2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2009,2010,2011,2012,2013,2014, 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 2.8.8)
36 # When we require cmake >= 2.8.12, it will provide
37 # CMAKE_MINIMUM_REQUIRED_VERSION automatically, but in the meantime we
38 # need to set a variable, and it must have a different name.
39 set(GMX_CMAKE_MINIMUM_REQUIRED_VERSION "2.8.8")
41 # CMake modules/macros are in a subdirectory to keep this file cleaner
42 # This needs to be set before project() in order to pick up toolchain files
43 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
47 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
48 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
49 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
51 # PROJECT_VERSION should have the following structure:
52 # VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
54 # The "-dev" suffix is important to keep because it makes possible to distinguish
55 # between a build from official release and a build from git release branch on a
56 # machine with no git.
58 # NOTE: when releasing the "-dev" suffix needs to be stripped off!
59 # REGRESSIONTEST_VERSION and REGRESSIONTEST_BRANCH should always be
61 set(PROJECT_VERSION "5.1-dev")
62 # If this is a released tarball, "-dev" will not be present in
63 # PROJECT_VERSION, and REGRESSIONTEST_VERSION specifies the version
64 # number of the regressiontest tarball against which the code tarball
65 # can be tested. This will be the version of the last patch release.
66 set(REGRESSIONTEST_VERSION "5.0.1-dev")
67 # If this is not a released tarball, "-dev" will be present in
68 # PROJECT_VERSION, and REGRESSIONTEST_BRANCH specifies the name of the
69 # gerrit.gromacs.org branch whose HEAD can test this code, *if* this
70 # code contains all recent fixes from the corresponding code branch.
71 set(REGRESSIONTEST_BRANCH "refs/heads/master")
73 set(CUSTOM_VERSION_STRING ""
74 CACHE STRING "Custom version string (if empty, use hard-coded default)")
75 mark_as_advanced(CUSTOM_VERSION_STRING)
76 if (CUSTOM_VERSION_STRING)
77 set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
79 set(LIBRARY_SOVERSION 1)
80 set(LIBRARY_VERSION ${LIBRARY_SOVERSION}.0.0)
81 # It is a bit irritating, but this has to be set separately for now!
82 SET(CPACK_PACKAGE_VERSION_MAJOR "5")
83 SET(CPACK_PACKAGE_VERSION_MINOR "1")
84 #SET(CPACK_PACKAGE_VERSION_PATCH "0")
86 # The numerical gromacs version. It is 40600 for 4.6.0.
87 # The #define GMX_VERSION in gromacs/version.h is set to this value.
89 "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
90 if(CPACK_PACKAGE_VERSION_PATCH)
92 "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
95 # The API version tracks the numerical Gromacs version (for now).
96 # It is potentially different from the Gromacs version in the future, if
97 # the programs/libraries diverge from the presumably more stable API.
98 # The #define GMX_API_VERSION in version.h is set to this value to
99 # provide backward compatibility of software written against the Gromacs API.
100 set(API_VERSION ${NUM_VERSION})
102 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
103 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
106 include(gmxBuildTypeReference)
107 include(gmxBuildTypeProfile)
108 include(gmxBuildTypeTSAN)
109 include(gmxBuildTypeASAN)
110 include(gmxBuildTypeReleaseWithAssert)
112 if(NOT CMAKE_BUILD_TYPE)
113 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile." FORCE)
114 # There's no need to offer a user the choice of ThreadSanitizer
115 # Set the possible values of build type for cmake-gui
116 set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
117 "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile")
119 if(CMAKE_CONFIGURATION_TYPES)
120 # Add appropriate GROMACS-specific build types for the Visual
121 # Studio generator (Debug, Release, MinSizeRel and RelWithDebInfo
122 # are already present by default).
