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 "5.0.1-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 # The MD5 checksum of the regressiontest tarball. Only used if "-dev"
68 # is not present in the PROJECT_VERSION
69 set(REGRESSIONTEST_MD5SUM "a07524afebca5013540d4f2f72df2dce")
70 # If this is not a released tarball, "-dev" will be present in
71 # PROJECT_VERSION, and REGRESSIONTEST_BRANCH specifies the name of the
72 # gerrit.gromacs.org branch whose HEAD can test this code, *if* this
73 # code contains all recent fixes from the corresponding code branch.
74 set(REGRESSIONTEST_BRANCH "refs/heads/release-5-0")
76 set(CUSTOM_VERSION_STRING ""
77 CACHE STRING "Custom version string (if empty, use hard-coded default)")
78 mark_as_advanced(CUSTOM_VERSION_STRING)
79 if (CUSTOM_VERSION_STRING)
80 set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
82 set(LIBRARY_SOVERSION 0)
83 set(LIBRARY_VERSION ${LIBRARY_SOVERSION}.0.0)
84 # It is a bit irritating, but this has to be set separately for now!
85 SET(CPACK_PACKAGE_VERSION_MAJOR "5")
86 SET(CPACK_PACKAGE_VERSION_MINOR "0")
87 #SET(CPACK_PACKAGE_VERSION_PATCH "0")
89 # The numerical gromacs version. It is 40600 for 4.6.0.
90 # The #define GMX_VERSION in gromacs/version.h is set to this value.
92 "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
93 if(CPACK_PACKAGE_VERSION_PATCH)
95 "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
98 # The API version tracks the numerical Gromacs version (for now).
99 # It is potentially different from the Gromacs version in the future, if
100 # the programs/libraries diverge from the presumably more stable API.
101 # The #define GMX_API_VERSION in version.h is set to this value to
102 # provide backward compatibility of software written against the Gromacs API.
103 set(API_VERSION ${NUM_VERSION})
105 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
106 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
109 include(gmxBuildTypeReference)
110 include(gmxBuildTypeTSAN)
111 include(gmxBuildTypeASAN)
112 include(gmxBuildTypeReleaseWithAssert)
114 if(NOT CMAKE_BUILD_TYPE)
115 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert." FORCE)
116 # There's no need to offer a user the choice of ThreadSanitizer
117 # Set the possible values of build type for cmake-gui
118 set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
119 "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert")
121 if(CMAKE_CONFIGURATION_TYPES)
122 # Add appropriate GROMACS-specific build types for the Visual
123 # Studio generator (Debug, Release, MinSizeRel and RelWithDebInfo
124 # are already present by default).
125 list(APPEND CMAKE_CONFIGURATION_TYPES "RelWithAssert" "Reference")
126 list(REMOVE_DUPLICATES CMAKE_CONFIGURATION_TYPES)
127 set(CMAKE_CONFIGURATION_TYPES "${CMAKE_CONFIGURATION_TYPES}" CACHE STRING
128 "List of configuration types"
131 set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBUGINFO RELWITHASSERT MINSIZEREL)
136 set(CPACK_PACKAGE_NAME "gromacs")
137 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
138 set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
139 set(CPACK_PACKAGE_VENDOR "gromacs.org")
140 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
141 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
142 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
143 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
144 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
145 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
146 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
147 # CPack source archives include only the directories we list here.
148 # This variable is a list of pairs of names of source and destination
149 # directories. Most of these are used for content GROMACS generates as
150 # part of the configuration or build.
151 set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/docs/man/man1;docs/man/man1;${CMAKE_BINARY_DIR}/docs/man/man7;docs/man/man7;${CMAKE_BINARY_DIR}/docs/old-html/final;docs/old-html/final;${CMAKE_BINARY_DIR}/docs/install-guide/final;/")
152 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
153 set(CPACK_GMX_BUILD_HELP "${GMX_BUILD_HELP}") #Works even though GMX_BUILD_HELP is defined later because it is off by default.
