(hardware)
84 add_subdirectory(linearalgebra)
85 add_subdirectory(math)
86 add_subdirectory(mdrun)
87 add_subdirectory(mdrunutility)
88 add_subdirectory(mdspan)
89 add_subdirectory(mdtypes)
90 add_subdirectory(onlinehelp)
91 add_subdirectory(options)
92 add_subdirectory(pbcutil)
93 add_subdirectory(random)
94 add_subdirectory(restraint)
95 add_subdirectory(tables)
96 add_subdirectory(taskassignment)
97 add_subdirectory(timing)
98 add_subdirectory(topology)
99 add_subdirectory(trajectory)
100 add_subdirectory(swap)
101 add_subdirectory(essentialdynamics)
102 add_subdirectory(pulling)
103 add_subdirectory(awh)
104 add_subdirectory(simd)
105 add_subdirectory(imd)
106 add_subdirectory(compat)
107 add_subdirectory(mimic)
108 add_subdirectory(modularsimulator)
109 if (NOT GMX_BUILD_MDRUN_ONLY)
110 add_subdirectory(gmxana)
111 add_subdirectory(gmxpreprocess)
112 add_subdirectory(correlationfunctions)
113 add_subdirectory(statistics)
114 add_subdirectory(analysisdata)
115 add_subdirectory(coordinateio)
116 add_subdirectory(trajectoryanalysis)
117 add_subdirectory(energyanalysis)
118 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)
133 gmx_target_compile_options(thread_mpi)
135 gmx_target_warning_suppression(thread_mpi /wd4996 HAS_NO_MSVC_UNSAFE_FUNCTION)
137 list(APPEND libgromacs_object_library_dependencies thread_mpi)
139 configure_file(version.h.cmakein version.h)
140 if(GMX_INSTALL_LEGACY_API)
142 ${CMAKE_CURRENT_BINARY_DIR}/version.h
143 DESTINATION include/gromacs)
146 # This code is here instead of utility/CMakeLists.txt, because CMake
147 # custom commands and source file properties can only be set in the directory
148 # that contains the target that uses them.
149 # TODO: Generate a header instead that can be included from baseversion.cpp.
150 # That probably simplifies things somewhat.
151 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
152 gmx_configure_version_file(
153 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
160 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
162 # Mark some shared GPU implementation files to compile with CUDA if needed
164 get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
165 set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
168 # set up CUDA compilation with clang
170 foreach (_file ${LIBGROMACS_SOURCES})
171 get_filename_component(_ext ${_file} EXT)
172 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
173 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
174 gmx_compile_cuda_file_with_clang(${_file})
180 # Work around FindCUDA that prevents using target_link_libraries()
181 # with keywords otherwise...
182 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
183 if (NOT GMX_CLANG_CUDA)
184 gmx_cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
186 add_library(libgromacs ${LIBGROMACS_SOURCES})
188 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
190 add_library(libgromacs ${LIBGROMACS_SOURCES})
193 # Add these contents first because linking their tests can take a lot
194 # of time, so we want lots of parallel work still available after
196 add_subdirectory(fileio)
197 add_subdirectory(selection)
199 # Suppress a warning about our abuse of t_inputrec
200 gmx_source_file_warning_suppression(mdtypes/inputrec.cpp -Wno-class-memaccess HAS_NO_CLASS_MEMACCESS)
202 # Handle the object libraries that contain the source file
203 # dependencies that need special handling because they are generated
205 foreach(object_library ${libgromacs_object_library_dependencies})
206 if (BUILD_SHARED_LIBS)
207 set_target_properties(${object_library} PROPERTIES POSITION_INDEPENDENT_CODE true)
209 target_include_directories(${object_library} SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
211 # Add the sources from the object libraries to the main library.
212 target_sources(libgromacs PRIVATE $<TARGET_OBJECTS:${object_library}>)
214 gmx_target_compile_options(libgromacs)
215 target_compile_definitions(libgromacs PRIVATE HAVE_CONFIG_H)
216 target_include_directories(libgromacs SYSTEM BEFORE PRIVATE ${PROJECT_SOURCE_DIR}/src/external/thread_mpi/include)
219 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
220 mark_as_advanced(GMX_EXTERNAL_CLFFT)
222 # Default to using clFFT found on the system
223 # switch to quiet at the second run.
224 if (DEFINED clFFT_LIBRARY)
225 set (clFFT_FIND_QUIETLY TRUE)
229 if (GMX_EXTERNAL_CLFFT)
230 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
235 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
236 requires clFFT, which was not found on your system. GROMACS does bundle
237 clFFT to help with building for OpenCL, but that clFFT has not yet been
238 ported to the more recent versions of that compiler that GROMACS itself
239 requires. Thus for now, OpenCL is not available with MSVC and the internal
240 build of clFFT in GROMACS 2019. Either change compiler, try installing
241 a clFFT package, or use the latest GROMACS 2018 point release.")