123 list(APPEND CMAKE_CONFIGURATION_TYPES "RelWithAssert" "Reference")
124 list(REMOVE_DUPLICATES CMAKE_CONFIGURATION_TYPES)
125 set(CMAKE_CONFIGURATION_TYPES "${CMAKE_CONFIGURATION_TYPES}" CACHE STRING
126 "List of configuration types"
129 set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBUGINFO RELWITHASSERT MINSIZEREL PROFILE)
134 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
135 set(CPACK_PACKAGE_VENDOR "gromacs.org")
136 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
137 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
138 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
139 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
140 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
141 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
142 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
143 # CPack source archives include only the directories we list here.
144 # This variable is a list of pairs of names of source and destination
145 # directories. Most of these are used for content GROMACS generates as
146 # part of the configuration or build.
147 set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/share/man/man1;share/man/man1;${CMAKE_BINARY_DIR}/share/man/man7;share/man/man7;${CMAKE_BINARY_DIR}/share/html/final;share/html/final;${CMAKE_BINARY_DIR}/install-guide/final;/")
148 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
150 #must come after all cpack settings!
153 # Set a default valgrind suppression file.
154 # This unfortunately needs to duplicate information from CTest to work as
156 set(MEMORYCHECK_SUPPRESSIONS_FILE
157 "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
159 "File that contains suppressions for the memory checker")
162 set(SOURCE_IS_GIT_REPOSITORY OFF)
163 set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
164 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
165 set(SOURCE_IS_GIT_REPOSITORY ON)
167 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
168 set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
171 ########################################################################
172 # Check and warn if cache generated on a different host is being reused
173 ########################################################################
175 execute_process(COMMAND hostname
176 OUTPUT_VARIABLE TMP_HOSTNAME
177 OUTPUT_STRIP_TRAILING_WHITESPACE)
178 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
180 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
181 is being reused! This could lead to inconsitencies; therefore, it is
182 recommended to regenerate the cache!")
184 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
185 "Hostname of the machine where the cache was generated.")
188 ########################################################################
189 # User input options #
190 ########################################################################
191 include(gmxOptionUtilities)
193 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
195 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
196 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
197 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
198 gmx_dependent_option(
200 "Enable MPI_IN_PLACE for MPIs that have it defined"
203 mark_as_advanced(GMX_MPI_IN_PLACE)
204 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
205 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
206 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
207 mark_as_advanced(GMX_FAHCORE)
209 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
210 mark_as_advanced(GMX_COOL_QUOTES)
211 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
213 # Decide on GPU settings based on user-settings and GPU/CUDA detection.
214 # We support CUDA >=v4.0 on *nix, but <= v4.1 doesn't work with MSVC
216 set(REQUIRED_CUDA_VERSION 4.1)
218 set(REQUIRED_CUDA_VERSION 4.0)
220 set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
221 include(gmxManageGPU)
223 # Detect the architecture the compiler is targetting, detect
224 # SIMD instructions possibilities on that hardware, suggest SIMD instruction set
225 # to use if none is specified, and populate the cache option for CPU
227 include(gmxDetectTargetArchitecture)
228 gmx_detect_target_architecture()
230 if(GMX_CPU_ACCELERATION)
231 # Stay compatible with old Jenkins command line options for specific SIMD acceleration
232 set(GMX_SIMD "${GMX_CPU_ACCELERATION}" CACHE STRING "SIMD instruction set level and compiler optimization" FORCE)
233 message("You set GMX_CPU_ACCELERATION, which is deprecated, and will be removed in a later version of GROMACS. It is replaced by GMX_SIMD. For now, copying the value from GMX_CPU_ACCELERATION to GMX_SIMD.")