155 #must come after all cpack settings!
158 # Set a default valgrind suppression file.
159 # This unfortunately needs to duplicate information from CTest to work as
161 set(MEMORYCHECK_SUPPRESSIONS_FILE
162 "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
164 "File that contains suppressions for the memory checker")
167 set(SOURCE_IS_GIT_REPOSITORY OFF)
168 set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
169 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
170 set(SOURCE_IS_GIT_REPOSITORY ON)
172 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
173 set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
176 ########################################################################
177 # Check and warn if cache generated on a different host is being reused
178 ########################################################################
180 execute_process(COMMAND hostname
181 OUTPUT_VARIABLE TMP_HOSTNAME
182 OUTPUT_STRIP_TRAILING_WHITESPACE)
183 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
185 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
186 is being reused! This could lead to inconsitencies; therefore, it is
187 recommended to regenerate the cache!")
189 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
190 "Hostname of the machine where the cache was generated.")
193 ########################################################################
194 # User input options #
195 ########################################################################
196 include(gmxOptionUtilities)
198 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
200 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
201 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
202 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
203 gmx_dependent_option(
205 "Enable MPI_IN_PLACE for MPIs that have it defined"
208 mark_as_advanced(GMX_MPI_IN_PLACE)
209 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
210 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
211 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
212 mark_as_advanced(GMX_FAHCORE)
214 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
215 mark_as_advanced(GMX_COOL_QUOTES)
216 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
218 # Decide on GPU settings based on user-settings and GPU/CUDA detection.
219 # We support CUDA >=v4.0 on *nix, but <= v4.1 doesn't work with MSVC
221 set(REQUIRED_CUDA_VERSION 4.1)
223 set(REQUIRED_CUDA_VERSION 4.0)
225 set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
226 include(gmxManageGPU)
228 # Detect the architecture the compiler is targetting, detect
229 # SIMD instructions possibilities on that hardware, suggest SIMD instruction set
230 # to use if none is specified, and populate the cache option for CPU
232 include(gmxDetectTargetArchitecture)
233 gmx_detect_target_architecture()
235 if(GMX_CPU_ACCELERATION)
236 # Stay compatible with old Jenkins command line options for specific SIMD acceleration
237 set(GMX_SIMD "${GMX_CPU_ACCELERATION}" CACHE STRING "SIMD instruction set level and compiler optimization" FORCE)
238 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.")
239 # TODO remove all references to GMX_CPU_ACCELERATION in master branch
242 if(NOT GMX_TARGET_MIC)
243 include(gmxDetectSimd)
244 gmx_detect_simd(GMX_SUGGESTED_SIMD)
246 set(GMX_SUGGESTED_SIMD "None")
249 gmx_option_multichoice(
251 "SIMD instruction set for CPU kernels and compiler optimization"
252 "${GMX_SUGGESTED_SIMD}"
253 None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 IBM_QPX Sparc64_HPC_ACE Reference)
255 gmx_option_multichoice(
259 fftw3 mkl "fftpack[built-in]")
260 gmx_dependent_option(
262 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
264 "GMX_FFT_LIBRARY STREQUAL FFTW3")
265 gmx_dependent_option(
266 GMX_DISABLE_FFTW_MEASURE
267 "Do not optimize FFTW setups (not needed with SSE)"
269 "GMX_FFT_LIBRARY STREQUAL FFTW3")
270 mark_as_advanced(GMX_BUILD_OWN_FFTW)
271 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
273 gmx_option_multichoice(
275 "QM package for QM/MM"
277 none gaussian mopac gamess orca)
279 gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
280 gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
282 # This should be moved to a separate NBNXN cmake module when that code is cleaned up and modularized
284 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
285 mark_as_advanced(GMX_BROKEN_CALLOC)
286 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
287 mark_as_advanced(GMX_LOAD_PLUGINS)
289 option(GMX_GPU "Enable GPU acceleration" ON)
290 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
292 option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
294 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
295 mark_as_advanced(GMX_GIT_VERSION_INFO)
298 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
300 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
302 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
303 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
305 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
306 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
308 option(GMX_BUILD_FOR_COVERAGE
309 "Tune build for better code coverage metrics (e.g., disable asserts)"
311 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
313 option(GMX_DEVELOPER_BUILD
314 "Enable Developer convenience features: always build unit-tests"
316 mark_as_advanced(GMX_DEVELOPER_BUILD)
318 ######################################################################
319 # Detect OpenMP support
320 ######################################################################
321 # The OpenMP detection _must_ come before tests for other CFLAGS.
