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(mdspan)
111 add_subdirectory(mdtypes)
112 add_subdirectory(onlinehelp)
113 add_subdirectory(options)
114 add_subdirectory(pbcutil)
115 add_subdirectory(random)
116 add_subdirectory(restraint)
117 add_subdirectory(tables)
118 add_subdirectory(taskassignment)
119 add_subdirectory(timing)
120 add_subdirectory(topology)
121 add_subdirectory(trajectory)
122 add_subdirectory(utility)
123 add_subdirectory(fileio)
124 add_subdirectory(swap)
125 add_subdirectory(essentialdynamics)
126 add_subdirectory(pulling)
127 add_subdirectory(awh)
128 add_subdirectory(simd)
129 add_subdirectory(imd)
130 add_subdirectory(compat)
131 add_subdirectory(mimic)
132 if (NOT GMX_BUILD_MDRUN_ONLY)
133 add_subdirectory(gmxana)
134 add_subdirectory(gmxpreprocess)
135 add_subdirectory(correlationfunctions)
136 add_subdirectory(statistics)
137 add_subdirectory(analysisdata)
138 add_subdirectory(selection)
139 add_subdirectory(trajectoryanalysis)
140 add_subdirectory(energyanalysis)
141 add_subdirectory(tools)
144 get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
145 list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
147 # This would be the standard way to include thread_mpi, but
148 # we want libgromacs to link the functions directly
150 # add_subdirectory(thread_mpi)
152 #target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
154 tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
155 target_sources(libgromacs_external PRIVATE ${THREAD_MPI_SOURCES})
157 configure_file(version.h.cmakein version.h)
166 ${CMAKE_CURRENT_BINARY_DIR}/version.h
169 # This code is here instead of utility/CMakeLists.txt, because CMake
170 # custom commands and source file properties can only be set in the directory
171 # that contains the target that uses them.
172 # TODO: Generate a header instead that can be included from baseversion.c.
173 # That probably simplifies things somewhat.
174 set(GENERATED_VERSION_FILE utility/baseversion-gen.cpp)
175 gmx_configure_version_file(
176 utility/baseversion-gen.cpp.cmakein ${GENERATED_VERSION_FILE}
181 list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE}
182 $<TARGET_OBJECTS:libgromacs_external>
183 $<TARGET_OBJECTS:libgromacs_generated>)
185 # Mark some shared GPU implementation files to compile with CUDA if needed
187 get_property(LIBGROMACS_GPU_IMPL_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_GPU_IMPL_SOURCES)
188 set_source_files_properties(${LIBGROMACS_GPU_IMPL_SOURCES} PROPERTIES CUDA_SOURCE_PROPERTY_FORMAT OBJ)
191 # set up CUDA compilation with clang
193 foreach (_file ${LIBGROMACS_SOURCES})
194 get_filename_component(_ext ${_file} EXT)
195 get_source_file_property(_cuda_source_format ${_file} CUDA_SOURCE_PROPERTY_FORMAT)
196 if ("${_ext}" STREQUAL ".cu" OR _cuda_source_format)
197 gmx_compile_cuda_file_with_clang(${_file})
203 # Work around FindCUDA that prevents using target_link_libraries()
204 # with keywords otherwise...
205 set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
206 if (NOT GMX_CLANG_CUDA)
207 cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
209 add_library(libgromacs ${LIBGROMACS_SOURCES})
211 target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
213 add_library(libgromacs ${LIBGROMACS_SOURCES})
217 option(GMX_EXTERNAL_CLFFT "True if an external clFFT is required to be used" FALSE)
218 mark_as_advanced(GMX_EXTERNAL_CLFFT)
220 # Default to using clFFT found on the system
221 # switch to quiet at the second run.
222 if (DEFINED clFFT_LIBRARY)
223 set (clFFT_FIND_QUIETLY TRUE)
227 if (GMX_EXTERNAL_CLFFT)
228 message(FATAL_ERROR "Did not find required external clFFT library, consider setting clFFT_ROOT_DIR")
233 "An OpenCL build was requested with Visual Studio compiler, but GROMACS
234 requires clFFT, which was not found on your system. GROMACS does bundle
235 clFFT to help with building for OpenCL, but that clFFT has not yet been
236 ported to the more recent versions of that compiler that GROMACS itself
237 requires. Thus for now, OpenCL is not available with MSVC and the internal
238 build of clFFT in GROMACS 2019. Either change compiler, try installing
239 a clFFT package, or use the latest GROMACS 2018 point release.")
