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
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14 # GROMACS is distributed in the hope that it will be useful,
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17 # Lesser General Public License for more details.
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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(nbnxm)
101 add_subdirectory(commandline)
102 add_subdirectory(domdec)
103 add_subdirectory(ewald)
104 add_subdirectory(fft)
105 add_subdirectory(gpu_utils)
106 add_subdirectory(hardware)
107 add_subdirectory(linearalgebra)
108 add_subdirectory(math)
109 add_subdirectory(mdrun)
110 add_subdirectory(mdrunutility)
111 add_subdirectory(mdspan)
112 add_subdirectory(mdtypes)
113 add_subdirectory(onlinehelp)
114 add_subdirectory(options)
115 add_subdirectory(pbcutil)
116 add_subdirectory(random)
117 add_subdirectory(restraint)
118 add_subdirectory(tables)
119 add_subdirectory(taskassignment)
120 add_subdirectory(timing)
121 add_subdirectory(topology)
122 add_subdirectory(trajectory)
123 add_subdirectory(utility)
124 add_subdirectory(fileio)
125 add_subdirectory(swap)
126 add_subdirectory(essentialdynamics)
127 add_subdirectory(pulling)
128 add_subdirectory(awh)
129 add_subdirectory(simd)
130 add_subdirectory(imd)
131 add_subdirectory(compat)
132 add_subdirectory(mimic)
133 if (NOT GMX_BUILD_MDRUN_ONLY)
134 add_subdirectory(gmxana)
135 add_subdirectory(gmxpreprocess)
136 add_subdirectory(correlationfunctions)
137 add_subdirectory(statistics)
138 add_subdirectory(analysisdata)
139 add_subdirectory(selection)
140 add_subdirectory(trajectoryanalysis)
141 add_subdirectory(energyanalysis)
142 add_subdirectory(tools)
145 get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
146 list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
148 # This would be the standard way to include thread_mpi, but
149 # we want libgromacs to link the functions directly
151 # add_subdirectory(thread_mpi)
153 #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
155 tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
156 target_sources(libgromacs_external PRIVATE ${THREAD_MPI_SOURCES})
158 configure_file(version.h.cmakein version.h)
167 ${CMAKE_CURRENT_BINARY_DIR}/version.h
170 # This code is here instead of utility/CMakeLists.txt, because CMake
171 # custom commands and source file properties can only be set in the directory
172 # that contains the target that uses them.
173 # TODO: Generate a header instead that can be included from baseversion.c.
174 # That probably simplifies things somewhat.
175 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
176 gmx_configure_version_file(
177 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
182 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE}
183 $<TARGET_OBJECTS:libgromacs_external>
184 $<TARGET_OBJECTS:libgromacs_generated>)
186 # Mark some shared GPU implementation files to compile with CUDA if needed
188 get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
189 set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
192 # set up CUDA compilation with clang
194 foreach (_file ${LIBGROMACS_SOURCES})
195 get_filename_component(_ext ${_file} EXT)
196 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
197 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
198 gmx_compile_cuda_file_with_clang(${_file})
204 # Work around FindCUDA that prevents using target_link_libraries()
205 # with keywords otherwise...
206 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
207 if (NOT GMX_CLANG_CUDA)
208 cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
210 add_library(libgromacs ${LIBGROMACS_SOURCES})
212 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
214 add_library(libgromacs ${LIBGROMACS_SOURCES})
218 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
219 mark_as_advanced(GMX_EXTERNAL_CLFFT)
221 # Default to using clFFT found on the system
222 # switch to quiet at the second run.
223 if (DEFINED clFFT_LIBRARY)
224 set (clFFT_FIND_QUIETLY TRUE)
228 if (GMX_EXTERNAL_CLFFT)
229 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
234 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
235 requires clFFT, which was not found on your system. GROMACS does bundle
236 clFFT to help with building for OpenCL, but that clFFT has not yet been
237 ported to the more recent versions of that compiler that GROMACS itself
238 requires. Thus for now, OpenCL is not available with MSVC and the internal
239 build of clFFT in GROMACS 2019. Either change compiler, try installing
240 a clFFT package, or use the latest GROMACS 2018 point release.")
243 # Fall back on the internal version
244 set (_clFFT_dir ../external/clFFT/src)
245 add_subdirectory(${_clFFT_dir} clFFT-build)
246 target_sources(libgromacs PRIVATE
247 $<TARGET_OBJECTS:clFFT>
249 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
250 # Use the magic variable for how to link any library needed for
251 # dlopen, etc. which is -ldl where needed, and empty otherwise
252 # (e.g. Windows, BSD, Mac).
253 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
255 target_link_libraries(libgromacs PRIVATE clFFT)
259 # Recent versions of gcc and clang give warnings on scanner.cpp, which
260 # is a generated source file. These are awkward to suppress inline, so
261 # we do it in the compilation command (after testing that the compiler
262 # supports the suppressions). Same issue exists for nonbonded kernels
263 # so we supress them for all generated files.