322 include(gmxManageOpenMP)
326 ######################################################################
328 # These need to be done early (before further tests).
329 #####################################################################
331 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
332 # are used with permission from CMake v3.0.0 so that GROMACS can detect
333 # invalid options with the Intel Compilers, and we have added a line
334 # to detect warnings with the Fujitsu compilers on K computer and ICC.
335 # CMake-3.0 also has a bug where the FAIL_REGEX pattern for AIX contains
336 # a semicolon. Since this is also used as a separator in lists inside CMake,
337 # that string ends up being split into two separate patterns, and the last
338 # part is just a single word that also matches other messages. We solved this
339 # by replacing the semicolon with a period that matches any character.
341 # These files should be removed from the source tree when a CMake version that
342 # includes the features in question becomes required for building GROMACS.
343 include(CheckCCompilerFlag)
344 include(CheckCXXCompilerFlag)
349 # This variable should be used for additional compiler flags which are not
350 # generated in gmxCFlags nor are SIMD or MPI related.
351 set(EXTRA_C_FLAGS "")
352 set(EXTRA_CXX_FLAGS "")
354 # Run through a number of tests for buggy compilers and other issues
355 include(gmxTestCompilerProblems)
356 gmx_test_compiler_problems()
357 # GMX_SIMD will not be set automatically until the second
358 # pass (which is not strictly guaranteed to occur), so putting this
359 # check here among logically-related tests is inefficient, but the
360 # potential loss is likely zero.
361 if(GMX_SIMD STREQUAL "AVX_256"
362 AND CMAKE_COMPILER_IS_GNUCC
363 AND (C_COMPILER_VERSION VERSION_EQUAL "4.6.1"
364 OR CXX_COMPILER_VERSION VERSION_EQUAL "4.6.1"))
365 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")
366 # See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002
373 add_definitions(-DGMX_DOUBLE)
374 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
376 if(GMX_SOFTWARE_INVSQRT)
377 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
380 if(WIN32 AND NOT CYGWIN)
381 set(GMX_WSOCKLIB_PATH CACHE PATH "Path to winsock (wsock32.lib) library.")
382 mark_as_advanced(GMX_WSOCKLIB_PATH)
383 find_library(WSOCK32_LIBRARY NAMES wsock32 PATHS ${GMX_WSOCKLIB_PATH})
385 list(APPEND GMX_EXTRA_LIBRARIES ${WSOCK32_LIBRARY})
386 add_definitions(-DGMX_HAVE_WINSOCK)
388 message(STATUS "No winsock found. Cannot use interactive molecular dynamics (IMD).")
389 endif(WSOCK32_LIBRARY)
394 ########################################################################
395 # Basic system tests (standard libraries, headers, functions, types) #
396 ########################################################################
397 include(CheckIncludeFiles)
398 include(CheckIncludeFileCXX)
399 check_include_files(unistd.h HAVE_UNISTD_H)
400 check_include_files(pwd.h HAVE_PWD_H)
401 check_include_files(dirent.h HAVE_DIRENT_H)
402 check_include_files(time.h HAVE_TIME_H)
403 check_include_files(sys/time.h HAVE_SYS_TIME_H)
404 check_include_files(io.h HAVE_IO_H)
405 check_include_files(sched.h HAVE_SCHED_H)
407 check_include_files(regex.h HAVE_POSIX_REGEX)
408 check_include_file_cxx(regex HAVE_CXX11_REGEX)
409 # TODO: It could be nice to inform the user if no regex support is found,
410 # as selections won't be fully functional.
