2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016,2017,2018,2019, 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 cmake_minimum_required(VERSION 3.9.6)
37 # CMake modules/macros are in a subdirectory to keep this file cleaner
38 # This needs to be set before project() in order to pick up toolchain files
39 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
43 include(gmxManageCcache)
45 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
46 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
47 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
49 # Set up common version variables, as well as general information about
50 # the build tree (whether the build is from a source package or from a git
51 # repository). Also declares a few functions that will be used for generating
52 # version info files later.
53 include(gmxBuildTreeInfo)
54 include(gmxVersionInfo)
56 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
57 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
59 if("${CMAKE_INSTALL_PREFIX}" STREQUAL "${CMAKE_BINARY_DIR}")
60 message(FATAL_ERROR "GROMACS cannot be installed into the build tree, choose a different location for CMAKE_INSTALL_PREFIX")
63 include(gmxBuildTypeReference)
64 include(gmxBuildTypeProfile)
65 include(gmxBuildTypeTSAN)
66 include(gmxBuildTypeASAN)
67 include(gmxBuildTypeMSAN)
68 include(gmxBuildTypeReleaseWithAssert)
70 if(NOT CMAKE_BUILD_TYPE)
71 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile TSAN ASAN MSAN." FORCE)
72 # Set the possible values of build type for cmake-gui
73 set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
74 "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile" "TSAN" "ASAN" "MSAN")
76 if(CMAKE_CONFIGURATION_TYPES)
77 # Add appropriate GROMACS-specific build types for the Visual
78 # Studio generator (Debug, Release, MinSizeRel and RelWithDebInfo
79 # are already present by default).
80 list(APPEND CMAKE_CONFIGURATION_TYPES "RelWithAssert" "Reference")
81 list(REMOVE_DUPLICATES CMAKE_CONFIGURATION_TYPES)
82 set(CMAKE_CONFIGURATION_TYPES "${CMAKE_CONFIGURATION_TYPES}" CACHE STRING
83 "List of configuration types"
86 set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBINFO RELWITHASSERT MINSIZEREL PROFILE)
88 set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
90 include(gmxCTestUtilities)
93 include(gmxCPackUtilities)
96 # Variables that accumulate stuff influencing the installed headers
97 set(INSTALLED_HEADER_INCLUDE_DIRS "")
98 set(INSTALLED_HEADER_DEFINITIONS "")
100 ########################################################################
101 # Global non-cache variables for implementing the build system
102 ########################################################################
104 # These variables collect libraries that GROMACS requires for
105 # linking. They should be appended to with list(APPEND ${name}
106 # new-library) calls. They are:
107 # - Libraries that are required for libgromacs (only)
108 set(GMX_EXTRA_LIBRARIES "")
109 # - Libraries that are required for all code in the repository
110 set(GMX_COMMON_LIBRARIES "")
111 # - Libraries that all code linked against libgromacs needs
112 # (i.e., something that is exposed in installed headers).
113 set(GMX_PUBLIC_LIBRARIES "")
115 ########################################################################
116 # Check and warn if cache generated on a different host is being reused
117 ########################################################################
119 execute_process(COMMAND hostname
120 OUTPUT_VARIABLE TMP_HOSTNAME
121 OUTPUT_STRIP_TRAILING_WHITESPACE)
122 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
124 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
125 is being reused! This could lead to inconsistencies; therefore, it is
126 recommended to regenerate the cache!")
128 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
129 "Hostname of the machine where the cache was generated.")
132 ########################################################################
133 # Detect architecture before setting options so we can alter defaults
134 ########################################################################
135 # Detect the architecture the compiler is targetting, detect
136 # SIMD instructions possibilities on that hardware, suggest SIMD instruction set
137 # to use if none is specified, and populate the cache option for CPU
139 include(gmxDetectTargetArchitecture)
140 gmx_detect_target_architecture()
142 # Permit the user to specify a particular standard library, e.g. compiling
143 # with "-stdlib=libc++" and linking with "-lc++abi -lc++" to get clang's libcxx.
