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.
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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 add_library(libgromacs_external OBJECT "")
47 if(CMAKE_COMPILER_IS_GNUCXX)
48 # Keep quiet about e.g. linearalgebra module
49 target_compile_options(libgromacs_external PRIVATE ${CXXFLAGS_NO_STRINGOP_TRUNCATION})
52 add_library(libgromacs_generated OBJECT "")
53 if (BUILD_SHARED_LIBS)
54 set_target_properties(libgromacs_external PROPERTIES POSITION_INDEPENDENT_CODE true)
55 set_target_properties(libgromacs_generated PROPERTIES POSITION_INDEPENDENT_CODE true)
58 function (_gmx_add_files_to_property PROPERTY)
59 foreach (_file ${ARGN})
60 if (IS_ABSOLUTE "${_file}")
61 set_property(GLOBAL APPEND PROPERTY ${PROPERTY} ${_file})
63 set_property(GLOBAL APPEND PROPERTY ${PROPERTY}
64 ${CMAKE_CURRENT_LIST_DIR}/${_file})
69 function (gmx_add_libgromacs_sources)
70 _gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
73 # TODO Reconsider this, as the CUDA driver API is probably a simpler
74 # approach, at least for the build system. See Redmine #2530
75 function (gmx_compile_cpp_as_cuda)
76 _gmx_add_files_to_property(GMX_LIBGROMACS_GPU_IMPL_SOURCES ${ARGN})
79 function (gmx_install_headers)
80 if (NOT GMX_BUILD_MDRUN_ONLY)
81 file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
83 DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${_dest}"
84 COMPONENT development)
86 _gmx_add_files_to_property(GMX_INSTALLED_HEADERS ${ARGN})
89 function (gmx_write_installed_header_list)
90 get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
91 string(REPLACE ";" "\n" _list "${_list}")
92 # TODO: Make this only update the file timestamp if the contents actually change.
93 file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
96 add_subdirectory(gmxlib)
97 add_subdirectory(mdlib)
98 add_subdirectory(applied-forces)
99 add_subdirectory(listed-forces)
100 add_subdirectory(commandline)
101 add_subdirectory(domdec)
102 add_subdirectory(ewald)
103 add_subdirectory(fft)
104 add_subdirectory(gpu_utils)
105 add_subdirectory(hardware)
106 add_subdirectory(linearalgebra)
107 add_subdirectory(math)
108 add_subdirectory(mdrun)
109 add_subdirectory(mdrunutility)
110 add_subdirectory(mdtypes)
111 add_subdirectory(onlinehelp)
112 add_subdirectory(options)
113 add_subdirectory(pbcutil)
114 add_subdirectory(random)
115 add_subdirectory(restraint)
116 add_subdirectory(tables)
117 add_subdirectory(taskassignment)
118 add_subdirectory(timing)
119 add_subdirectory(topology)
120 add_subdirectory(trajectory)
121 add_subdirectory(utility)
122 add_subdirectory(fileio)
123 add_subdirectory(swap)
124 add_subdirectory(essentialdynamics)
125 add_subdirectory(pulling)
126 add_subdirectory(awh)
127 add_subdirectory(simd)
128 add_subdirectory(imd)
129 add_subdirectory(compat)
130 add_subdirectory(mimic)
131 if (NOT GMX_BUILD_MDRUN_ONLY)
132 add_subdirectory(gmxana)
133 add_subdirectory(gmxpreprocess)
134 add_subdirectory(correlationfunctions)
135 add_subdirectory(statistics)
136 add_subdirectory(analysisdata)
137 add_subdirectory(selection)
138 add_subdirectory(trajectoryanalysis)
139 add_subdirectory(energyanalysis)
140 add_subdirectory(tools)
143 get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
144 list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
146 # This would be the standard way to include thread_mpi, but
147 # we want libgromacs to link the functions directly
149 # add_subdirectory(thread_mpi)
151 #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
153 tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
154 target_sources(libgromacs_external PRIVATE ${THREAD_MPI_SOURCES})
156 configure_file(version.h.cmakein version.h)
165 ${CMAKE_CURRENT_BINARY_DIR}/version.h
168 # This code is here instead of utility/CMakeLists.txt, because CMake
169 # custom commands and source file properties can only be set in the directory
170 # that contains the target that uses them.
171 # TODO: Generate a header instead that can be included from baseversion.c.
172 # That probably simplifies things somewhat.
173 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
174 gmx_configure_version_file(
175 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
180 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE}
181 $<TARGET_OBJECTS:libgromacs_external>
182 $<TARGET_OBJECTS:libgromacs_generated>)
184 # Mark some shared GPU implementation files to compile with CUDA if needed
186 get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
187 set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
190 # set up CUDA compilation with clang
192 foreach (_file ${LIBGROMACS_SOURCES})
193 get_filename_component(_ext ${_file} EXT)
194 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
195 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
196 gmx_compile_cuda_file_with_clang(${_file})
202 # Work around FindCUDA that prevents using target_link_libraries()
203 # with keywords otherwise...
204 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
205 if (NOT GMX_CLANG_CUDA)
206 cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
208 add_library(libgromacs ${LIBGROMACS_SOURCES})
210 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
212 add_library(libgromacs ${LIBGROMACS_SOURCES})
216 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
217 mark_as_advanced(GMX_EXTERNAL_CLFFT)
219 # Default to using clFFT found on the system
220 # switch to quiet at the second run.