412 include(CheckFunctionExists)
413 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
414 check_function_exists(memalign HAVE_MEMALIGN)
415 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
416 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
417 check_function_exists(fsync HAVE_FSYNC)
418 check_function_exists(_fileno HAVE__FILENO)
419 check_function_exists(fileno HAVE_FILENO)
420 check_function_exists(_commit HAVE__COMMIT)
421 check_function_exists(sigaction HAVE_SIGACTION)
422 check_function_exists(sysconf HAVE_SYSCONF)
423 check_function_exists(rsqrt HAVE_RSQRT)
424 check_function_exists(rsqrtf HAVE_RSQRTF)
425 check_function_exists(sqrtf HAVE_SQRTF)
427 include(CheckLibraryExists)
428 check_library_exists(m sqrt "" HAVE_LIBM)
429 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
431 include(TestSchedAffinity)
432 test_sched_affinity(HAVE_SCHED_AFFINITY)
434 include(TestBigEndian)
435 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
437 # Management of GROMACS options for specific toolchains should go
438 # here. Because the initial settings for some of the main options have
439 # already happened, but things like library detection and MPI compiler
440 # feature detection have not, the docstrings for any over-rides of
441 # GROMACS defaults or user settings will make sense. Also, any
442 # toolchain-related reasons for choosing whether to detect various
443 # things can be sorted out now, before the detection takes place.
444 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
445 include(gmxManageBlueGene)
448 ########################################################################
449 #Process MPI settings
450 ########################################################################
451 include(gmxManageMPI)
454 ########################################################################
455 #Process shared/static library settings
456 ########################################################################
457 include(gmxManageSharedLibraries)
460 ########################################################################
461 # Find external packages #
462 ########################################################################
464 # Unconditionally find the package, as it is also required for unit
465 # tests. This exports LIBXML2_FOUND, which we should not use because
466 # it does not tell us that linking will succeed. Instead, we test that
468 if(DEFINED LIBXML2_LIBRARIES)
469 set(LibXml2_FIND_QUIETLY TRUE)
471 find_package(LibXml2)
472 include(gmxTestLibXml2)
473 gmx_test_libxml2(HAVE_LIBXML2)
474 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${HAVE_LIBXML2})
476 mark_as_advanced(GMX_XML)
477 # Don't actually do anything, since libxml2 is currently not used by libgromacs
478 #if(GMX_XML AND NOT HAVE_LIBXML2)
479 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
482 # include_directories(${LIBXML2_INCLUDE_DIR})
483 # set(PKG_XML libxml-2.0)
484 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
487 option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
488 mark_as_advanced(GMX_EXTRAE)
493 include_directories(${EXTRAE_INCLUDE_DIR})
496 message(FATAL_ERROR "EXTRAE library was not found. Please add the correct path to CMAKE_PREFIX_PATH")
500 option(GMX_X11 "Use X window system" OFF)
503 # X11 includes/libraries are only set in the ngmx subdirectory!
506 "X11 include files and/or libraries were not found. "
507 "Set GMX_X11=OFF to compile without X11 support. "
508 "gmx view will not be available.")
510 include_directories(${X11_INCLUDE_DIR})
514 # Enable core threading facilities
515 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include")
516 # Enable tMPI C++ support
519 # enable MPI functions
522 set(MPI_IN_PLACE_EXISTS 1)
524 # If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
525 if (TMPI_ATOMICS_DISABLED)
526 add_definitions(-DTMPI_ATOMICS_DISABLED)
530 # now that we have detected the dependencies, do the second configure pass
538 if(WIN32 AND NOT CYGWIN)
539 set(GMX_NATIVE_WINDOWS 1)
540 # This makes windows.h not declare min/max as macros that would break
541 # C++ code using std::min/std::max.