144 set(GMX_STDLIB_CXX_FLAGS "" CACHE STRING "Compiler flag for a C++ standard library flavour")
145 set(GMX_STDLIB_LIBRARIES "" CACHE STRING "Linker libraries for a particular C++ standard library")
146 mark_as_advanced(GMX_STDLIB_CXX_FLAGS)
147 mark_as_advanced(GMX_STDLIB_LIBRARIES)
149 include(CheckCCompilerFlag)
150 include(CheckCXXCompilerFlag)
152 # This must come early, since some of our configuration flag tests
153 # depend on being able to compile C++11 source files.
154 include(gmxTestCXX11)
155 gmx_test_cxx11(GMX_CXX11_FLAGS GMX_STDLIB_CXX_FLAGS GMX_STDLIB_LIBRARIES)
157 # Make sure all C++ code will be compiled in C++11 mode, with the
158 # expected standard library.
159 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GMX_CXX11_FLAGS} ${GMX_STDLIB_CXX_FLAGS}")
161 ########################################################################
162 # User input options #
163 ########################################################################
164 include(gmxOptionUtilities)
166 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
168 # Fujitsu only has SIMD in double precision, so this will be faster
169 gmx_set_boolean(GMX_DOUBLE_DEFAULT GMX_TARGET_FUJITSU_SPARC64)
170 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" ${GMX_DOUBLE_DEFAULT})
171 option(GMX_RELAXED_DOUBLE_PRECISION "Accept single precision 1/sqrt(x) when using Fujitsu HPC-ACE SIMD" OFF)
172 mark_as_advanced(GMX_RELAXED_DOUBLE_PRECISION)
174 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
175 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
176 gmx_dependent_option(
178 "Enable MPI_IN_PLACE for MPIs that have it defined"
181 mark_as_advanced(GMX_MPI_IN_PLACE)
183 option(GMX_MIMIC "Enable MiMiC QM/MM interface (CPMD is required)" OFF)
185 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
186 mark_as_advanced(GMX_FAHCORE)
188 option(GMX_COOL_QUOTES "Enable GROMACS cool quotes" ON)
189 mark_as_advanced(GMX_COOL_QUOTES)
190 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
192 option(GMX_USE_OPENCL "Enable OpenCL acceleration" OFF)
194 # Decide on GPU settings based on user-settings and GPU/CUDA
195 # detection. VS2017 requires CUDA 9.0, for the other arch/compilers
196 # rest we require CUDA 7.0 or later (including for clang-CUDA).
198 set(REQUIRED_CUDA_VERSION 9.0)
200 set(REQUIRED_CUDA_VERSION 7.0)
202 set(REQUIRED_CUDA_COMPUTE_CAPABILITY 3.0)
204 # OpenCL required version: 1.2 or newer
205 set(REQUIRED_OPENCL_MIN_VERSION_MAJOR 1)
206 set(REQUIRED_OPENCL_MIN_VERSION_MINOR 2)
207 set(REQUIRED_OPENCL_MIN_VERSION ${REQUIRED_OPENCL_MIN_VERSION_MAJOR}.${REQUIRED_OPENCL_MIN_VERSION_MINOR})
209 if(NOT GMX_USE_OPENCL)
210 # CUDA detection is done only if GMX_USE_OPENCL is OFF.
