2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2009,2010,2011,2012,2013,2014,2015, 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 "5.0.5-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 "5.0.5-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 "81e8ff1600495ce2a57706dca9d73482")
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 RELWITHDEBINFO 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 inconsistencies; 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 # Detect architecture before setting options so we can alter defaults
196 ########################################################################
197 # Detect the architecture the compiler is targetting, detect
198 # SIMD instructions possibilities on that hardware, suggest SIMD instruction set
199 # to use if none is specified, and populate the cache option for CPU
201 include(gmxDetectTargetArchitecture)
202 gmx_detect_target_architecture()
204 ########################################################################
205 # User input options #
206 ########################################################################
207 include(gmxOptionUtilities)
209 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
211 if(GMX_TARGET_FUJITSU_SPARC64)
212 # Fujitsu only has SIMD in double precision, so this will be faster
213 set(GMX_DOUBLE_DEFAULT ON)
215 set(GMX_DOUBLE_DEFAULT OFF)
217 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" ${GMX_DOUBLE_DEFAULT})
218 option(GMX_RELAXED_DOUBLE_PRECISION "Accept single precision 1/sqrt(x) when using Fujitsu HPC-ACE SIMD" OFF)
219 mark_as_advanced(GMX_RELAXED_DOUBLE_PRECISION)
221 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
222 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
223 gmx_dependent_option(
225 "Enable MPI_IN_PLACE for MPIs that have it defined"
228 mark_as_advanced(GMX_MPI_IN_PLACE)
229 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
230 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
231 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
232 mark_as_advanced(GMX_FAHCORE)
234 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
235 mark_as_advanced(GMX_COOL_QUOTES)
236 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
238 # Decide on GPU settings based on user-settings and GPU/CUDA detection.
239 # We support CUDA >=v4.0 on *nix, but <= v4.1 doesn't work with MSVC
241 set(REQUIRED_CUDA_VERSION 4.1)
243 set(REQUIRED_CUDA_VERSION 4.0)
245 set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
246 include(gmxManageGPU)
248 if(GMX_CPU_ACCELERATION)
249 # Stay compatible with old Jenkins command line options for specific SIMD acceleration
250 set(GMX_SIMD "${GMX_CPU_ACCELERATION}" CACHE STRING "SIMD instruction set level and compiler optimization" FORCE)
251 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.")
252 # TODO remove all references to GMX_CPU_ACCELERATION in master branch
255 if(NOT GMX_TARGET_MIC)
256 include(gmxDetectSimd)
257 gmx_detect_simd(GMX_SUGGESTED_SIMD)
259 set(GMX_SUGGESTED_SIMD "None")
262 gmx_option_multichoice(
264 "SIMD instruction set for CPU kernels and compiler optimization"
265 "${GMX_SUGGESTED_SIMD}"
266 None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 IBM_QPX Sparc64_HPC_ACE Reference)
268 gmx_option_multichoice(
272 fftw3 mkl "fftpack[built-in]")
273 gmx_dependent_option(
275 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
277 "GMX_FFT_LIBRARY STREQUAL FFTW3")
278 gmx_dependent_option(
279 GMX_DISABLE_FFTW_MEASURE
280 "Do not optimize FFTW setups (not needed with SSE)"
282 "GMX_FFT_LIBRARY STREQUAL FFTW3")
283 mark_as_advanced(GMX_BUILD_OWN_FFTW)
284 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
286 gmx_option_multichoice(
288 "QM package for QM/MM"
290 none gaussian mopac gamess orca)
292 gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
293 gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
295 # This should be moved to a separate NBNXN cmake module when that code is cleaned up and modularized
297 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
298 mark_as_advanced(GMX_BROKEN_CALLOC)
299 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
300 mark_as_advanced(GMX_LOAD_PLUGINS)
302 option(GMX_GPU "Enable GPU acceleration" ON)
303 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
305 option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
307 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
308 mark_as_advanced(GMX_GIT_VERSION_INFO)
311 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
313 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
315 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
316 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
318 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
319 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
321 option(GMX_BUILD_FOR_COVERAGE
322 "Tune build for better code coverage metrics (e.g., disable asserts)"
324 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
326 option(GMX_DEVELOPER_BUILD
327 "Enable Developer convenience features: always build unit-tests"
329 mark_as_advanced(GMX_DEVELOPER_BUILD)
331 ######################################################################
332 # Detect OpenMP support
333 ######################################################################
334 # The OpenMP detection _must_ come before tests for other CFLAGS.