242 # Fall back on the internal version
243 set (_clFFT_dir ../external/clFFT/src)
244 add_subdirectory(${_clFFT_dir} clFFT-build)
245 target_sources(libgromacs PRIVATE
246 $<TARGET_OBJECTS:clFFT>
248 target_include_directories(libgromacs SYSTEM PRIVATE ${_clFFT_dir}/include)
249 # Use the magic variable for how to link any library needed for
250 # dlopen, etc. which is -ldl where needed, and empty otherwise
251 # (e.g. Windows, BSD, Mac).
252 target_link_libraries(libgromacs PRIVATE "${CMAKE_DL_LIBS}")
254 target_link_libraries(libgromacs PRIVATE clFFT)
258 # Recent versions of gcc and clang give warnings on scanner.cpp, which
259 # is a generated source file. These are awkward to suppress inline, so
260 # we do it in the compilation command (after testing that the compiler
261 # supports the suppressions). Same issue exists for nonbonded kernels
262 # so we supress them for all generated files.
263 include(CheckCXXCompilerFlag)
264 check_cxx_compiler_flag("-Wno-unused -Wno-unused-parameter" HAS_NO_UNUSED)
265 check_cxx_compiler_flag(-Wno-missing-declarations HAS_NO_MISSING_DECL)
266 check_cxx_compiler_flag(-Wno-missing-prototypes HAS_NO_MISSING_PROTO)
267 check_cxx_compiler_flag(/wd4101 HAS_NO_MSVC_UNUSED)
269 check_cxx_compiler_flag(-wd1419 HAS_DECL_IN_SOURCE)
272 target_compile_options(libgromacs_generated PRIVATE "-Wno-unused;-Wno-unused-parameter")
274 if (HAS_NO_MISSING_DECL)
275 target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-declarations")
277 # TODO The group scheme kernels don't use proper function prototype
278 # declarations, and clang warns about such use, which we suppress
279 # rather than fix. We would prefer to use no suppressions. However
280 # other compilers do not support such a warning suppression for C++
281 # source files, and issue warnings about that. Remove the use of
282 # -Wno-missing-prototypes here and above when the group scheme is
284 if (HAS_NO_MISSING_PROTO AND "${CMAKE_CXX_COMPILER_ID}" STREQUAL "Clang")
285 target_compile_options(libgromacs_generated PRIVATE "-Wno-missing-prototypes")
287 if (HAS_NO_MSVC_UNUSED)
288 target_compile_options(libgromacs_generated PRIVATE "/wd4101")
290 if (HAS_DECL_IN_SOURCE)
291 target_compile_options(libgromacs_generated PRIVATE "-wd1419")
294 if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
295 # Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
296 # On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
297 # with the SIMD_AVX_512_CXX_FLAGS flags.
298 set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
301 gmx_setup_tng_for_libgromacs()
303 target_link_libraries(libgromacs
306 ${GMX_EXTRA_LIBRARIES}
307 ${GMX_COMMON_LIBRARIES}
308 ${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
309 ${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS}
312 ${GMX_PUBLIC_LIBRARIES}
315 target_link_libraries(libgromacs PUBLIC OpenMP::OpenMP_CXX)
317 set_target_properties(libgromacs PROPERTIES
318 OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
319 SOVERSION ${LIBRARY_SOVERSION_MAJOR}
320 VERSION ${LIBRARY_VERSION}
324 target_link_libraries(libgromacs PRIVATE lmfit)
326 if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" AND CMAKE_CXX_COMPILER_VERSION MATCHES "^6\.0")
327 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Weverything ${IGNORED_CLANG_ALL_WARNINGS}>)
329 if (CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
330 target_compile_options(libgromacs PRIVATE $<$<COMPILE_LANGUAGE:CXX>:/analyze /analyze:stacksize 70000
331 #Control flow warnings are disabled because the commond line output is insufficient. There is no tool
332 #to convert the xml report to e.g. HTML and even in Visual Studio the viewer doesn't work with cmake support.