211 include(gmxManageGPU)
212 set(GMX_USE_CUDA ${GMX_GPU})
214 set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_CUDA")
216 set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_NONE")
219 #Now the OpenCL path (for both AMD and NVIDIA)
221 include(gmxManageOpenCL)
222 set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_OPENCL")
224 message(FATAL_ERROR "OpenCL requested but GPU option is not enabled (try -DGMX_GPU=on) ")
228 gmx_option_multichoice(
230 "SIMD instruction set for CPU kernels and compiler optimization"
232 AUTO None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX2_128 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
235 set(GMX_FFT_LIBRARY_DEFAULT "mkl")
237 set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
240 gmx_option_multichoice(
243 "${GMX_FFT_LIBRARY_DEFAULT}"
244 fftw3 mkl "fftpack[built-in]")
245 gmx_dependent_option(
247 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
249 "GMX_FFT_LIBRARY STREQUAL FFTW3")
250 gmx_dependent_option(
251 GMX_DISABLE_FFTW_MEASURE
252 "Do not optimize FFTW setups (not needed with SSE)"
254 "GMX_FFT_LIBRARY STREQUAL FFTW3")
255 mark_as_advanced(GMX_BUILD_OWN_FFTW)
256 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
258 gmx_option_multichoice(
260 "QM package for QM/MM"
262 none gaussian mopac gamess orca)
264 gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
265 gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
267 # This should be moved to a separate NBNXN cmake module when that code is cleaned up and modularized
269 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
270 mark_as_advanced(GMX_BROKEN_CALLOC)
272 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
274 option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
276 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
278 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
279 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
281 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
282 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
284 option(GMX_BUILD_FOR_COVERAGE
285 "Tune build for better code coverage metrics (e.g., disable asserts)"
287 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
289 option(GMX_DEVELOPER_BUILD
290 "Enable Developer convenience features: always build unit-tests"
292 mark_as_advanced(GMX_DEVELOPER_BUILD)
294 gmx_set_boolean(GMX_COMPILER_WARNINGS_DEFAULT "NOT SOURCE_IS_SOURCE_DISTRIBUTION")
295 option(GMX_COMPILER_WARNINGS
296 "Enable a default set of compiler warnings"
297 ${GMX_COMPILER_WARNINGS_DEFAULT})
298 mark_as_advanced(GMX_COMPILER_WARNINGS)
299 # Always turn on compiler warnings with a developer build.
300 gmx_add_cache_dependency(GMX_COMPILER_WARNINGS BOOL "NOT GMX_DEVELOPER_BUILD" ON)
302 option(GMX_BUILD_SHARED_EXE
303 "Build exectuables as shared binaries. If not set, this disables rpath and dynamic linker flags in an attempt to build a static binary, but this may require setting up the toolchain properly and making appropriate libraries available."
305 mark_as_advanced(GMX_BUILD_SHARED_EXE)
307 option(GMX_PHYSICAL_VALIDATION
308 "Include physical validation tests in ctest environment. These can then be called using 'make check-phys' or
309 'make check-all'. Warning: Running the physical validation tests takes significantly more time than other tests!"
311 mark_as_advanced(GMX_PHYSICAL_VALIDATION)
313 ######################################################################
314 # Detect OpenMP support
315 ######################################################################
316 # The OpenMP detection _must_ come before tests for other CFLAGS.
317 include(gmxManageOpenMP)
321 ######################################################################
323 # These need to be done early (before further tests).
324 #####################################################################
329 # This variable should be used for additional compiler flags which are not
330 # generated in gmxCFlags nor are SIMD or MPI related.
332 # TODO These variables should be consolidated into
333 # EXTRA_COMPILER_FLAGS so that we we don't perpetrate bugs where
334 # things that work in C compilation (e.g. merging from old branches)
335 # also work for C++ compilation.