264 include(CheckCXXCompilerFlag)
265 check_cxx_compiler_flag("-Wno-unused -Wno-unused-parameter" HAS_NO_UNUSED)
266 check_cxx_compiler_flag(-Wno-missing-declarations HAS_NO_MISSING_DECL)
267 check_cxx_compiler_flag(-Wno-missing-prototypes HAS_NO_MISSING_PROTO)
268 check_cxx_compiler_flag(/wd4101 HAS_NO_MSVC_UNUSED)
270 check_cxx_compiler_flag(-wd1419 HAS_DECL_IN_SOURCE)
273 target_compile_options(libgromacs_generated PRIVATE "-Wno-unused;-Wno-unused-parameter")
275 if (HAS_NO_MISSING_DECL)
276 target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-declarations")
278 # TODO The group scheme kernels don't use proper function prototype
279 # declarations, and clang warns about such use, which we suppress
280 # rather than fix. We would prefer to use no suppressions. However
281 # other compilers do not support such a warning suppression for C++
282 # source files, and issue warnings about that. Remove the use of
283 # -Wno-missing-prototypes here and above when the group scheme is
285 if (HAS_NO_MISSING_PROTO AND "${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
286 target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-prototypes")
288 if (HAS_NO_MSVC_UNUSED)
289 target_compile_options(libgromacs_generated PRIVATE "/wd4101")
291 if (HAS_DECL_IN_SOURCE)
292 target_compile_options(libgromacs_generated PRIVATE "-wd1419")
295 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
296 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
297 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
298 # with the SIMD_AVX_512_CXX_FLAGS flags.
299 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
302 gmx_setup_tng_for_libgromacs()
304 target_link_libraries(libgromacs
307 ${GMX_EXTRA_LIBRARIES}
308 ${GMX_COMMON_LIBRARIES}
309 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
310 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
313 ${GMX_PUBLIC_LIBRARIES}
316 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
318 set_target_properties(libgromacs PROPERTIES
319 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
320 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
321 VERSION ${LIBRARY_VERSION}
325 target_link_libraries(libgromacs PRIVATE lmfit)
327 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^6\.0")
328 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
330 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
331 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
332 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
333 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
334 /wd6001 #unitialized memory
335 /wd6011 #derefencing NULL
336 /wd6053 #prior call not zero-terminate
337 /wd6054 #might not be zero-terminated
338 /wd6385 #reading invalid data
339 /wd6386 #buffer overrun
340 /wd6387 #could be '0'
341 /wd28199 #uninitialized memory
342 # For compile time constant (e.g. templates) the following warnings have flase postives
343 /wd6239 #(<non-zero> && <expr>)
344 /wd6240 #(<expr> && <non-zero>)
345 /wd6294 #Ill-defined for-loop
346 /wd6326 #comparison of constant with other constant
347 /wd28020 #expression involving paramter is not true
349 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
350 /wd6993 #OpenMP ignored
352 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
353 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
354 /wd6246 #hides declaration
360 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
361 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
364 gmx_write_installed_header_list()
366 # Only install the library in mdrun-only mode if it is actually necessary
368 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
369 install(TARGETS libgromacs
371 LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
372 RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
373 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
377 if (NOT GMX_BUILD_MDRUN_ONLY)
378 include(InstallLibInfo.cmake)
381 # Technically, the user could want to do this for an OpenCL build
382 # using the CUDA runtime, but currently there's no reason to want to
384 if (INSTALL_CUDART_LIB) #can be set manual by user
386 foreach(CUDA_LIB ${CUDA_LIBRARIES})
387 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
388 if(IS_CUDART) #libcuda should not be installed
389 #install also name-links (linker uses those)
390 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
391 install(FILES ${CUDA_LIBS} DESTINATION
392 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
396 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
401 # Install the utility headers
402 file(GLOB OPENCL_INSTALLED_FILES
403 gpu_utils/vectype_ops.clh
404 gpu_utils/device_utils.clh
406 install(FILES ${OPENCL_INSTALLED_FILES}
407 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
409 file(GLOB OPENCL_INSTALLED_FILES
412 install(FILES ${OPENCL_INSTALLED_FILES}
413 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
416 # Install the NBNXM source and headers
417 file(GLOB OPENCL_INSTALLED_FILES
420 install(FILES ${OPENCL_INSTALLED_FILES}
421 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm
423 file(GLOB OPENCL_INSTALLED_FILES
424 nbnxm/opencl/nbnxm_ocl_kernels.cl
425 nbnxm/opencl/nbnxm_ocl_kernel.clh
426 nbnxm/opencl/nbnxm_ocl_kernel_pruneonly.clh
427 nbnxm/opencl/nbnxm_ocl_kernels.clh
428 nbnxm/opencl/nbnxm_ocl_kernels_fastgen.clh
429 nbnxm/opencl/nbnxm_ocl_kernels_fastgen_add_twincut.clh
430 nbnxm/opencl/nbnxm_ocl_kernel_utils.clh
431 nbnxm/opencl/nbnxm_ocl_consts.h
433 install(FILES ${OPENCL_INSTALLED_FILES}
434 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/nbnxm/opencl
437 # Install the PME source and headers
438 file(GLOB OPENCL_INSTALLED_FILES
442 ewald/pme_gpu_utils.clh
444 ewald/pme_gpu_types.h
446 install(FILES ${OPENCL_INSTALLED_FILES}
447 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald