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)
135 set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
137 set(CPACK_PACKAGE_NAME "gromacs")
138 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
139 set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
140 set(CPACK_PACKAGE_VENDOR "gromacs.org")
141 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
142 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
143 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
144 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
145 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
146 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
147 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
148 # CPack source archives include only the directories we list here.
149 # This variable is a list of pairs of names of source and destination
150 # directories. Most of these are used for content GROMACS generates as
151 # part of the configuration or build.
152 set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${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;${CMAKE_BINARY_DIR}/docs/install-guide/final;/")
153 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
154 set(CPACK_GMX_BUILD_HELP "${GMX_BUILD_HELP}") #Works even though GMX_BUILD_HELP is defined later because it is off by default.
156 #must come after all cpack settings!
159 # Set a default valgrind suppression file.
160 # This unfortunately needs to duplicate information from CTest to work as
162 set(MEMORYCHECK_SUPPRESSIONS_FILE
163 "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
165 "File that contains suppressions for the memory checker")
168 set(SOURCE_IS_GIT_REPOSITORY OFF)
169 set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
170 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
171 set(SOURCE_IS_GIT_REPOSITORY ON)
173 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
174 set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
177 ########################################################################
178 # Check and warn if cache generated on a different host is being reused
179 ########################################################################
181 execute_process(COMMAND hostname
182 OUTPUT_VARIABLE TMP_HOSTNAME
183 OUTPUT_STRIP_TRAILING_WHITESPACE)
184 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
186 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
187 is being reused! This could lead to inconsitencies; therefore, it is
188 recommended to regenerate the cache!")
190 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
191 "Hostname of the machine where the cache was generated.")
194 ########################################################################
195 # User input options #
196 ########################################################################
197 include(gmxOptionUtilities)
199 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
201 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
202 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
203 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
204 gmx_dependent_option(
206 "Enable MPI_IN_PLACE for MPIs that have it defined"
209 mark_as_advanced(GMX_MPI_IN_PLACE)
210 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
211 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
212 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
213 mark_as_advanced(GMX_FAHCORE)
215 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
216 mark_as_advanced(GMX_COOL_QUOTES)
217 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
219 # Decide on GPU settings based on user-settings and GPU/CUDA detection.
220 # We support CUDA >=v4.0 on *nix, but <= v4.1 doesn't work with MSVC
222 set(REQUIRED_CUDA_VERSION 4.1)
224 set(REQUIRED_CUDA_VERSION 4.0)
226 set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
227 include(gmxManageGPU)
229 # Detect the architecture the compiler is targetting, detect
230 # SIMD instructions possibilities on that hardware, suggest SIMD instruction set
231 # to use if none is specified, and populate the cache option for CPU
233 include(gmxDetectTargetArchitecture)
234 gmx_detect_target_architecture()
236 if(GMX_CPU_ACCELERATION)
237 # Stay compatible with old Jenkins command line options for specific SIMD acceleration
238 set(GMX_SIMD "${GMX_CPU_ACCELERATION}" CACHE STRING "SIMD instruction set level and compiler optimization" FORCE)
239 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.")