336 set(EXTRA_C_FLAGS "")
337 set(EXTRA_CXX_FLAGS "")
339 # Run through a number of tests for buggy compilers and other issues
340 include(gmxTestCompilerProblems)
341 gmx_test_compiler_problems()
343 # Implement double-precision option. This is complicated because we
344 # need installed headers to use the precision mode of the build that
345 # produced the library, but cannot use config.h in that case. We also
346 # want such variables to always have a definition, because #if is more
347 # robust than #ifdef. So, we put this value on the compiler command
350 # GMX_RELAXED_DOUBLE_PRECISION does not need to be handled here,
351 # because no installed header needs it
353 set(GMX_DOUBLE_VALUE 1)
355 set(GMX_DOUBLE_VALUE 0)
357 add_definitions(-DGMX_DOUBLE=${GMX_DOUBLE_VALUE})
358 list(APPEND INSTALLED_HEADER_DEFINITIONS "-DGMX_DOUBLE=${GMX_DOUBLE_VALUE}")
361 list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
362 add_definitions(-DGMX_HAVE_WINSOCK)
367 ########################################################################
368 # Basic system tests (standard libraries, headers, functions, types) #
369 ########################################################################
370 include(CheckIncludeFiles)
371 include(CheckIncludeFileCXX)
372 check_include_files(unistd.h HAVE_UNISTD_H)
373 check_include_files(pwd.h HAVE_PWD_H)
374 check_include_files(dirent.h HAVE_DIRENT_H)
375 check_include_files(time.h HAVE_TIME_H)
376 check_include_files(sys/time.h HAVE_SYS_TIME_H)
377 check_include_files(io.h HAVE_IO_H)
378 check_include_files(sched.h HAVE_SCHED_H)
380 check_include_files(regex.h HAVE_POSIX_REGEX)
381 # TODO: It could be nice to inform the user if no regex support is found,
382 # as selections won't be fully functional.
384 include(CheckCXXSymbolExists)
385 check_cxx_symbol_exists(gettimeofday sys/time.h HAVE_GETTIMEOFDAY)
386 check_cxx_symbol_exists(sysconf unistd.h HAVE_SYSCONF)
387 check_cxx_symbol_exists(nice unistd.h HAVE_NICE)
388 check_cxx_symbol_exists(fsync unistd.h HAVE_FSYNC)
389 check_cxx_symbol_exists(_fileno stdio.h HAVE__FILENO)
390 check_cxx_symbol_exists(fileno stdio.h HAVE_FILENO)
391 check_cxx_symbol_exists(_commit io.h HAVE__COMMIT)
392 check_cxx_symbol_exists(sigaction signal.h HAVE_SIGACTION)
394 # We cannot check for the __builtins as symbols, but check if code compiles
395 check_cxx_source_compiles("int main(){ return __builtin_clz(1);}" HAVE_BUILTIN_CLZ)
396 check_cxx_source_compiles("int main(){ return __builtin_clzll(1);}" HAVE_BUILTIN_CLZLL)
398 check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned long i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE)
399 check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned __int64 i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE64)
400 elseif(CMAKE_CXX_COMPILER_ID MATCHES "XL")
401 check_cxx_source_compiles("int main(){ return __cntlz4(1);}" HAVE_CNTLZ4)
402 check_cxx_source_compiles("int main(){ return __cntlz8(1);}" HAVE_CNTLZ8)
405 include(CheckLibraryExists)
406 find_library(HAVE_LIBM m)
407 mark_as_advanced(HAVE_LIBM)
408 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
409 check_library_exists(m feenableexcept "" HAVE_FEENABLEEXCEPT)
410 check_library_exists(m fedisableexcept "" HAVE_FEDISABLEEXCEPT)
412 include(TestSchedAffinity)
413 test_sched_affinity(HAVE_SCHED_AFFINITY)
415 # Aligned memory allocation. We need to check for both mm_malloc(),
416 # posix_memalign(), memalign(), and on windows also _aligned_malloc()
417 include(gmxTestMMMalloc)
418 gmx_test_mm_malloc(HAVE__MM_MALLOC)
419 check_cxx_symbol_exists(posix_memalign stdlib.h HAVE_POSIX_MEMALIGN)
420 check_cxx_symbol_exists(memalign stdlib.h HAVE_MEMALIGN)
422 # No need to waste time on this test on platforms where it will never be true
423 check_cxx_symbol_exists(_aligned_malloc stdlib.h HAVE__ALIGNED_MALLOC)
426 include(TestBigEndian)
427 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
429 gmx_set_boolean(GMX_USE_NICE "HAVE_UNISTD_H AND HAVE_NICE")
431 # Management of GROMACS options for specific toolchains should go
432 # here. Because the initial settings for some of the main options have
433 # already happened, but things like library detection and MPI compiler
434 # feature detection have not, the docstrings for any over-rides of
435 # GROMACS defaults or user settings will make sense. Also, any
436 # toolchain-related reasons for choosing whether to detect various
437 # things can be sorted out now, before the detection takes place.