234 # TODO remove all references to GMX_CPU_ACCELERATION in master branch
237 if(NOT GMX_TARGET_MIC)
238 include(gmxDetectSimd)
239 gmx_detect_simd(GMX_SUGGESTED_SIMD)
241 set(GMX_SUGGESTED_SIMD "None")
244 gmx_option_multichoice(
246 "SIMD instruction set for CPU kernels and compiler optimization"
247 "${GMX_SUGGESTED_SIMD}"
248 None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 IBM_QPX Sparc64_HPC_ACE Reference)
250 gmx_option_multichoice(
254 fftw3 mkl "fftpack[built-in]")
255 gmx_dependent_option(
257 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
259 "GMX_FFT_LIBRARY STREQUAL FFTW3")
260 gmx_dependent_option(
261 GMX_DISABLE_FFTW_MEASURE
262 "Do not optimize FFTW setups (not needed with SSE)"
264 "GMX_FFT_LIBRARY STREQUAL FFTW3")
265 mark_as_advanced(GMX_BUILD_OWN_FFTW)
266 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
268 gmx_option_multichoice(
270 "QM package for QM/MM"
272 none gaussian mopac gamess orca)
274 gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
275 gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
277 # This should be moved to a separate NBNXN cmake module when that code is cleaned up and modularized
279 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
280 mark_as_advanced(GMX_BROKEN_CALLOC)
281 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
282 mark_as_advanced(GMX_LOAD_PLUGINS)
284 option(GMX_GPU "Enable GPU acceleration" ON)
285 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
287 option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
289 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
290 mark_as_advanced(GMX_GIT_VERSION_INFO)
293 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
295 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
297 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
298 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
300 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
301 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
303 option(GMX_BUILD_FOR_COVERAGE
304 "Tune build for better code coverage metrics (e.g., disable asserts)"
306 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
309 ######################################################################
310 # Detect OpenMP support
311 ######################################################################
312 # The OpenMP detection _must_ come before tests for other CFLAGS.
313 include(gmxManageOpenMP)
317 ######################################################################
319 # These need to be done early (before further tests).
320 #####################################################################
322 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
323 # are used with permission from CMake v2.8.9 so that GROMACS can detect
324 # invalid options with the Intel Compilers.
325 # These files should be removed from the source tree when a CMake version that
326 # includes the features in question becomes required for building GROMACS.
327 include(CheckCCompilerFlag)
328 include(CheckCXXCompilerFlag)
334 # This variable should be used for additional compiler flags which are not
335 # generated in gmxCFlags nor are SIMD or MPI related.
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()
342 # GMX_SIMD will not be set automatically until the second
343 # pass (which is not strictly guaranteed to occur), so putting this
344 # check here among logically-related tests is inefficient, but the
345 # potential loss is likely zero.
346 if(GMX_SIMD STREQUAL "AVX_256"
347 AND CMAKE_COMPILER_IS_GNUCC
348 AND (C_COMPILER_VERSION VERSION_EQUAL "4.6.1"
349 OR CXX_COMPILER_VERSION VERSION_EQUAL "4.6.1"))
350 message(FATAL_ERROR "gcc 4.6.1 has buggy support for AVX, and GROMACS mdrun will not work. If you want simulation performance, use a more recent compiler. Otherwise, use GMX_SIMD=SSE4.1")
351 # See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002
358 add_definitions(-DGMX_DOUBLE)
359 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
361 if(GMX_SOFTWARE_INVSQRT)
362 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
365 if(WIN32 AND NOT CYGWIN)
366 set(GMX_WSOCKLIB_PATH CACHE PATH "Path to winsock (wsock32.lib) library.")
367 mark_as_advanced(GMX_WSOCKLIB_PATH)
368 find_library(WSOCK32_LIBRARY NAMES wsock32 PATHS ${GMX_WSOCKLIB_PATH})
370 list(APPEND GMX_EXTRA_LIBRARIES ${WSOCK32_LIBRARY})
371 add_definitions(-DGMX_HAVE_WINSOCK)
373 message(STATUS "No winsock found. Cannot use interactive molecular dynamics (IMD).")
374 endif(WSOCK32_LIBRARY)
379 ########################################################################
380 # Basic system tests (standard libraries, headers, functions, types) #
381 ########################################################################
382 include(CheckIncludeFiles)
383 include(CheckIncludeFileCXX)
384 check_include_files(unistd.h HAVE_UNISTD_H)
385 check_include_files(pwd.h HAVE_PWD_H)
386 check_include_files(dirent.h HAVE_DIRENT_H)
387 check_include_files(time.h HAVE_TIME_H)
388 check_include_files(sys/time.h HAVE_SYS_TIME_H)
389 check_include_files(io.h HAVE_IO_H)
390 check_include_files(sched.h HAVE_SCHED_H)
392 check_include_files(regex.h HAVE_POSIX_REGEX)
393 check_include_file_cxx(regex HAVE_CXX11_REGEX)
394 # TODO: It could be nice to inform the user if no regex support is found,
395 # as selections won't be fully functional.