542 add_definitions(-DNOMINMAX)
545 # only bother with finding git and using version.h if the source is a git repo
546 if(GMX_GIT_VERSION_INFO)
547 if (NOT SOURCE_IS_GIT_REPOSITORY)
549 "Cannot generate git version information from source tree not under git. "
550 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
552 # We need at least git v1.5.3 be able to parse git's date output. If not
553 # found or the version is too small, we can't generate version information.
556 if(NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
558 "No compatible git version found (>= 1.5.3 required). "
559 "Won't be able to generate development version information. "
560 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
564 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
565 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
566 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
567 find_package(Boost 1.44.0)
568 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
569 set(Boost_FOUND FALSE)
571 # Print the notification only on first run, when determining the default
572 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
573 message("Boost >= 1.44 not found. Using minimal internal version. "
574 "This may cause trouble if you plan on compiling/linking other "
575 "software that uses Boost against Gromacs.")
578 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
580 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
582 "Boost >= 1.44 not found. "
583 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
584 "version of Boost included with Gromacs.")
587 if(NOT DEFINED GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
588 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.")
590 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${HAVE_LIBXML2})
591 mark_as_advanced(GMX_BUILD_UNITTESTS)
592 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
593 if (GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
595 "Cannot build unit tests without libxml2. "
596 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version of libxml2.")
599 if(GMX_USE_TNG AND NOT GMX_EXTERNAL_TNG)
600 # TNG wants zlib if it is available
601 find_package(ZLIB QUIET)
603 gmx_test_zlib(HAVE_ZLIB)
606 ########################################################################
607 # Generate development version info for cache
608 ########################################################################
609 # set(GEN_VERSION_INFO_INTERNAL "ON")
610 # include(gmxGenerateVersionString)
612 ########################################################################
613 # Our own GROMACS tests
614 ########################################################################
616 add_definitions( -DHAVE_CONFIG_H )
617 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
618 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
619 # Required for config.h, maybe should only be set in src/CMakeLists.txt
620 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
621 # Required for gmx_header_config_gen.h to be found before installation
622 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src/gromacs/utility)
623 # Required for now to make old code compile
624 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
626 include(gmxTestInlineASM)
627 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
629 include(gmxSetBuildInformation)
630 gmx_set_build_information()
632 # - the build system's CPU supports it
633 # - the acceleration is set to AVX as all AVX-capable CPUs support AVX (which
634 # at this point means that the user set it).
635 # Note: it's better to not use the later set value of GMX_SIMD because
636 # it reflects the system's capability of both compiling and running AVX code.
637 # TODO: After merge with 5.0 one could implement a cache variable dependency
638 # such that GMX_USE_RDTSCP can change if GMX_SIMD is changed to AVX
639 # after the first cmake pass.
640 if (BUILD_CPU_FEATURES MATCHES "rdtscp" OR GMX_SIMD MATCHES "AVX")
641 set(GMX_USE_RDTSCP_DEFAULT_VALUE ON)
643 set(GMX_USE_RDTSCP_DEFAULT_VALUE OFF)
645 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)" ${GMX_USE_RDTSCP_DEFAULT_VALUE})
646 mark_as_advanced(GMX_USE_RDTSCP)
651 include(gmxTestFloatFormat)
652 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
653 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
654 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
656 include(gmxTestLargeFiles)
657 gmx_test_large_files(GMX_LARGEFILES)
659 include(gmxTestSignal)
660 gmx_test_sigusr1(HAVE_SIGUSR1)
662 include(gmxTestPipes)
663 gmx_test_pipes(HAVE_PIPES)
665 include(gmxTestIsfinite)
666 gmx_test_isfinite(HAVE_ISFINITE)
667 gmx_test__isfinite(HAVE__ISFINITE)
668 gmx_test__finite(HAVE__FINITE)
670 include(gmxTestCXX11)
671 gmx_test_cxx11(GMX_CXX11_SUPPORTED GMX_CXX11_FLAGS)
672 include(CMakeDependentOption)
673 # nvcc does not support C++11 flags, so with GPUs we prefer to skip C++11 flags
674 # entirely to keep the compilation environment uniform.