438 if(GMX_TARGET_FUJITSU_SPARC64)
439 include(gmxManageFujitsuSparc64)
442 ########################################################################
443 #Process MPI settings
444 ########################################################################
445 include(gmxManageMPI)
447 ########################################################################
448 #Process MiMiC settings
449 ########################################################################
450 include(gmxManageMimic)
452 ########################################################################
453 #Process shared/static library settings
454 ########################################################################
455 include(gmxManageSharedLibraries)
458 ########################################################################
459 # Find external packages #
460 ########################################################################
462 # Unconditionally find the package, as it is also required for unit
463 # tests. This exports LIBXML2_FOUND, which we should not use because
464 # it does not tell us that linking will succeed. Instead, we test that
466 #if(DEFINED LIBXML2_LIBRARIES)
467 # set(LibXml2_FIND_QUIETLY TRUE)
469 #find_package(LibXml2)
470 #include(gmxTestLibXml2)
471 #gmx_test_libxml2(HAVE_LIBXML2)
472 #option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${HAVE_LIBXML2})
474 #mark_as_advanced(GMX_XML)
475 # Don't actually do anything, since libxml2 is currently not used by libgromacs
476 #if(GMX_XML AND NOT HAVE_LIBXML2)
477 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
480 # include_directories(${LIBXML2_INCLUDE_DIR})
481 # set(PKG_XML libxml-2.0)
482 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
487 "Use hwloc portable hardware locality library"
491 # Find quietly the second time.
492 if(DEFINED HWLOC_LIBRARIES)
493 set(Hwloc_FIND_QUIETLY TRUE)
495 find_package(Hwloc 1.5)
498 if (HWLOC_LIBRARIES MATCHES ".a$")
499 set(_STATIC_HWLOC TRUE)
502 gmx_check_if_changed(HWLOC_FOUND_CHANGED HWLOC_FOUND)
503 if (_STATIC_HWLOC AND HWLOC_FOUND_CHANGED)
504 message(STATUS "Static hwloc library found, will not attempt using it as it could lead to link-time errors. To use the detected library, manually set GMX_HWLOC=ON and you will likely have to pass appropriate linker flags too to satisfy the link-time dependencies of your hwloc library. Try \"pkg-config --libs --static hwloc\" for suggestions on what you will need.")
505 set(GMX_USE_HWLOC OFF)
507 set(GMX_USE_HWLOC ON)
511 include_directories(SYSTEM ${HWLOC_INCLUDE_DIRS})
512 list(APPEND GMX_EXTRA_LIBRARIES ${HWLOC_LIBRARIES})
514 elseif(GMX_HWLOC_FORCE)
515 message(FATAL_ERROR "Hwloc package support required, but not found.")
519 option(GMX_EXTERNAL_TINYXML2 "Use external TinyXML-2 instead of compiling the version bundled with GROMACS." OFF)
520 mark_as_advanced(GMX_EXTERNAL_TINYXML2)
521 if(GMX_EXTERNAL_TINYXML2)
522 # Find an external TinyXML-2 library.
523 find_package(TinyXML-2 3.0.0)
524 set(HAVE_TINYXML2 ${TinyXML2_FOUND})
525 if(NOT HAVE_TINYXML2)
526 message(FATAL_ERROR "External TinyXML-2 could not be found, please adjust your search paths")
530 option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
531 mark_as_advanced(GMX_EXTRAE)
536 include_directories(SYSTEM ${EXTRAE_INCLUDE_DIR})
539 message(FATAL_ERROR "EXTRAE library was not found. Please add the correct path to CMAKE_PREFIX_PATH")
543 option(GMX_X11 "Use X window system" OFF)
546 # X11 includes/libraries are only set in the ngmx subdirectory!