244 # Fall back on the internal version
245 set (_clFFT_dir ../external/clFFT/src)
246 add_subdirectory(${_clFFT_dir} clFFT-build)
247 target_sources(libgromacs PRIVATE
248 $<TARGET_OBJECTS:clFFT>
250 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
251 # Use the magic variable for how to link any library needed for
252 # dlopen, etc. which is -ldl where needed, and empty otherwise
253 # (e.g. Windows, BSD, Mac).
254 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
256 target_link_libraries(libgromacs PRIVATE clFFT)
260 # Permit GROMACS code to include externally developed headers, such as
261 # the functionality from the nonstd project that we use for
262 # gmx::compat::optional. These are included as system headers so that
263 # no warnings are issued from them.
265 # TODO Perhaps generalize this for all headers from src/external
266 target_include_directories(libgromacs SYSTEM PRIVATE ${PROJECT_SOURCE_DIR}/src/external)
268 # Temporary fix to allow external access to restraintpotentail
269 target_include_directories(libgromacs PUBLIC
270 $<INSTALL_INTERFACE:include>
273 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
274 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
275 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
276 # with the SIMD_AVX_512_CXX_FLAGS flags.
277 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
280 gmx_setup_tng_for_libgromacs()
282 target_link_libraries(libgromacs
285 ${GMX_EXTRA_LIBRARIES}
286 ${GMX_COMMON_LIBRARIES}
287 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
288 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
291 ${GMX_PUBLIC_LIBRARIES}
294 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
296 set_target_properties(libgromacs PROPERTIES
297 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
298 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
299 VERSION ${LIBRARY_VERSION}
303 target_link_libraries(libgromacs PRIVATE lmfit)
305 # Fix everything found by the latest version of clang that we use in
306 # Jenkins testing. This should be updated when we update the latest
307 # tested version of clang.
308 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^7\.0")
309 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
311 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
312 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
313 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
314 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
315 /wd6001 #unitialized memory
316 /wd6011 #derefencing NULL
317 /wd6053 #prior call not zero-terminate
318 /wd6054 #might not be zero-terminated
319 /wd6385 #reading invalid data
320 /wd6386 #buffer overrun
321 /wd6387 #could be '0'
322 /wd28199 #uninitialized memory
323 # For compile time constant (e.g. templates) the following warnings have flase postives
324 /wd6239 #(<non-zero> && <expr>)
325 /wd6240 #(<expr> && <non-zero>)
326 /wd6294 #Ill-defined for-loop
327 /wd6326 #comparison of constant with other constant
328 /wd28020 #expression involving paramter is not true
330 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
331 /wd6993 #OpenMP ignored
333 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
334 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
335 /wd6246 #hides declaration
341 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
342 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
345 # Only install the library in mdrun-only mode if it is actually necessary
347 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
348 install(TARGETS libgromacs
350 LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
351 RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
352 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
353 INCLUDES DESTINATION include
357 if (NOT GMX_BUILD_MDRUN_ONLY)
358 include(InstallLibInfo.cmake)
361 # Technically, the user could want to do this for an OpenCL build
362 # using the CUDA runtime, but currently there's no reason to want to
364 if (INSTALL_CUDART_LIB) #can be set manual by user
366 foreach(CUDA_LIB ${CUDA_LIBRARIES})
367 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
368 if(IS_CUDART) #libcuda should not be installed
369 #install also name-links (linker uses those)
370 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
371 install(FILES ${CUDA_LIBS} DESTINATION
372 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
376 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
381 # Install the utility headers
382 file(GLOB OPENCL_INSTALLED_FILES
383 gpu_utils/vectype_ops.clh
384 gpu_utils/device_utils.clh
386 install(FILES ${OPENCL_INSTALLED_FILES}
387 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
389 file(GLOB OPENCL_INSTALLED_FILES
392 install(FILES ${OPENCL_INSTALLED_FILES}
393 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
396 # Install the NBNXM source and headers
397 file(GLOB OPENCL_INSTALLED_FILES
400 install(FILES ${OPENCL_INSTALLED_FILES}
401 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
403 file(GLOB OPENCL_INSTALLED_FILES
404 nbnxm/opencl/nbnxm_ocl_kernels.cl
405 nbnxm/opencl/nbnxm_ocl_kernel.clh
406 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
407 nbnxm/opencl/nbnxm_ocl_kernels.clh
408 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
409 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
410 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
411 nbnxm/opencl/nbnxm_ocl_consts.h
413 install(FILES ${OPENCL_INSTALLED_FILES}
414 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
417 # Install the PME source and headers
418 file(GLOB OPENCL_INSTALLED_FILES
422 ewald/pme_gpu_utils.clh
424 ewald/pme_gpu_types.h
426 install(FILES ${OPENCL_INSTALLED_FILES}
427 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald