Newer
Older
#
# This file is part of the GROMACS molecular simulation package.
#
# Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
# Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
# and including many others, as listed in the AUTHORS file in the
# top-level source directory and at http://www.gromacs.org.
#
# GROMACS is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public License
# as published by the Free Software Foundation; either version 2.1
# of the License, or (at your option) any later version.
#
# GROMACS is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
# License along with GROMACS; if not, see
# http://www.gnu.org/licenses, or write to the Free Software Foundation,
# Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# If you want to redistribute modifications to GROMACS, please
# consider that scientific software is very special. Version
# control is crucial - bugs must be traceable. We will be happy to
# consider code for inclusion in the official distribution, but
# derived work must not be called official GROMACS. Details are found
# in the README & COPYING files - if they are missing, get the
# official version at http://www.gromacs.org.
#
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
include(${CMAKE_SOURCE_DIR}/Plumed.cmake)
set(LIBGROMACS_SOURCES)
if (GMX_CLANG_CUDA)
include(gmxClangCudaUtils)
endif()
set_property(GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
set_property(GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
set_property(GLOBAL PROPERTY GMX_AVX_512_SOURCE)
function (_gmx_add_files_to_property PROPERTY)
foreach (_file ${ARGN})
if (IS_ABSOLUTE "${_file}")
set_property(GLOBAL APPEND PROPERTY ${PROPERTY} ${_file})
else()
set_property(GLOBAL APPEND PROPERTY ${PROPERTY}
${CMAKE_CURRENT_LIST_DIR}/${_file})
endif()
endforeach()
endfunction ()
function (gmx_add_libgromacs_sources)
_gmx_add_files_to_property(GMX_LIBGROMACS_SOURCES ${ARGN})
endfunction ()
function (gmx_install_headers)
if (NOT GMX_BUILD_MDRUN_ONLY)
file(RELATIVE_PATH _dest ${PROJECT_SOURCE_DIR}/src ${CMAKE_CURRENT_LIST_DIR})
install(FILES ${ARGN}
DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${_dest}"
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
COMPONENT development)
endif()
_gmx_add_files_to_property(GMX_INSTALLED_HEADERS ${ARGN})
endfunction ()
function (gmx_write_installed_header_list)
get_property(_list GLOBAL PROPERTY GMX_INSTALLED_HEADERS)
string(REPLACE ";" "\n" _list "${_list}")
# TODO: Make this only update the file timestamp if the contents actually change.
file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/installed-headers.txt "${_list}")
endfunction()
add_subdirectory(gmxlib)
add_subdirectory(mdlib)
add_subdirectory(applied-forces)
add_subdirectory(listed-forces)
add_subdirectory(commandline)
add_subdirectory(domdec)
add_subdirectory(ewald)
add_subdirectory(fft)
add_subdirectory(gpu_utils)
add_subdirectory(hardware)
add_subdirectory(linearalgebra)
add_subdirectory(math)
add_subdirectory(mdrunutility)
add_subdirectory(mdtypes)
add_subdirectory(onlinehelp)
add_subdirectory(options)
add_subdirectory(pbcutil)
add_subdirectory(random)
add_subdirectory(tables)
add_subdirectory(taskassignment)
add_subdirectory(timing)
add_subdirectory(topology)
add_subdirectory(trajectory)
add_subdirectory(utility)
add_subdirectory(fileio)
add_subdirectory(swap)
add_subdirectory(essentialdynamics)
add_subdirectory(pulling)
add_subdirectory(awh)
add_subdirectory(simd)
add_subdirectory(imd)
if (NOT GMX_BUILD_MDRUN_ONLY)
add_subdirectory(gmxana)
add_subdirectory(gmxpreprocess)
add_subdirectory(correlationfunctions)
add_subdirectory(statistics)
add_subdirectory(analysisdata)
add_subdirectory(selection)
add_subdirectory(trajectoryanalysis)
add_subdirectory(energyanalysis)
add_subdirectory(tools)
endif()
get_property(PROPERTY_SOURCES GLOBAL PROPERTY GMX_LIBGROMACS_SOURCES)
list(APPEND LIBGROMACS_SOURCES ${GMXLIB_SOURCES} ${MDLIB_SOURCES} ${PROPERTY_SOURCES})
# This would be the standard way to include thread_mpi, but
# we want libgromacs to link the functions directly
#if(GMX_THREAD_MPI)
# add_subdirectory(thread_mpi)
#endif()
#target_link_libraries(gmx ${GMX_EXTRA_LIBRARIES} ${THREAD_MPI_LIB})
tmpi_get_source_list(THREAD_MPI_SOURCES ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/src)
list(APPEND LIBGROMACS_SOURCES ${THREAD_MPI_SOURCES})
get_lmfit_properties(LMFIT_SOURCES LMFIT_LIBRARIES_TO_LINK LMFIT_INCLUDE_DIRECTORY LMFIT_INCLUDE_DIR_ORDER)
include_directories(${LMFIT_INCLUDE_DIR_ORDER} SYSTEM "${LMFIT_INCLUDE_DIRECTORY}")
list(APPEND LIBGROMACS_SOURCES ${LMFIT_SOURCES})
configure_file(version.h.cmakein version.h)
gmx_install_headers(
analysisdata.h
commandline.h
options.h
random.h
selection.h
trajectoryanalysis.h
utility.h
${CMAKE_CURRENT_BINARY_DIR}/version.h
)
# This code is here instead of utility/CMakeLists.txt, because CMake
# custom commands and source file properties can only be set in the directory
# that contains the target that uses them.
# TODO: Generate a header instead that can be included from baseversion.c.
# That probably simplifies things somewhat.
set(GENERATED_VERSION_FILE utility/baseversion-gen.c)
gmx_configure_version_file(
utility/baseversion-gen.c.cmakein ${GENERATED_VERSION_FILE}
REMOTE_HASH)
list(APPEND LIBGROMACS_SOURCES ${GENERATED_VERSION_FILE})
# set up CUDA compilation with clang
if (GMX_CLANG_CUDA)
foreach (_file ${LIBGROMACS_SOURCES})
get_filename_component(_ext ${_file} EXT)
if (${_ext} STREQUAL ".cu")
gmx_compile_cuda_file_with_clang(${_file})
endif()
endforeach()
endif()
if (GMX_USE_CUDA)
# Work around FindCUDA that prevents using target_link_libraries()
# with keywords otherwise...
set(CUDA_LIBRARIES PRIVATE ${CUDA_LIBRARIES})
if (NOT GMX_CLANG_CUDA)
cuda_add_library(libgromacs ${LIBGROMACS_SOURCES})
else()
add_library(libgromacs ${LIBGROMACS_SOURCES})
endif()
target_link_libraries(libgromacs PRIVATE ${CUDA_CUFFT_LIBRARIES})
else()
add_library(libgromacs ${LIBGROMACS_SOURCES})
endif()
# Recent versions of gcc and clang give warnings on scanner.cpp, which
# is a generated source file. These are awkward to suppress inline, so
# we do it in the compilation command (after testing that the compiler
# supports the suppressions).
include(CheckCXXCompilerFlag)
check_cxx_compiler_flag(-Wno-unused HAS_NO_UNUSED)
if (HAS_NO_UNUSED)
set(_scanner_cpp_compiler_flags "${_scanner_cpp_compiler_flags} -Wno-unused-parameter -Wno-unused-function")
endif()
set_source_files_properties(selection/scanner.cpp PROPERTIES COMPILE_FLAGS "${_scanner_cpp_compiler_flags}")
if(SIMD_AVX_512_CXX_SUPPORTED AND NOT ("${GMX_SIMD_ACTIVE}" STREQUAL "AVX_512_KNL"))
# Since we might be overriding -march=core-avx2, add a flag so we don't warn for this specific file.
# On KNL this can cause illegal instruction because the compiler might use non KNL AVX instructions
# with the SIMD_AVX_512_CXX_FLAGS flags.
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
set_source_files_properties(hardware/identifyavx512fmaunits.cpp PROPERTIES COMPILE_FLAGS "${SIMD_AVX_512_CXX_FLAGS} ${CXX_NO_UNUSED_OPTION_WARNING_FLAGS}")
endif()
gmx_setup_tng_for_libgromacs()
target_link_libraries(libgromacs
PRIVATE
${EXTRAE_LIBRARIES}
${GMX_EXTRA_LIBRARIES}
${GMX_COMMON_LIBRARIES}
${FFT_LIBRARIES} ${LINEAR_ALGEBRA_LIBRARIES}
${LMFIT_LIBRARIES_TO_LINK}
${THREAD_LIB} ${GMX_SHARED_LINKER_FLAGS} ${OPENCL_LIBRARIES}
${GMX_STDLIB_LIBRARIES}
PUBLIC
${GMX_PUBLIC_LIBRARIES}
${PLUMED_LOAD}
)
set_target_properties(libgromacs PROPERTIES
OUTPUT_NAME "gromacs${GMX_LIBS_SUFFIX}"
SOVERSION ${LIBRARY_SOVERSION_MAJOR}
VERSION ${LIBRARY_VERSION}
COMPILE_FLAGS "${OpenMP_C_FLAGS}")
gmx_write_installed_header_list()
# Only install the library in mdrun-only mode if it is actually necessary
# for the binary
if (NOT GMX_BUILD_MDRUN_ONLY OR BUILD_SHARED_LIBS)
install(TARGETS libgromacs
EXPORT libgromacs
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
COMPONENT libraries)
endif()
if (NOT GMX_BUILD_MDRUN_ONLY)
include(InstallLibInfo.cmake)
endif()
# Technically, the user could want to do this for an OpenCL build
# using the CUDA runtime, but currently there's no reason to want to
# do that.
if (INSTALL_CUDART_LIB) #can be set manual by user
if (GMX_USE_CUDA)
foreach(CUDA_LIB ${CUDA_LIBRARIES})
string(REGEX MATCH "cudart" IS_CUDART ${CUDA_LIB})
if(IS_CUDART) #libcuda should not be installed
#install also name-links (linker uses those)
file(GLOB CUDA_LIBS ${CUDA_LIB}*)
install(FILES ${CUDA_LIBS} DESTINATION
${CMAKE_INSTALL_LIBDIR} COMPONENT libraries)
endif()
endforeach()
else()
message(WARNING "INSTALL_CUDART_LIB only makes sense when configuring for CUDA support")
endif()
endif()
if(GMX_USE_OPENCL)
set(OPENCL_KERNELS ${MDLIB_OPENCL_KERNELS})
install(FILES ${OPENCL_KERNELS} DESTINATION
endif()
if (BUILD_TESTING)
add_subdirectory(compat/tests)
endif()