549 "X11 include files and/or libraries were not found. "
550 "Set GMX_X11=OFF to compile without X11 support. "
551 "gmx view will not be available.")
553 include_directories(SYSTEM ${X11_INCLUDE_DIR})
557 # Enable core threading facilities
558 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include")
560 # enable MPI functions
562 set(MPI_IN_PLACE_EXISTS 1)
564 # If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
565 if (TMPI_ATOMICS_DISABLED)
566 add_definitions(-DTMPI_ATOMICS_DISABLED)
569 include(gmxManageTNG)
571 include(gmxManageLmfit)
574 # now that we have detected the dependencies, do the second configure pass
577 list(APPEND GMX_EXTRA_LIBRARIES ${GMX_CUDA_CLANG_LINK_LIBS})
578 link_directories("${GMX_CUDA_CLANG_LINK_DIRS}")
587 set(GMX_NATIVE_WINDOWS 1)
588 # This makes windows.h not declare min/max as macros that would break
589 # C++ code using std::min/std::max.
590 add_definitions(-DNOMINMAX)
593 if(CMAKE_SYSTEM_NAME STREQUAL "Darwin") #Work-around for cmake bug #10837
594 if (CMAKE_COMPILER_IS_GNUCC OR CMAKE_C_COMPILER_ID MATCHES "Intel" OR CMAKE_C_COMPILER_ID MATCHES "Clang")
595 set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
597 if (CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Intel" OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
598 set(CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem ")
602 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING" ON)
603 mark_as_advanced(GMX_BUILD_UNITTESTS)
604 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
606 ########################################################################
607 # Our own GROMACS tests
608 ########################################################################
610 add_definitions( -DHAVE_CONFIG_H )
611 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
612 # TODO required at high level because both libgromacs and progs/mdrun
613 # require it, both for thread-MPI and its atomics and mutexes.
614 include_directories(BEFORE SYSTEM ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
615 # Required for config.h, maybe should only be set in src/CMakeLists.txt
616 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
618 include(gmxTestInlineASM)
619 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
621 include(gmxSetBuildInformation)
622 gmx_set_build_information()
624 gmx_option_multichoice(
626 "Use low-latency RDTSCP instruction for CPU-based timers for mdrun execution; might need to be off when compiling for heterogeneous environments)"
629 mark_as_advanced(GMX_USE_RDTSCP)
631 macro(gmx_check_rdtscp)
632 if (CPU_DETECTION_FEATURES MATCHES "rdtscp")
634 set(RDTSCP_DETECTION_MESSAGE " - detected on the build host")
636 set(RDTSCP_DETECTION_MESSAGE " - not detected on the build host")
641 if (GMX_USE_RDTSCP STREQUAL "ON")
643 elseif(GMX_USE_RDTSCP STREQUAL "DETECT")
645 elseif(GMX_USE_RDTSCP STREQUAL "AUTO")
646 # If the user specified automated SIMD selection, that the choice
647 # is made based on detection on the build host. If so, then RDTSCP
648 # should be chosen the same way.
650 # If the user specified an AVX SIMD level (e.g. when
651 # cross-compiling GROMACS) then they will get our best guess, ie
652 # that in practice AVX mostly correlates with rdtscp (and anyway
653 # is only relevant in rather old x86 hardware).