397 include(CheckFunctionExists)
398 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
399 check_function_exists(memalign HAVE_MEMALIGN)
400 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
401 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
402 check_function_exists(fsync HAVE_FSYNC)
403 check_function_exists(_fileno HAVE__FILENO)
404 check_function_exists(fileno HAVE_FILENO)
405 check_function_exists(_commit HAVE__COMMIT)
406 check_function_exists(sigaction HAVE_SIGACTION)
407 check_function_exists(sysconf HAVE_SYSCONF)
408 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
409 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
410 check_function_exists(rsqrt HAVE_RSQRT)
411 check_function_exists(rsqrtf HAVE_RSQRTF)
412 check_function_exists(sqrtf HAVE_SQRTF)
414 include(CheckLibraryExists)
415 check_library_exists(m sqrt "" HAVE_LIBM)
416 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
418 include(TestBigEndian)
419 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
421 # Management of GROMACS options for specific toolchains should go
422 # here. Because the initial settings for some of the main options have
423 # already happened, but things like library detection and MPI compiler
424 # feature detection have not, the docstrings for any over-rides of
425 # GROMACS defaults or user settings will make sense. Also, any
426 # toolchain-related reasons for choosing whether to detect various
427 # things can be sorted out now, before the detection takes place.
428 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
429 include(gmxManageBlueGene)
432 ########################################################################
433 #Process MPI settings
434 ########################################################################
435 include(gmxManageMPI)
438 ########################################################################
439 #Process shared/static library settings
440 ########################################################################
441 include(gmxManageSharedLibraries)
444 ########################################################################
445 # Find external packages #
446 ########################################################################
448 # Unconditionally find the package, as it is also required for unit
449 # tests. This exports LIBXML2_FOUND, which we should not use because
450 # it does not tell us that linking will succeed. Instead, we test that
452 find_package(LibXml2)
453 include(gmxTestLibXml2)
454 gmx_test_libxml2(HAVE_LIBXML2)
455 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${HAVE_LIBXML2})
457 mark_as_advanced(GMX_XML)
458 # Don't actually do anything, since libxml2 is currently not used by libgromacs
459 #if(GMX_XML AND NOT HAVE_LIBXML2)
460 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
463 # include_directories(${LIBXML2_INCLUDE_DIR})
464 # set(PKG_XML libxml-2.0)
465 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
468 option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
469 mark_as_advanced(GMX_EXTRAE)
474 include_directories(${EXTRAE_INCLUDE_DIR})
477 message(FATAL_ERROR "EXTRAE library was not found. Please add the correct path to CMAKE_PREFIX_PATH")
481 option(GMX_X11 "Use X window system" OFF)
484 # X11 includes/libraries are only set in the ngmx subdirectory!
487 "X11 include files and/or libraries were not found. "
488 "Set GMX_X11=OFF to compile without X11 support. "
489 "gmx view will not be available.")
491 include_directories(${X11_INCLUDE_DIR})
495 # Enable core threading facilities
496 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include")
497 # Enable tMPI C++ support
500 # enable MPI functions
503 set(MPI_IN_PLACE_EXISTS 1)
505 # If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
506 if (TMPI_ATOMICS_DISABLED)
507 add_definitions(-DTMPI_ATOMICS_DISABLED)
511 # now that we have detected the dependencies, do the second configure pass
519 if(WIN32 AND NOT CYGWIN)
520 set(GMX_NATIVE_WINDOWS 1)
521 # This makes windows.h not declare min/max as macros that would break
522 # C++ code using std::min/std::max.