240 # TODO remove all references to GMX_CPU_ACCELERATION in master branch
243 if(NOT GMX_TARGET_MIC)
244 include(gmxDetectSimd)
245 gmx_detect_simd(GMX_SUGGESTED_SIMD)
247 set(GMX_SUGGESTED_SIMD "None")
250 gmx_option_multichoice(
252 "SIMD instruction set for CPU kernels and compiler optimization"
253 "${GMX_SUGGESTED_SIMD}"
254 None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 IBM_QPX Sparc64_HPC_ACE Reference)
256 gmx_option_multichoice(
260 fftw3 mkl "fftpack[built-in]")
261 gmx_dependent_option(
263 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
265 "GMX_FFT_LIBRARY STREQUAL FFTW3")
266 gmx_dependent_option(
267 GMX_DISABLE_FFTW_MEASURE
268 "Do not optimize FFTW setups (not needed with SSE)"
270 "GMX_FFT_LIBRARY STREQUAL FFTW3")
271 mark_as_advanced(GMX_BUILD_OWN_FFTW)
272 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
274 gmx_option_multichoice(
276 "QM package for QM/MM"
278 none gaussian mopac gamess orca)
280 gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
281 gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
283 # This should be moved to a separate NBNXN cmake module when that code is cleaned up and modularized
285 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
286 mark_as_advanced(GMX_BROKEN_CALLOC)
287 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
288 mark_as_advanced(GMX_LOAD_PLUGINS)
290 option(GMX_GPU "Enable GPU acceleration" ON)
291 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
293 option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
295 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
296 mark_as_advanced(GMX_GIT_VERSION_INFO)
299 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
301 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
303 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
304 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
306 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
307 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
309 option(GMX_BUILD_FOR_COVERAGE
310 "Tune build for better code coverage metrics (e.g., disable asserts)"
312 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
314 option(GMX_DEVELOPER_BUILD
315 "Enable Developer convenience features: always build unit-tests"
317 mark_as_advanced(GMX_DEVELOPER_BUILD)
319 ######################################################################
320 # Detect OpenMP support
321 ######################################################################
322 # The OpenMP detection _must_ come before tests for other CFLAGS.
323 include(gmxManageOpenMP)
327 ######################################################################
329 # These need to be done early (before further tests).
330 #####################################################################
332 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
333 # are used with permission from CMake v3.0.0 so that GROMACS can detect
334 # invalid options with the Intel Compilers, and we have added a line
335 # to detect warnings with the Fujitsu compilers on K computer and ICC.
336 # CMake-3.0 also has a bug where the FAIL_REGEX pattern for AIX contains
337 # a semicolon. Since this is also used as a separator in lists inside CMake,
338 # that string ends up being split into two separate patterns, and the last
339 # part is just a single word that also matches other messages. We solved this
340 # by replacing the semicolon with a period that matches any character.
342 # These files should be removed from the source tree when a CMake version that
343 # includes the features in question becomes required for building GROMACS.
344 include(CheckCCompilerFlag)
345 include(CheckCXXCompilerFlag)
350 # This variable should be used for additional compiler flags which are not
351 # generated in gmxCFlags nor are SIMD or MPI related.
352 set(EXTRA_C_FLAGS "")
353 set(EXTRA_CXX_FLAGS "")
355 # Run through a number of tests for buggy compilers and other issues
356 include(gmxTestCompilerProblems)
357 gmx_test_compiler_problems()
358 # GMX_SIMD will not be set automatically until the second
359 # pass (which is not strictly guaranteed to occur), so putting this
360 # check here among logically-related tests is inefficient, but the
361 # potential loss is likely zero.
362 if(GMX_SIMD STREQUAL "AVX_256"
363 AND CMAKE_COMPILER_IS_GNUCC
364 AND (C_COMPILER_VERSION VERSION_EQUAL "4.6.1"
365 OR CXX_COMPILER_VERSION VERSION_EQUAL "4.6.1"))
366 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")
367 # See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002
374 add_definitions(-DGMX_DOUBLE)
375 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
377 if(GMX_SOFTWARE_INVSQRT)
378 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
381 if(WIN32 AND NOT CYGWIN)
382 list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
383 add_definitions(-DGMX_HAVE_WINSOCK)
388 ########################################################################
389 # Basic system tests (standard libraries, headers, functions, types) #
390 ########################################################################
391 include(CheckIncludeFiles)
392 include(CheckIncludeFileCXX)
393 check_include_files(unistd.h HAVE_UNISTD_H)
394 check_include_files(pwd.h HAVE_PWD_H)
395 check_include_files(dirent.h HAVE_DIRENT_H)
396 check_include_files(time.h HAVE_TIME_H)
397 check_include_files(sys/time.h HAVE_SYS_TIME_H)
398 check_include_files(io.h HAVE_IO_H)
399 check_include_files(sched.h HAVE_SCHED_H)
401 check_include_files(regex.h HAVE_POSIX_REGEX)
402 check_include_file_cxx(regex HAVE_CXX11_REGEX)
403 # TODO: It could be nice to inform the user if no regex support is found,
404 # as selections won't be fully functional.
406 include(CheckFunctionExists)
407 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
408 check_function_exists(memalign HAVE_MEMALIGN)
409 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
410 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
411 check_function_exists(fsync HAVE_FSYNC)
412 check_function_exists(_fileno HAVE__FILENO)
413 check_function_exists(fileno HAVE_FILENO)
414 check_function_exists(_commit HAVE__COMMIT)
415 check_function_exists(sigaction HAVE_SIGACTION)
416 check_function_exists(sysconf HAVE_SYSCONF)
417 check_function_exists(rsqrt HAVE_RSQRT)
418 check_function_exists(rsqrtf HAVE_RSQRTF)
419 check_function_exists(sqrtf HAVE_SQRTF)
421 include(CheckLibraryExists)
422 check_library_exists(m sqrt "" HAVE_LIBM)
423 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
425 include(TestSchedAffinity)
426 test_sched_affinity(HAVE_SCHED_AFFINITY)
428 include(TestBigEndian)
429 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
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(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
439 include(gmxManageBlueGene)
442 ########################################################################
443 #Process MPI settings
444 ########################################################################
445 include(gmxManageMPI)
448 ########################################################################
449 #Process shared/static library settings
450 ########################################################################
451 include(gmxManageSharedLibraries)
454 ########################################################################
455 # Find external packages #
456 ########################################################################
458 # Unconditionally find the package, as it is also required for unit
459 # tests. This exports LIBXML2_FOUND, which we should not use because
460 # it does not tell us that linking will succeed. Instead, we test that
462 if(DEFINED LIBXML2_LIBRARIES)
463 set(LibXml2_FIND_QUIETLY TRUE)
465 find_package(LibXml2)
466 include(gmxTestLibXml2)
467 gmx_test_libxml2(HAVE_LIBXML2)
468 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${HAVE_LIBXML2})
470 mark_as_advanced(GMX_XML)
471 # Don't actually do anything, since libxml2 is currently not used by libgromacs
472 #if(GMX_XML AND NOT HAVE_LIBXML2)
473 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
476 # include_directories(${LIBXML2_INCLUDE_DIR})
477 # set(PKG_XML libxml-2.0)
478 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
481 option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
482 mark_as_advanced(GMX_EXTRAE)
487 include_directories(${EXTRAE_INCLUDE_DIR})
490 message(FATAL_ERROR "EXTRAE library was not found. Please add the correct path to CMAKE_PREFIX_PATH")
494 option(GMX_X11 "Use X window system" OFF)
497 # X11 includes/libraries are only set in the ngmx subdirectory!
500 "X11 include files and/or libraries were not found. "
501 "Set GMX_X11=OFF to compile without X11 support. "
502 "gmx view will not be available.")
504 include_directories(${X11_INCLUDE_DIR})
508 # Enable core threading facilities
509 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include")
510 # Enable tMPI C++ support
513 # enable MPI functions
516 set(MPI_IN_PLACE_EXISTS 1)
518 # If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
519 if (TMPI_ATOMICS_DISABLED)
520 add_definitions(-DTMPI_ATOMICS_DISABLED)
524 # now that we have detected the dependencies, do the second configure pass
532 if(WIN32 AND NOT CYGWIN)
533 set(GMX_NATIVE_WINDOWS 1)
534 # This makes windows.h not declare min/max as macros that would break
535 # C++ code using std::min/std::max.