654 if (GMX_SIMD STREQUAL "AUTO")
656 elseif (GMX_SIMD MATCHES "AVX")
660 gmx_check_if_changed(HAVE_RDTSCP_CHANGED HAVE_RDTSCP)
661 if (HAVE_RDTSCP_CHANGED)
663 message(STATUS "Enabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
665 message(STATUS "Disabling RDTSCP support${RDTSCP_DETECTION_MESSAGE}")
669 include(gmxTestLargeFiles)
670 gmx_test_large_files(GMX_LARGEFILES)
672 include(gmxTestSignal)
673 gmx_test_sigusr1(HAVE_SIGUSR1)
675 include(gmxTestPipes)
676 gmx_test_pipes(HAVE_PIPES)
678 check_include_file_cxx(regex HAVE_CXX11_REGEX)
681 gmx_test_xdr(GMX_SYSTEM_XDR)
682 # Darwin has system XDR, but it uses a three-argument flavour of
683 # xdrproc_t that it guarantees will still work if you pass the normal
684 # two-argument xdr filters, but gcc 8 warns about the cast necessary
685 # to do that, so it's simpler to just use our own XDR library.
687 # TODO It would be better to craft a cmake test which fails if such
688 # XDR operations cause warnings, and succeeds otherwise, because it is
689 # generally preferable to use system libraries where possible.
690 if(NOT GMX_SYSTEM_XDR OR CMAKE_SYSTEM_NAME STREQUAL "Darwin")
691 set(GMX_INTERNAL_XDR 1)
695 ##################################################
696 # Process SIMD instruction settings
697 ##################################################
698 # This checks what flags to add in order to
699 # support the SIMD instructions we need, it sets
700 # correct defines for the SIMD instructions supported,
701 # and adds advanced options to control accuracy
702 # for SIMD math operations.
703 include(gmxManageSimd)
706 include(gmxManageCycleCounters)
707 gmx_manage_cycle_counters()
709 # Process QM/MM Settings
710 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
711 set(GMX_QMMM_GAUSSIAN 1)
712 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
713 set(GMX_QMMM_MOPAC 1)
714 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
715 set(GMX_QMMM_GAMESS 1)
716 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
718 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
721 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
725 ##################################################
726 # Process FFT library settings
727 ##################################################
728 include(gmxManageFFTLibraries)
731 include(gmxManageLinearAlgebraLibraries)
733 include(gmxManagePluginSupport)
736 if(NOT GMX_VMD_PLUGIN_PATH)
741 # Link real-time library for POSIX timers. The check for clock_gettime
742 # confirms the linkability of rt.
743 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
744 list(APPEND GMX_EXTRA_LIBRARIES rt)
747 # Math and thread libraries must often come after all others when linking...
749 list(APPEND GMX_PUBLIC_LIBRARIES m)
752 option(GMX_NACL "Configure for Native Client builds" OFF)
754 list(APPEND GMX_EXTRA_LIBRARIES nosys)
755 set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
756 # TODO: Is this still necessary with the check for its presence?
760 mark_as_advanced(GMX_NACL)
763 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
764 "Path to swindirect.h")
765 include_directories(${COREWRAP_INCLUDE_DIR})
768 # Value of GMX_BUILD_HELP=AUTO tries to generate things, but will only
769 # produce warnings if that fails.
770 set(build_help_default AUTO)
771 if (SOURCE_IS_SOURCE_DISTRIBUTION OR CMAKE_CROSSCOMPILING)
772 set(build_help_default OFF)
774 gmx_option_trivalue(GMX_BUILD_HELP "Build completions automatically (requires that compiled binaries can be executed on the build host) and install man pages if built (requires building the 'man' target manually)" ${build_help_default})
775 mark_as_advanced(GMX_BUILD_HELP)
776 if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND BUILD_IS_INSOURCE)
778 "Rebuilding shell completions or man pages is not supported for "
779 "in-source builds from a source distribution. "
780 "Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
783 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
784 # these are set after everything else
785 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
786 set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
787 set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
788 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
789 set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
791 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
792 message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
793 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
794 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
795 message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
796 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
797 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
798 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
799 message("CMAKE_SHARED_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
802 ########################################################################
803 # Specify install locations
804 ########################################################################
805 # Use GNUInstallDirs to set paths on multiarch systems.