523 add_definitions(-DNOMINMAX)
526 # only bother with finding git and using version.h if the source is a git repo
527 if(GMX_GIT_VERSION_INFO)
528 if (NOT SOURCE_IS_GIT_REPOSITORY)
530 "Cannot generate git version information from source tree not under git. "
531 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
533 # We need at least git v1.5.3 be able to parse git's date output. If not
534 # found or the version is too small, we can't generate version information.
537 if(NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
539 "No compatible git version found (>= 1.5.3 required). "
540 "Won't be able to generate development version information. "
541 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
545 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
546 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
547 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
548 find_package(Boost 1.44.0)
549 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
550 set(Boost_FOUND FALSE)
552 # Print the notification only on first run, when determining the default
553 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
554 message("Boost >= 1.44 not found. Using minimal internal version. "
555 "This may cause trouble if you plan on compiling/linking other "
556 "software that uses Boost against Gromacs.")
559 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
561 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
563 "Boost >= 1.44 not found. "
564 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
565 "version of Boost included with Gromacs.")
568 if(NOT DEFINED GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
569 message(WARNING "libxml2 not found. Will build GROMACS without unit-tests. This is not recommended, because the unit-tests help to verify that GROMACS functions correctly. Most likely you are missing the libxml2-dev(el) package. After you installed it, set GMX_BUILD_UNITTESTS=ON.")
571 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${HAVE_LIBXML2})
572 mark_as_advanced(GMX_BUILD_UNITTESTS)
573 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
574 if (GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
576 "Cannot build unit tests without libxml2. "
577 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version of libxml2.")
580 ########################################################################
581 # Generate development version info for cache
582 ########################################################################
583 # set(GEN_VERSION_INFO_INTERNAL "ON")
584 # include(gmxGenerateVersionString)
586 ########################################################################
587 # Our own GROMACS tests
588 ########################################################################
590 add_definitions( -DHAVE_CONFIG_H )
591 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
592 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
593 # Required for config.h, maybe should only be set in src/CMakeLists.txt
594 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
595 # Required for now to make old code compile
596 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
598 include(gmxTestInlineASM)
599 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
601 include(gmxSetBuildInformation)
602 gmx_set_build_information()
604 # - the build system's CPU supports it
605 # - the acceleration is set to AVX as all AVX-capable CPUs support AVX (which
606 # at this point means that the user set it).
607 # Note: it's better to not use the later set value of GMX_SIMD because
608 # it reflects the system's capability of both compiling and running AVX code.
609 # TODO: After merge with 5.0 one could implement a cache variable dependency
610 # such that GMX_USE_RDTSCP can change if GMX_SIMD is changed to AVX
611 # after the first cmake pass.
612 if (BUILD_CPU_FEATURES MATCHES "rdtscp" OR GMX_SIMD MATCHES "AVX")
613 set(GMX_USE_RDTSCP_DEFAULT_VALUE ON)
615 set(GMX_USE_RDTSCP_DEFAULT_VALUE OFF)
617 option(GMX_USE_RDTSCP "Use RDTSCP for better CPU-based timers (available on recent x86 CPUs; might need to be off when compiling for heterogeneous environments)" ${GMX_USE_RDTSCP_DEFAULT_VALUE})
618 mark_as_advanced(GMX_USE_RDTSCP)
623 include(gmxTestFloatFormat)
624 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
625 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
626 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
628 include(gmxTestLargeFiles)
629 gmx_test_large_files(GMX_LARGEFILES)
631 include(gmxTestSignal)
632 gmx_test_sigusr1(HAVE_SIGUSR1)
634 include(gmxTestPipes)
635 gmx_test_pipes(HAVE_PIPES)
637 include(gmxTestIsfinite)
638 gmx_test_isfinite(HAVE_ISFINITE)
639 gmx_test__isfinite(HAVE__ISFINITE)
640 gmx_test__finite(HAVE__FINITE)
642 include(gmxTestCXX11)
643 gmx_test_cxx11(GMX_CXX11_SUPPORTED GMX_CXX11_FLAGS)
644 include(CMakeDependentOption)
645 # nvcc does not support C++11 flags, so with GPUs we prefer to skip C++11 flags
646 # entirely to keep the compilation environment uniform.