536 add_definitions(-DNOMINMAX)
539 # only bother with finding git and using version.h if the source is a git repo
540 if(GMX_GIT_VERSION_INFO)
541 if (NOT SOURCE_IS_GIT_REPOSITORY)
543 "Cannot generate git version information from source tree not under git. "
544 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
546 # We need at least git v1.5.3 be able to parse git's date output. If not
547 # found or the version is too small, we can't generate version information.
550 if(NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
552 "No compatible git version found (>= 1.5.3 required). "
553 "Won't be able to generate development version information. "
554 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
558 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
559 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
560 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
561 find_package(Boost 1.44.0)
562 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
563 set(Boost_FOUND FALSE)
565 # Print the notification only on first run, when determining the default
566 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
567 message("Boost >= 1.44 not found. Using minimal internal version. "
568 "This may cause trouble if you plan on compiling/linking other "
569 "software that uses Boost against Gromacs.")
572 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
574 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
576 "Boost >= 1.44 not found. "
577 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
578 "version of Boost included with Gromacs.")
581 if(NOT DEFINED GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
582 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.")
584 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${HAVE_LIBXML2})
585 mark_as_advanced(GMX_BUILD_UNITTESTS)
586 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
587 if (GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
589 "Cannot build unit tests without libxml2. "
590 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version of libxml2.")
593 if(GMX_USE_TNG AND NOT GMX_EXTERNAL_TNG)
594 # TNG wants zlib if it is available
595 find_package(ZLIB QUIET)
597 gmx_test_zlib(HAVE_ZLIB)
600 ########################################################################
601 # Generate development version info for cache
602 ########################################################################
603 # set(GEN_VERSION_INFO_INTERNAL "ON")
604 # include(gmxGenerateVersionString)
606 ########################################################################
607 # Our own GROMACS tests
608 ########################################################################
610 add_definitions( -DHAVE_CONFIG_H )
611 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
612 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
613 # Required for config.h, maybe should only be set in src/CMakeLists.txt
614 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
615 # Required for gmx_header_config_gen.h to be found before installation
616 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src/gromacs/utility)
617 # Required for now to make old code compile
618 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
620 include(gmxTestInlineASM)
621 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
623 include(gmxSetBuildInformation)
624 gmx_set_build_information()
626 # - the build system's CPU supports it
627 # - the acceleration is set to AVX as all AVX-capable CPUs support AVX (which
628 # at this point means that the user set it).
629 # Note: it's better to not use the later set value of GMX_SIMD because
630 # it reflects the system's capability of both compiling and running AVX code.
631 # TODO: After merge with 5.0 one could implement a cache variable dependency
632 # such that GMX_USE_RDTSCP can change if GMX_SIMD is changed to AVX
633 # after the first cmake pass.
634 if (BUILD_CPU_FEATURES MATCHES "rdtscp" OR GMX_SIMD MATCHES "AVX")
635 set(GMX_USE_RDTSCP_DEFAULT_VALUE ON)
637 set(GMX_USE_RDTSCP_DEFAULT_VALUE OFF)
639 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)" ${GMX_USE_RDTSCP_DEFAULT_VALUE})
640 mark_as_advanced(GMX_USE_RDTSCP)
645 include(gmxTestFloatFormat)
646 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
647 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
648 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
650 include(gmxTestLargeFiles)
651 gmx_test_large_files(GMX_LARGEFILES)
653 include(gmxTestSignal)
654 gmx_test_sigusr1(HAVE_SIGUSR1)
656 include(gmxTestPipes)
657 gmx_test_pipes(HAVE_PIPES)
659 include(gmxTestIsfinite)
660 gmx_test_isfinite(HAVE_ISFINITE)
661 gmx_test__isfinite(HAVE__ISFINITE)
662 gmx_test__finite(HAVE__FINITE)
664 include(gmxTestCXX11)
665 gmx_test_cxx11(GMX_CXX11_SUPPORTED GMX_CXX11_FLAGS)
666 include(CMakeDependentOption)
667 # nvcc does not support C++11 flags, so with GPUs we prefer to skip C++11 flags
668 # entirely to keep the compilation environment uniform.