675 cmake_dependent_option(GMX_CXX11
677 ON "GMX_CXX11_SUPPORTED AND NOT GMX_GPU" OFF)
678 mark_as_advanced(GMX_CXX11)
680 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} ${GMX_CXX11_FLAGS}")
685 gmx_test_xdr(GMX_SYSTEM_XDR)
686 if(NOT GMX_SYSTEM_XDR)
687 set(GMX_INTERNAL_XDR 1)
691 ##################################################
692 # Process SIMD instruction settings
693 ##################################################
694 # This checks what flags to add in order to
695 # support the SIMD instructions we need, and sets
696 # correct defines for the SIMD instructions supported.
701 # Process QM/MM Settings
702 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
703 set(GMX_QMMM_GAUSSIAN 1)
704 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
705 set(GMX_QMMM_MOPAC 1)
706 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
707 set(GMX_QMMM_GAMESS 1)
708 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
710 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
713 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
717 ##################################################
718 # Process FFT library settings
719 ##################################################
720 include(gmxManageFFTLibraries)
723 include(gmxManageLinearAlgebraLibraries)
725 # Whether GROMACS will really try to compile support for VMD plugins
726 set(GMX_USE_PLUGINS OFF)
729 if(CYGWIN OR NOT WIN32)
730 # Native Windows does not have, nor need dlopen
731 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
732 include(gmxTestdlopen)
733 gmx_test_dlopen(HAVE_DLOPEN)
736 # so, should we use plug-ins?
737 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
739 MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
741 if(NOT GMX_VMD_PLUGIN_PATH)
744 set(GMX_USE_PLUGINS ON)
745 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
746 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
751 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
753 # Link real-time library for POSIX timers. The check for clock_gettime
754 # confirms the linkability of rt.
755 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
756 list(APPEND GMX_EXTRA_LIBRARIES rt)
759 # Math and thread libraries must often come after all others when linking...
761 list(APPEND GMX_EXTRA_LIBRARIES m)
764 option(GMX_NACL "Configure for Native Client builds" OFF)
766 list(APPEND GMX_EXTRA_LIBRARIES nosys)
767 set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
771 mark_as_advanced(GMX_NACL)
774 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
775 "Path to swindirect.h")
776 include_directories(${COREWRAP_INCLUDE_DIR})
779 option(GMX_BUILD_HELP "Build man pages, HTML help, and completions automatically (requires that compiled binaries can be executed on the build host)" OFF)
780 mark_as_advanced(GMX_BUILD_HELP)
781 if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND
782 "${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
785 "Rebuilding HTML and man pages is not supported for in-source "
786 "builds from a source distribution. "
787 "Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
790 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
791 # these are set after everything else
792 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
793 set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
794 set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
795 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
796 set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
798 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
799 message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
800 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
801 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
802 message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
803 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
804 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
805 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
806 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
810 #Unset all OpenMP flags in case OpenMP was disabled either by the user
811 #or because it was only partially detected (e.g. only for C but not C++ compiler)
812 unset(OpenMP_C_FLAGS CACHE)
813 unset(OpenMP_CXX_FLAGS CACHE)
815 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
816 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
818 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
820 ########################################################################
821 # Specify install locations
822 ########################################################################
823 # Use GNUInstallDirs to set paths on multiarch systems.
824 include(GNUInstallDirs)
826 # Customization for the installation tree paths.
827 set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
828 "Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
829 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
830 "Data installation directory under share/ (default: gromacs)")
831 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
833 # These variables are used internally to provide a central location for
834 # customizing the install locations.