647 cmake_dependent_option(GMX_CXX11
649 ON "GMX_CXX11_SUPPORTED AND NOT GMX_GPU" OFF)
650 mark_as_advanced(GMX_CXX11)
652 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} ${GMX_CXX11_FLAGS}")
657 gmx_test_xdr(GMX_SYSTEM_XDR)
658 if(NOT GMX_SYSTEM_XDR)
659 set(GMX_INTERNAL_XDR 1)
663 ##################################################
664 # Process SIMD instruction settings
665 ##################################################
666 # This checks what flags to add in order to
667 # support the SIMD instructions we need, and sets
668 # correct defines for the SIMD instructions supported.
673 # Process QM/MM Settings
674 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
675 set(GMX_QMMM_GAUSSIAN 1)
676 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
677 set(GMX_QMMM_MOPAC 1)
678 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
679 set(GMX_QMMM_GAMESS 1)
680 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
682 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
685 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
689 ##################################################
690 # Process FFT library settings
691 ##################################################
692 include(gmxManageFFTLibraries)
695 include(gmxManageLinearAlgebraLibraries)
697 # Whether GROMACS will really try to compile support for VMD plugins
698 set(GMX_USE_PLUGINS OFF)
701 if(CYGWIN OR NOT WIN32)
702 # Native Windows does not have, nor need dlopen
703 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
704 include(gmxTestdlopen)
705 gmx_test_dlopen(HAVE_DLOPEN)
708 # so, should we use plug-ins?
709 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
712 "Found the ability to use plug-ins when building shared libaries, "
713 "so will compile to use plug-ins (e.g. to read VMD-supported file "
716 if(NOT GMX_VMD_PLUGIN_PATH)
719 set(GMX_USE_PLUGINS ON)
720 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
721 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
726 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
728 # Link real-time library for POSIX timers. The check for clock_gettime
729 # confirms the linkability of rt.
730 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
731 list(APPEND GMX_EXTRA_LIBRARIES rt)
734 # Math and thread libraries must often come after all others when linking...
736 list(APPEND GMX_EXTRA_LIBRARIES m)
739 option(GMX_NACL "Configure for Native Client builds" OFF)
741 list(APPEND GMX_EXTRA_LIBRARIES nosys)
742 set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
746 mark_as_advanced(GMX_NACL)
749 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
750 "Path to swindirect.h")
751 include_directories(${COREWRAP_INCLUDE_DIR})
754 option(GMX_BUILD_HELP "Build man pages, HTML help, and completions automatically (requires that compiled binaries can be executed on the build host)" OFF)
755 mark_as_advanced(GMX_BUILD_HELP)
756 if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND
757 "${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
760 "Rebuilding HTML and man pages is not supported for in-source "
761 "builds from a source distribution. "
762 "Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
765 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
766 # these are set after everything else
767 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
768 set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
769 set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
770 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
771 set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
773 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
774 message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
775 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
776 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
777 message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
778 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
779 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
780 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
781 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
785 #Unset all OpenMP flags in case OpenMP was disabled either by the user
786 #or because it was only partially detected (e.g. only for C but not C++ compiler)
787 unset(OpenMP_C_FLAGS CACHE)
788 unset(OpenMP_CXX_FLAGS CACHE)
790 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
791 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
793 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
795 ########################################################################
796 # Specify install locations
797 ########################################################################
798 # Use GNUInstallDirs to set paths on multiarch systems.
799 include(GNUInstallDirs)
801 # Customization for the installation tree paths.
802 set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
803 "Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
804 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
805 "Data installation directory under share/ (default: gromacs)")
806 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
808 # These variables are used internally to provide a central location for
809 # customizing the install locations.