669 cmake_dependent_option(GMX_CXX11
671 ON "GMX_CXX11_SUPPORTED AND NOT GMX_GPU" OFF)
672 mark_as_advanced(GMX_CXX11)
674 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} ${GMX_CXX11_FLAGS}")
679 gmx_test_xdr(GMX_SYSTEM_XDR)
680 if(NOT GMX_SYSTEM_XDR)
681 set(GMX_INTERNAL_XDR 1)
685 ##################################################
686 # Process SIMD instruction settings
687 ##################################################
688 # This checks what flags to add in order to
689 # support the SIMD instructions we need, and sets
690 # correct defines for the SIMD instructions supported.
695 # Process QM/MM Settings
696 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
697 set(GMX_QMMM_GAUSSIAN 1)
698 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
699 set(GMX_QMMM_MOPAC 1)
700 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
701 set(GMX_QMMM_GAMESS 1)
702 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
704 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
707 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
711 ##################################################
712 # Process FFT library settings
713 ##################################################
714 include(gmxManageFFTLibraries)
717 include(gmxManageLinearAlgebraLibraries)
719 # Whether GROMACS will really try to compile support for VMD plugins
720 set(GMX_USE_PLUGINS OFF)
723 if(CYGWIN OR NOT WIN32)
724 # Native Windows does not have, nor need dlopen
725 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
726 include(gmxTestdlopen)
727 gmx_test_dlopen(HAVE_DLOPEN)
730 # so, should we use plug-ins?
731 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
733 MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
735 if(NOT GMX_VMD_PLUGIN_PATH)
738 set(GMX_USE_PLUGINS ON)
739 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
740 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
745 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
747 # Link real-time library for POSIX timers. The check for clock_gettime
748 # confirms the linkability of rt.
749 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
750 list(APPEND GMX_EXTRA_LIBRARIES rt)
753 # Math and thread libraries must often come after all others when linking...
755 list(APPEND GMX_EXTRA_LIBRARIES m)
758 option(GMX_NACL "Configure for Native Client builds" OFF)
760 list(APPEND GMX_EXTRA_LIBRARIES nosys)
761 set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
765 mark_as_advanced(GMX_NACL)
768 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
769 "Path to swindirect.h")
770 include_directories(${COREWRAP_INCLUDE_DIR})
773 option(GMX_BUILD_HELP "Build man pages, HTML help, and completions automatically (requires that compiled binaries can be executed on the build host)" OFF)
774 mark_as_advanced(GMX_BUILD_HELP)
775 if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND
776 "${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
779 "Rebuilding HTML and man pages is not supported for in-source "
780 "builds from a source distribution. "
781 "Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
784 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
785 # these are set after everything else
786 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
787 set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
788 set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
789 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
790 set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
792 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
793 message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
794 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
795 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
796 message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
797 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
798 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
799 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
800 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
804 #Unset all OpenMP flags in case OpenMP was disabled either by the user
805 #or because it was only partially detected (e.g. only for C but not C++ compiler)
806 unset(OpenMP_C_FLAGS CACHE)
807 unset(OpenMP_CXX_FLAGS CACHE)
809 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
810 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
812 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
814 ########################################################################
815 # Specify install locations
816 ########################################################################
817 # Use GNUInstallDirs to set paths on multiarch systems.
818 include(GNUInstallDirs)
820 # Customization for the installation tree paths.
821 set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
822 "Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
823 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
824 "Data installation directory under share/ (default: gromacs)")
825 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
827 # These variables are used internally to provide a central location for
828 # customizing the install locations.