333 /wd6001 #unitialized memory
334 /wd6011 #derefencing NULL
335 /wd6053 #prior call not zero-terminate
336 /wd6054 #might not be zero-terminated
337 /wd6385 #reading invalid data
338 /wd6386 #buffer overrun
339 /wd6387 #could be '0'
340 /wd28199 #uninitialized memory
341 # For compile time constant (e.g. templates) the following warnings have flase postives
342 /wd6239 #(<non-zero> && <expr>)
343 /wd6240 #(<expr> && <non-zero>)
344 /wd6294 #Ill-defined for-loop
345 /wd6326 #comparison of constant with other constant
346 /wd28020 #expression involving paramter is not true
348 /wd6330 #incorrect type to function (warns for char (instead of unsigned) for isspace/isalpha/isdigit/..))
349 /wd6993 #OpenMP ignored
351 /wd6031 #return value ignored (important - mostly warnigns about sscanf)
352 /wd6244 #hides declaration (known issue - we ingore similar warnings for other compilers)
353 /wd6246 #hides declaration
359 set_target_properties(libgromacs PROPERTIES CXX_CLANG_TIDY
360 "${CLANG_TIDY_EXE};-warnings-as-errors=*")
363 gmx_write_installed_header_list()
365 # Only install the library in mdrun-only mode if it is actually necessary
367 if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
368 install(TARGETS libgromacs
370 LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
371 RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
372 ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
376 if (NOT GMX_BUILD_MDRUN_ONLY)
377 include(InstallLibInfo.cmake)
380 # Technically, the user could want to do this for an OpenCL build
381 # using the CUDA runtime, but currently there's no reason to want to
383 if (INSTALL_CUDART_LIB) #can be set manual by user
385 foreach(CUDA_LIB ${CUDA_LIBRARIES})
386 string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
387 if(IS_CUDART) #libcuda should not be installed
388 #install also name-links (linker uses those)
389 file(GLOB CUDA_LIBS ${CUDA_LIB}*)
390 install(FILES ${CUDA_LIBS} DESTINATION
391 ${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
395 message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
400 # Install the utility headers
401 file(GLOB OPENCL_INSTALLED_FILES
402 gpu_utils/vectype_ops.clh
403 gpu_utils/device_utils.clh
405 install(FILES ${OPENCL_INSTALLED_FILES}
406 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/gpu_utils
408 file(GLOB OPENCL_INSTALLED_FILES
411 install(FILES ${OPENCL_INSTALLED_FILES}
412 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/pbcutil
415 # Install the NB source and headers
416 file(GLOB OPENCL_INSTALLED_FILES
419 install(FILES ${OPENCL_INSTALLED_FILES}
420 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/mdlib
422 file(GLOB OPENCL_INSTALLED_FILES
423 mdlib/nbnxn_ocl/nbnxn_ocl_kernels.cl
424 mdlib/nbnxn_ocl/nbnxn_ocl_kernel.clh
425 mdlib/nbnxn_ocl/nbnxn_ocl_kernel_pruneonly.clh
426 mdlib/nbnxn_ocl/nbnxn_ocl_kernels.clh
427 mdlib/nbnxn_ocl/nbnxn_ocl_kernels_fastgen.clh
428 mdlib/nbnxn_ocl/nbnxn_ocl_kernels_fastgen_add_twincut.clh
429 mdlib/nbnxn_ocl/nbnxn_ocl_kernel_utils.clh
430 mdlib/nbnxn_ocl/nbnxn_ocl_consts.h
432 install(FILES ${OPENCL_INSTALLED_FILES}
433 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/mdlib/nbnxn_ocl
436 # Install the PME source and headers
437 file(GLOB OPENCL_INSTALLED_FILES
441 ewald/pme-gpu-utils.clh
443 ewald/pme-gpu-types.h
445 install(FILES ${OPENCL_INSTALLED_FILES}
446 DESTINATION ${GMX_INSTALL_OCLDIR}/gromacs/ewald