810 set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
811 set(BIN_INSTALL_DIR bin)
812 set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
813 set(MAN_INSTALL_DIR share/man)
814 set(INCL_INSTALL_DIR include)
816 # These variables get written into config.h for use in finding the data
818 set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
819 set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
821 # Binary and library suffix options
822 include(gmxManageSuffixes)
824 ################################################################
825 # Shared library load path settings
826 ################################################################
827 # CMake supports RPATH on OS X only from 2.8.12 upwards.
828 # CMAKE_SYSTEM_VERSION > 8.0 matches OS X 10.5 and above, where RPATH support
830 if((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR
831 ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (NOT CMAKE_VERSION VERSION_LESS 2.8.12)))
832 # The build folder always has bin/ and lib/; if we are also going to
833 # install to lib/, then the installation RPATH works also in the build
834 # tree. This makes installation slightly faster (no need to rewrite the
835 # RPATHs), and makes the binaries in the build tree relocatable.
836 if(GMX_LIB_INSTALL_DIR STREQUAL "lib")
837 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
839 # Set the RPATH as relative to the executable location to make the
840 # binaries relocatable.
841 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
842 set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
844 set(CMAKE_INSTALL_RPATH "@executable_path/../${GMX_LIB_INSTALL_DIR}")
846 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
847 set(CMAKE_MACOSX_RPATH 1)
849 # We are on Darwin/OSX, and CMake cannot handle RPATHs automatically.
850 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0)
851 # Set the RPATH options manually.
852 set(CMAKE_INSTALL_NAME_DIR "@rpath")
853 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../${GMX_LIB_INSTALL_DIR}")
855 # Use the old INSTALL_NAME_DIR mechanism if RPATH is not supported.
856 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
860 #COPYING file: Only necessary for binary distributions.
861 #Simpler to always install.
862 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
864 if(GMX_EXTERNAL_BOOST)
865 include_directories(${Boost_INCLUDE_DIRS})
866 set(PKG_CFLAGS "${PKG_CFLAGS} -I${Boost_INCLUDE_DIRS}")
868 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/boost)
869 # typeid not supported for minimal internal version
870 # (would add significant amount of code)
871 add_definitions(-DBOOST_NO_TYPEID)
872 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
873 # (from share/template/)
874 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${CMAKE_INSTALL_PREFIX}/${INCL_INSTALL_DIR}/gromacs/external/boost")
875 if (NOT GMX_BUILD_MDRUN_ONLY)
876 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
877 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
878 COMPONENT development)
882 if (GMX_BUILD_FOR_COVERAGE)
883 # Code heavy with asserts makes conditional coverage close to useless metric,
884 # as by design most of the false branches are impossible to trigger in
885 # correctly functioning code. And the benefit of testing those that could
886 # be triggered by using an API against its specification isn't usually
888 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
892 # "tests" target builds all the separate test binaries.
893 add_custom_target(tests)
894 # "run-ctest" is an internal target that actually runs the tests.
895 # This is necessary to be able to add separate targets that execute as part
896 # of 'make check', but are ensured to be executed after the actual tests.
897 add_custom_target(run-ctest
898 COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
899 COMMENT "Running all tests"
901 add_dependencies(run-ctest tests)
902 # "check" target builds and runs all tests.
903 add_custom_target(check DEPENDS run-ctest)
906 if (NOT GMX_BUILD_MDRUN_ONLY)
907 add_subdirectory(doxygen)
908 add_subdirectory(install-guide)
909 add_subdirectory(share)
910 add_subdirectory(scripts)
912 add_subdirectory(src)
915 add_subdirectory(tests)
918 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
919 # Don't bother the user after the first configure pass.
920 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
921 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
923 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
925 #######################
927 #######################
928 CONFIGURE_FILE( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
929 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
931 ###########################
932 ADD_CUSTOM_TARGET(uninstall
933 "${CMAKE_COMMAND}" -P
934 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
935 ###########################
936 set_directory_properties(PROPERTIES
937 ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")
939 ########################################################################
941 ########################################################################
943 option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF)
944 mark_as_advanced(GMX_BUILD_MANUAL)
946 # Make sure we only do detection of manual-building dependencies
947 # when the user opted in for that.
948 add_subdirectory(manual)