335 include(gmxManageOpenMP)
339 ######################################################################
341 # These need to be done early (before further tests).
342 #####################################################################
344 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
345 # are used with permission from CMake v3.0.0 so that GROMACS can detect
346 # invalid options with the Intel Compilers, and we have added a line
347 # to detect warnings with the Fujitsu compilers on K computer and ICC.
348 # CMake-3.0 also has a bug where the FAIL_REGEX pattern for AIX contains
349 # a semicolon. Since this is also used as a separator in lists inside CMake,
350 # that string ends up being split into two separate patterns, and the last
351 # part is just a single word that also matches other messages. We solved this
352 # by replacing the semicolon with a period that matches any character.
354 # These files should be removed from the source tree when a CMake version that
355 # includes the features in question becomes required for building GROMACS.
356 include(CheckCCompilerFlag)
357 include(CheckCXXCompilerFlag)
362 # This variable should be used for additional compiler flags which are not
363 # generated in gmxCFlags nor are SIMD or MPI related.
364 set(EXTRA_C_FLAGS "")
365 set(EXTRA_CXX_FLAGS "")
367 # Run through a number of tests for buggy compilers and other issues
368 include(gmxTestCompilerProblems)
369 gmx_test_compiler_problems()
370 # GMX_SIMD will not be set automatically until the second
371 # pass (which is not strictly guaranteed to occur), so putting this
372 # check here among logically-related tests is inefficient, but the
373 # potential loss is likely zero.
374 if(GMX_SIMD STREQUAL "AVX_256"
375 AND CMAKE_COMPILER_IS_GNUCC
376 AND (C_COMPILER_VERSION VERSION_EQUAL "4.6.1"
377 OR CXX_COMPILER_VERSION VERSION_EQUAL "4.6.1"))
378 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")
379 # See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002
386 add_definitions(-DGMX_DOUBLE)
387 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
388 if(GMX_RELAXED_DOUBLE_PRECISION)
389 add_definitions(-DGMX_RELAXED_DOUBLE_PRECISION)
392 if(GMX_SOFTWARE_INVSQRT)
393 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
396 if(WIN32 AND NOT CYGWIN)
397 list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
398 add_definitions(-DGMX_HAVE_WINSOCK)
403 ########################################################################
404 # Basic system tests (standard libraries, headers, functions, types) #
405 ########################################################################
406 include(CheckIncludeFiles)
407 include(CheckIncludeFileCXX)
408 check_include_files(unistd.h HAVE_UNISTD_H)
409 check_include_files(pwd.h HAVE_PWD_H)
410 check_include_files(dirent.h HAVE_DIRENT_H)
411 check_include_files(time.h HAVE_TIME_H)
412 check_include_files(sys/time.h HAVE_SYS_TIME_H)
413 check_include_files(io.h HAVE_IO_H)
414 check_include_files(sched.h HAVE_SCHED_H)
416 check_include_files(regex.h HAVE_POSIX_REGEX)
417 # TODO: It could be nice to inform the user if no regex support is found,
418 # as selections won't be fully functional.