806 include(GNUInstallDirs)
808 set(GMX_INSTALL_DATASUBDIR "gromacs" CACHE STRING "Subdirectory for GROMACS data under CMAKE_INSTALL_DATADIR")
809 mark_as_advanced(GMX_INSTALL_DATASUBDIR)
811 # Internal convenience so we do not have to join two path segments in the code
812 set(GMX_INSTALL_GMXDATADIR ${CMAKE_INSTALL_DATADIR}/${GMX_INSTALL_DATASUBDIR})
814 # If the nesting level wrt. the installation root is changed,
815 # gromacs-config.cmake.cmakein needs to be adapted.
816 set(GMX_INSTALL_CMAKEDIR ${CMAKE_INSTALL_DATAROOTDIR}/cmake)
818 # TODO: Make GMXRC adapt if this is changed
819 set(GMX_INSTALL_PKGCONFIGDIR ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
820 set(GMX_INSTALL_OCLDIR ${GMX_INSTALL_GMXDATADIR}/opencl)
822 list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${CMAKE_INSTALL_INCLUDEDIR})
824 # Binary and library suffix options
825 include(gmxManageSuffixes)
827 ################################################################
828 # Shared library load path settings
829 ################################################################
830 if(NOT GMX_BUILD_SHARED_EXE)
832 set(CMAKE_SKIP_RPATH TRUE)
833 set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) # remove -Wl,-Bdynamic
834 set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
836 # The build folder always has bin/ and lib/; if we are also going to
837 # install to lib/, then the installation RPATH works also in the build
838 # tree. This makes installation slightly faster (no need to rewrite the
839 # RPATHs), and makes the binaries in the build tree relocatable.
840 if(CMAKE_INSTALL_LIBDIR STREQUAL "lib")
841 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
843 cmake_policy(SET CMP0068 NEW) # From CMake-3.9
844 set(CMAKE_BUILD_WITH_INSTALL_NAME_DIR TRUE)
847 # Set the RPATH as relative to the executable location to make the
848 # binaries relocatable.
849 if(CMAKE_SYSTEM_NAME STREQUAL "Darwin") #Assume OS X >=10.5
850 set(CMAKE_INSTALL_RPATH "@loader_path/../${CMAKE_INSTALL_LIBDIR}")
851 set(CMAKE_INSTALL_NAME_DIR ${CMAKE_INSTALL_RPATH})
853 set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${CMAKE_INSTALL_LIBDIR}")
855 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
856 set(CMAKE_MACOSX_RPATH 1)
859 #COPYING file: Only necessary for binary distributions.
860 #Simpler to always install.
861 install(FILES COPYING DESTINATION ${GMX_INSTALL_GMXDATADIR} COMPONENT data)
863 if (GMX_BUILD_FOR_COVERAGE)
864 # Code heavy with asserts makes conditional coverage close to useless metric,
865 # as by design most of the false branches are impossible to trigger in
866 # correctly functioning code. And the benefit of testing those that could
867 # be triggered by using an API against its specification isn't usually
869 add_definitions(-DNDEBUG -DGMX_DISABLE_ASSERTS)
873 include(tests/CheckTarget.cmake)
876 if (NOT GMX_BUILD_MDRUN_ONLY)
877 find_package(ImageMagick QUIET COMPONENTS convert)
878 include(gmxTestImageMagick)
879 GMX_TEST_IMAGEMAGICK(IMAGE_CONVERT_POSSIBLE)
880 add_subdirectory(docs)
881 add_subdirectory(share)
882 add_subdirectory(scripts)
884 add_subdirectory(src)
887 add_subdirectory(tests)
890 gmx_cpack_write_config()
892 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
893 # Don't bother the user after the first configure pass.
894 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
895 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
897 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
899 #######################
901 #######################
902 CONFIGURE_FILE( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
903 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
905 ###########################
906 ADD_CUSTOM_TARGET(uninstall
907 "${CMAKE_COMMAND}" -P
908 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
909 ###########################
910 set_directory_properties(PROPERTIES
911 ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")