221 if (DEFINED clFFT_LIBRARY)
222 set (clFFT_FIND_QUIETLY TRUE)
226 if (GMX_EXTERNAL_CLFFT)
227 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
232 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
233 requires clFFT, which was not found on your system. GROMACS does bundle
234 clFFT to help with building for OpenCL, but that clFFT has not yet been
235 ported to the more recent versions of that compiler that GROMACS itself
236 requires. Thus for now, OpenCL is not available with MSVC and the internal
237 build of clFFT in GROMACS 2019. Either change compiler, try installing
238 a clFFT package, or use the latest GROMACS 2018 point release.")
241 # Fall back on the internal version
242 set (_clFFT_dir ../external/clFFT/src)
243 add_subdirectory(${_clFFT_dir} clFFT-build)
244 target_sources(libgromacs PRIVATE
245 $<TARGET_OBJECTS:clFFT>
247 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
248 # Use the magic variable for how to link any library needed for
249 # dlopen, etc. which is -ldl where needed, and empty otherwise
250 # (e.g. Windows, BSD, Mac).
251 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
253 target_link_libraries(libgromacs PRIVATE clFFT)
257 # Recent versions of gcc and clang give warnings on scanner.cpp, which
258 # is a generated source file. These are awkward to suppress inline, so
259 # we do it in the compilation command (after testing that the compiler
260 # supports the suppressions). Same issue exists for nonbonded kernels
261 # so we supress them for all generated files.
262 include(CheckCXXCompilerFlag)
263 check_cxx_compiler_flag("-Wno-unused -Wno-unused-parameter" HAS_NO_UNUSED)
264 check_cxx_compiler_flag(-Wno-missing-declarations HAS_NO_MISSING_DECL)
265 check_cxx_compiler_flag(-Wno-missing-prototypes HAS_NO_MISSING_PROTO)
266 check_cxx_compiler_flag(/wd4101 HAS_NO_MSVC_UNUSED)
268 check_cxx_compiler_flag(-wd1419 HAS_DECL_IN_SOURCE)
271 target_compile_options(libgromacs_generated PRIVATE "-Wno-unused;-Wno-unused-parameter")
273 if (HAS_NO_MISSING_DECL)
274 target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-declarations")
276 # TODO The group scheme kernels don't use proper function prototype
277 # declarations, and clang warns about such use, which we suppress
278 # rather than fix. We would prefer to use no suppressions. However
279 # other compilers do not support such a warning suppression for C++
280 # source files, and issue warnings about that. Remove the use of
281 # -Wno-missing-prototypes here and above when the group scheme is
283 if (HAS_NO_MISSING_PROTO AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
284 target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-prototypes")
286 if (HAS_NO_MSVC_UNUSED)
287 target_compile_options(libgromacs_generated PRIVATE "/wd4101")
289 if (HAS_DECL_IN_SOURCE)
290 target_compile_options(libgromacs_generated PRIVATE "-wd1419")
293 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
294 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
295 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
296 # with the SIMD_AVX_512_CXX_FLAGS flags.
297 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
300 gmx_setup_tng_for_libgromacs()
302 target_link_libraries(libgromacs
305 ${GMX_EXTRA_LIBRARIES}
306 ${GMX_COMMON_LIBRARIES}
307 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
308 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
310 ${GMX_STDLIB_LIBRARIES}
312 ${GMX_PUBLIC_LIBRARIES}
314 set_target_properties(libgromacs PROPERTIES
315 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
316 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
317 VERSION ${LIBRARY_VERSION}
318 COMPILE_FLAGS "${OpenMP_C_FLAGS}")
321 target_link_libraries(libgromacs PRIVATE lmfit)
323 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^6\.0")
324 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
326 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
327 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
328 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
329 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
330 /wd6001 #unitialized memory
331 /wd6011 #derefencing NULL
332 /wd6053 #prior call not zero-terminate
333 /wd6054 #might not be zero-terminated
334 /wd6385 #reading invalid data
335 /wd6386 #buffer overrun
336 /wd6387 #could be '0'
337 /wd28199 #uninitialized memory
338 # For compile time constant (e.g. templates) the following warnings have flase postives
339 /wd6239 #(<non-zero> && <expr>)
340 /wd6240 #(<expr> && <non-zero>)
341 /wd6294 #Ill-defined for-loop
342 /wd6326 #comparison of constant with other constant
343 /wd28020 #expression involving paramter is not true
345 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
346 /wd6993 #OpenMP ignored
348 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
349 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
350 /wd6246 #hides declaration
356 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
357 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
360 gmx_write_installed_header_list()
362 # Only install the library in mdrun-only mode if it is actually necessary
364 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
365 install(TARGETS libgromacs
367 LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
368 RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
369 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
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 NB source and headers
413 file(GLOB OPENCL_INSTALLED_FILES
416 install(FILES ${OPENCL_INSTALLED_FILES}
417 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/mdlib
419 file(GLOB OPENCL_INSTALLED_FILES
420 mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl
421 mdlib/nbnxn_ocl/nbnxn_ocl_kernel.clh
422 mdlib/nbnxn_ocl/nbnxn_ocl_kernel_pruneonly.clh
423 mdlib/nbnxn_ocl/nbnxn_ocl_kernels.clh
424 mdlib/nbnxn_ocl/nbnxn_ocl_kernels_fastgen.clh
425 mdlib/nbnxn_ocl/nbnxn_ocl_kernels_fastgen_add_twincut.clh
426 mdlib/nbnxn_ocl/nbnxn_ocl_kernel_utils.clh
427 mdlib/nbnxn_ocl/nbnxn_ocl_consts.h
429 install(FILES ${OPENCL_INSTALLED_FILES}
430 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/mdlib/nbnxn_ocl
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