420 include(CheckFunctionExists)
421 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
422 check_function_exists(memalign HAVE_MEMALIGN)
423 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
424 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
425 check_function_exists(fsync HAVE_FSYNC)
426 check_function_exists(_fileno HAVE__FILENO)
427 check_function_exists(fileno HAVE_FILENO)
428 check_function_exists(_commit HAVE__COMMIT)
429 check_function_exists(sigaction HAVE_SIGACTION)
430 check_function_exists(sysconf HAVE_SYSCONF)
431 check_function_exists(rsqrt HAVE_RSQRT)
432 check_function_exists(rsqrtf HAVE_RSQRTF)
433 check_function_exists(sqrtf HAVE_SQRTF)
435 include(CheckLibraryExists)
436 check_library_exists(m sqrt "" HAVE_LIBM)
437 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
439 include(TestSchedAffinity)
440 test_sched_affinity(HAVE_SCHED_AFFINITY)
442 include(TestBigEndian)
443 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
445 # Management of GROMACS options for specific toolchains should go
446 # here. Because the initial settings for some of the main options have
447 # already happened, but things like library detection and MPI compiler
448 # feature detection have not, the docstrings for any over-rides of
449 # GROMACS defaults or user settings will make sense. Also, any
450 # toolchain-related reasons for choosing whether to detect various
451 # things can be sorted out now, before the detection takes place.
452 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
453 include(gmxManageBlueGene)
456 if(GMX_TARGET_FUJITSU_SPARC64)
457 include(gmxManageFujitsuSparc64)
460 ########################################################################
461 #Process MPI settings
462 ########################################################################
463 include(gmxManageMPI)
466 ########################################################################
467 #Process shared/static library settings
468 ########################################################################
469 include(gmxManageSharedLibraries)
472 ########################################################################
473 # Find external packages #
474 ########################################################################
476 # TNG wants zlib if it is available. And static libxml2 might have a dependency
477 find_package(ZLIB QUIET)
479 gmx_test_zlib(HAVE_ZLIB)
481 # Unconditionally find the package, as it is also required for unit
482 # tests. This exports LIBXML2_FOUND, which we should not use because
483 # it does not tell us that linking will succeed. Instead, we test that
485 if(DEFINED LIBXML2_LIBRARIES)
486 set(LibXml2_FIND_QUIETLY TRUE)
488 find_package(LibXml2)
489 include(gmxTestLibXml2)
490 gmx_test_libxml2(HAVE_LIBXML2)
491 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${HAVE_LIBXML2})
493 mark_as_advanced(GMX_XML)
494 # Don't actually do anything, since libxml2 is currently not used by libgromacs
495 #if(GMX_XML AND NOT HAVE_LIBXML2)
496 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
499 # include_directories(${LIBXML2_INCLUDE_DIR})
500 # set(PKG_XML libxml-2.0)
501 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
504 option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
505 mark_as_advanced(GMX_EXTRAE)
510 include_directories(${EXTRAE_INCLUDE_DIR})
513 message(FATAL_ERROR "EXTRAE library was not found. Please add the correct path to CMAKE_PREFIX_PATH")
517 option(GMX_X11 "Use X window system" OFF)
520 # X11 includes/libraries are only set in the ngmx subdirectory!
523 "X11 include files and/or libraries were not found. "
524 "Set GMX_X11=OFF to compile without X11 support. "
525 "gmx view will not be available.")
527 include_directories(${X11_INCLUDE_DIR})
531 # Enable core threading facilities
532 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include")
533 # Enable tMPI C++ support
536 # enable MPI functions
539 set(MPI_IN_PLACE_EXISTS 1)
541 # If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
542 if (TMPI_ATOMICS_DISABLED)
543 add_definitions(-DTMPI_ATOMICS_DISABLED)
547 # now that we have detected the dependencies, do the second configure pass
555 if(WIN32 AND NOT CYGWIN)
556 set(GMX_NATIVE_WINDOWS 1)
557 # This makes windows.h not declare min/max as macros that would break
558 # C++ code using std::min/std::max.
559 add_definitions(-DNOMINMAX)
562 # only bother with finding git and using version.h if the source is a git repo
563 if(GMX_GIT_VERSION_INFO)
564 if (NOT SOURCE_IS_GIT_REPOSITORY)
566 "Cannot generate git version information from source tree not under git. "
567 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
569 # We need at least git v1.5.3 be able to parse git's date output. If not
570 # found or the version is too small, we can't generate version information.
573 if(NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
575 "No compatible git version found (>= 1.5.3 required). "
576 "Won't be able to generate development version information. "
577 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
581 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
582 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
583 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
584 find_package(Boost 1.44.0)
585 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
586 set(Boost_FOUND FALSE)
588 # Print the notification only on first run, when determining the default
589 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
590 message("Boost >= 1.44 not found. Using minimal internal version. "
591 "This may cause trouble if you plan on compiling/linking other "
592 "software that uses Boost against Gromacs.")