835 set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
836 set(BIN_INSTALL_DIR bin)
837 set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
838 set(MAN_INSTALL_DIR share/man)
839 set(INCL_INSTALL_DIR include)
841 # These variables get written into config.h for use in finding the data
843 set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
844 set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
846 # Binary and library suffix options
847 include(gmxManageSuffixes)
849 ################################################################
850 # Shared library load path settings
851 ################################################################
852 # CMake supports RPATH on OS X only from 2.8.12 upwards.
853 # CMAKE_SYSTEM_VERSION > 8.0 matches OS X 10.5 and above, where RPATH support
855 if((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR
856 ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (NOT CMAKE_VERSION VERSION_LESS 2.8.12)))
857 # The build folder always has bin/ and lib/; if we are also going to
858 # install to lib/, then the installation RPATH works also in the build
859 # tree. This makes installation slightly faster (no need to rewrite the
860 # RPATHs), and makes the binaries in the build tree relocatable.
861 if(GMX_LIB_INSTALL_DIR STREQUAL "lib")
862 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
864 # Set the RPATH as relative to the executable location to make the
865 # binaries relocatable.
866 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
867 set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
869 set(CMAKE_INSTALL_RPATH "@executable_path/../${GMX_LIB_INSTALL_DIR}")
871 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
872 set(CMAKE_MACOSX_RPATH 1)
874 # We are on Darwin/OSX, and CMake cannot handle RPATHs automatically.
875 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0)
876 # Set the RPATH options manually.
877 set(CMAKE_INSTALL_NAME_DIR "@rpath")
878 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../${GMX_LIB_INSTALL_DIR}")
880 # Use the old INSTALL_NAME_DIR mechanism if RPATH is not supported.
881 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
885 #COPYING file: Only necessary for binary distributions.
886 #Simpler to always install.
887 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
889 if(GMX_EXTERNAL_BOOST)
890 include_directories(${Boost_INCLUDE_DIRS})
891 set(PKG_CFLAGS "${PKG_CFLAGS} -I${Boost_INCLUDE_DIRS}")
893 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/boost)
894 # typeid not supported for minimal internal version
895 # (would add significant amount of code)
896 add_definitions(-DBOOST_NO_TYPEID)
897 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
898 # (from share/template/)
899 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${CMAKE_INSTALL_PREFIX}/${INCL_INSTALL_DIR}/gromacs/external/boost")
900 if (NOT GMX_BUILD_MDRUN_ONLY)
901 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
902 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
903 COMPONENT development)
907 if (GMX_BUILD_FOR_COVERAGE)
908 # Code heavy with asserts makes conditional coverage close to useless metric,
909 # as by design most of the false branches are impossible to trigger in
910 # correctly functioning code. And the benefit of testing those that could
911 # be triggered by using an API against its specification isn't usually
913 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
917 # "tests" target builds all the separate test binaries.
918 add_custom_target(tests)
919 # "run-ctest" is an internal target that actually runs the tests.
920 # This is necessary to be able to add separate targets that execute as part
921 # of 'make check', but are ensured to be executed after the actual tests.
922 add_custom_target(run-ctest
923 COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
924 COMMENT "Running all tests"
926 add_dependencies(run-ctest tests)
927 # "check" target builds and runs all tests.
928 add_custom_target(check DEPENDS run-ctest)
931 if (NOT GMX_BUILD_MDRUN_ONLY)
932 add_subdirectory(docs)
933 add_subdirectory(share)
934 add_subdirectory(scripts)
936 add_subdirectory(src)
939 add_subdirectory(tests)
942 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
943 # Don't bother the user after the first configure pass.
944 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
945 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
947 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
949 #######################
951 #######################
952 CONFIGURE_FILE( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
953 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
955 ###########################
956 ADD_CUSTOM_TARGET(uninstall
957 "${CMAKE_COMMAND}" -P
958 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
959 ###########################
960 set_directory_properties(PROPERTIES
961 ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")