829 set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
830 set(BIN_INSTALL_DIR bin)
831 set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
832 set(MAN_INSTALL_DIR share/man)
833 set(INCL_INSTALL_DIR include)
835 # These variables get written into config.h for use in finding the data
837 set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
838 set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
840 # Binary and library suffix options
841 include(gmxManageSuffixes)
843 ################################################################
844 # Shared library load path settings
845 ################################################################
846 # CMake supports RPATH on OS X only from 2.8.12 upwards.
847 # CMAKE_SYSTEM_VERSION > 8.0 matches OS X 10.5 and above, where RPATH support
849 if((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR
850 ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (NOT CMAKE_VERSION VERSION_LESS 2.8.12)))
851 # The build folder always has bin/ and lib/; if we are also going to
852 # install to lib/, then the installation RPATH works also in the build
853 # tree. This makes installation slightly faster (no need to rewrite the
854 # RPATHs), and makes the binaries in the build tree relocatable.
855 if(GMX_LIB_INSTALL_DIR STREQUAL "lib")
856 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
858 # Set the RPATH as relative to the executable location to make the
859 # binaries relocatable.
860 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
861 set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
863 set(CMAKE_INSTALL_RPATH "@executable_path/../${GMX_LIB_INSTALL_DIR}")
865 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
866 set(CMAKE_MACOSX_RPATH 1)
868 # We are on Darwin/OSX, and CMake cannot handle RPATHs automatically.
869 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0)
870 # Set the RPATH options manually.
871 set(CMAKE_INSTALL_NAME_DIR "@rpath")
872 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../${GMX_LIB_INSTALL_DIR}")
874 # Use the old INSTALL_NAME_DIR mechanism if RPATH is not supported.
875 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
879 #COPYING file: Only necessary for binary distributions.
880 #Simpler to always install.
881 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
883 if(GMX_EXTERNAL_BOOST)
884 include_directories(${Boost_INCLUDE_DIRS})
885 set(PKG_CFLAGS "${PKG_CFLAGS} -I${Boost_INCLUDE_DIRS}")
887 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/boost)
888 # typeid not supported for minimal internal version
889 # (would add significant amount of code)
890 add_definitions(-DBOOST_NO_TYPEID)
891 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
892 # (from share/template/)
893 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${CMAKE_INSTALL_PREFIX}/${INCL_INSTALL_DIR}/gromacs/external/boost")
894 if (NOT GMX_BUILD_MDRUN_ONLY)
895 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
896 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
897 COMPONENT development)
901 if (GMX_BUILD_FOR_COVERAGE)
902 # Code heavy with asserts makes conditional coverage close to useless metric,
903 # as by design most of the false branches are impossible to trigger in
904 # correctly functioning code. And the benefit of testing those that could
905 # be triggered by using an API against its specification isn't usually
907 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
911 # "tests" target builds all the separate test binaries.
912 add_custom_target(tests)
913 # "run-ctest" is an internal target that actually runs the tests.
914 # This is necessary to be able to add separate targets that execute as part
915 # of 'make check', but are ensured to be executed after the actual tests.
916 add_custom_target(run-ctest
917 COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
918 COMMENT "Running all tests"
920 add_dependencies(run-ctest tests)
921 # "check" target builds and runs all tests.
922 add_custom_target(check DEPENDS run-ctest)
925 if (NOT GMX_BUILD_MDRUN_ONLY)
926 add_subdirectory(docs)
927 add_subdirectory(share)
928 add_subdirectory(scripts)
930 add_subdirectory(src)
933 add_subdirectory(tests)
936 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
937 # Don't bother the user after the first configure pass.
938 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
939 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
941 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
943 #######################
945 #######################
946 CONFIGURE_FILE( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
947 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
949 ###########################
950 ADD_CUSTOM_TARGET(uninstall
951 "${CMAKE_COMMAND}" -P
952 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
953 ###########################
954 set_directory_properties(PROPERTIES
955 ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")