595 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
597 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
599 "Boost >= 1.44 not found. "
600 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
601 "version of Boost included with Gromacs.")
604 if(NOT DEFINED GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
605 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.")
607 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${HAVE_LIBXML2})
608 mark_as_advanced(GMX_BUILD_UNITTESTS)
609 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
610 if (GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
612 "Cannot build unit tests without libxml2. "
613 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version of libxml2.")
616 ########################################################################
617 # Generate development version info for cache
618 ########################################################################
619 # set(GEN_VERSION_INFO_INTERNAL "ON")
620 # include(gmxGenerateVersionString)
622 ########################################################################
623 # Our own GROMACS tests
624 ########################################################################
626 add_definitions( -DHAVE_CONFIG_H )
627 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
628 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
629 # Required for config.h, maybe should only be set in src/CMakeLists.txt
630 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
631 # Required for gmx_header_config_gen.h to be found before installation
632 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src/gromacs/utility)
633 # Required for now to make old code compile
634 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
636 include(gmxTestInlineASM)
637 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
639 include(gmxSetBuildInformation)
640 gmx_set_build_information()
642 # - the build system's CPU supports it
643 # - the acceleration is set to AVX as all AVX-capable CPUs support AVX (which
644 # at this point means that the user set it).
645 # Note: it's better to not use the later set value of GMX_SIMD because
646 # it reflects the system's capability of both compiling and running AVX code.
647 # TODO: After merge with 5.0 one could implement a cache variable dependency
648 # such that GMX_USE_RDTSCP can change if GMX_SIMD is changed to AVX
649 # after the first cmake pass.
650 if (BUILD_CPU_FEATURES MATCHES "rdtscp" OR GMX_SIMD MATCHES "AVX")
651 set(GMX_USE_RDTSCP_DEFAULT_VALUE ON)
653 set(GMX_USE_RDTSCP_DEFAULT_VALUE OFF)
655 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)" ${GMX_USE_RDTSCP_DEFAULT_VALUE})
656 mark_as_advanced(GMX_USE_RDTSCP)
661 include(gmxTestFloatFormat)
662 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
663 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
664 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
666 include(gmxTestLargeFiles)
667 gmx_test_large_files(GMX_LARGEFILES)
669 include(gmxTestSignal)
670 gmx_test_sigusr1(HAVE_SIGUSR1)
672 include(gmxTestPipes)
673 gmx_test_pipes(HAVE_PIPES)
675 include(gmxTestIsfinite)
676 gmx_test_isfinite(HAVE_ISFINITE)
677 gmx_test__isfinite(HAVE__ISFINITE)
678 gmx_test__finite(HAVE__FINITE)
680 include(gmxTestCXX11)
681 gmx_test_cxx11(GMX_CXX11_SUPPORTED GMX_CXX11_FLAGS)
682 include(CMakeDependentOption)
683 # clang with some older versions of boost fail to work with C++11
684 if(CMAKE_CXX_COMPILER_ID MATCHES Clang AND
685 (Boost_VERSION VERSION_EQUAL 104601 OR Boost_VERSION VERSION_EQUAL 104700))
686 set(CLANG_AND_OLD_EXTERNAL_BOOST TRUE)
688 # nvcc does not support C++11 flags, so with GPUs we prefer to skip C++11 flags
689 # entirely to keep the compilation environment uniform.
690 cmake_dependent_option(GMX_CXX11
692 ON "GMX_CXX11_SUPPORTED AND NOT GMX_GPU AND NOT CLANG_AND_OLD_EXTERNAL_BOOST" OFF)
693 mark_as_advanced(GMX_CXX11)
695 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} ${GMX_CXX11_FLAGS}")
698 # Now we can test for CXX11_REGEX include file
699 check_include_file_cxx(regex HAVE_CXX11_REGEX)
702 gmx_test_xdr(GMX_SYSTEM_XDR)
703 if(NOT GMX_SYSTEM_XDR)
704 set(GMX_INTERNAL_XDR 1)
708 ##################################################
709 # Process SIMD instruction settings
710 ##################################################
711 # This checks what flags to add in order to
712 # support the SIMD instructions we need, and sets
713 # correct defines for the SIMD instructions supported.
718 # Process QM/MM Settings
719 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
720 set(GMX_QMMM_GAUSSIAN 1)
721 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
722 set(GMX_QMMM_MOPAC 1)
723 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
724 set(GMX_QMMM_GAMESS 1)
725 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
727 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
730 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
734 ##################################################
735 # Process FFT library settings
736 ##################################################
737 include(gmxManageFFTLibraries)
740 include(gmxManageLinearAlgebraLibraries)
742 # Whether GROMACS will really try to compile support for VMD plugins
743 set(GMX_USE_PLUGINS OFF)
746 if(CYGWIN OR NOT WIN32)
747 # Native Windows does not have, nor need dlopen
748 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
749 include(gmxTestdlopen)
750 gmx_test_dlopen(HAVE_DLOPEN)
753 # so, should we use plug-ins?
754 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
756 MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
758 if(NOT GMX_VMD_PLUGIN_PATH)
761 set(GMX_USE_PLUGINS ON)
762 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
763 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
768 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
770 # Link real-time library for POSIX timers. The check for clock_gettime
771 # confirms the linkability of rt.
772 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
773 list(APPEND GMX_EXTRA_LIBRARIES rt)
776 # Math and thread libraries must often come after all others when linking...
778 list(APPEND GMX_EXTRA_LIBRARIES m)
781 option(GMX_NACL "Configure for Native Client builds" OFF)
783 list(APPEND GMX_EXTRA_LIBRARIES nosys)
784 set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
788 mark_as_advanced(GMX_NACL)
791 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
792 "Path to swindirect.h")
793 include_directories(${COREWRAP_INCLUDE_DIR})
796 option(GMX_BUILD_HELP "Build man pages, HTML help, and completions automatically (requires that compiled binaries can be executed on the build host)" OFF)
797 mark_as_advanced(GMX_BUILD_HELP)
798 if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND
799 "${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
802 "Rebuilding HTML and man pages is not supported for in-source "
803 "builds from a source distribution. "
804 "Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
807 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
808 # these are set after everything else
809 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
810 set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
811 set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
812 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
813 set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
815 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
816 message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
817 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
818 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
819 message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
820 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
821 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
822 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
823 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
827 #Unset all OpenMP flags in case OpenMP was disabled either by the user
828 #or because it was only partially detected (e.g. only for C but not C++ compiler)
829 unset(OpenMP_C_FLAGS CACHE)
830 unset(OpenMP_CXX_FLAGS CACHE)
832 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
833 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
835 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
837 ########################################################################
838 # Specify install locations
839 ########################################################################
840 # Use GNUInstallDirs to set paths on multiarch systems.
841 include(GNUInstallDirs)
843 # Customization for the installation tree paths.
844 set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
845 "Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
846 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
847 "Data installation directory under share/ (default: gromacs)")
848 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
850 # These variables are used internally to provide a central location for
851 # customizing the install locations.
852 set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
853 set(BIN_INSTALL_DIR bin)
854 set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
855 set(MAN_INSTALL_DIR share/man)
856 set(INCL_INSTALL_DIR include)
858 # These variables get written into config.h for use in finding the data
860 set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
861 set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
863 # Binary and library suffix options
864 include(gmxManageSuffixes)
866 ################################################################
867 # Shared library load path settings
868 ################################################################
869 # CMake supports RPATH on OS X only from 2.8.12 upwards.
870 # CMAKE_SYSTEM_VERSION > 8.0 matches OS X 10.5 and above, where RPATH support
872 if((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR
873 ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (NOT CMAKE_VERSION VERSION_LESS 2.8.12)))
874 # The build folder always has bin/ and lib/; if we are also going to
875 # install to lib/, then the installation RPATH works also in the build
876 # tree. This makes installation slightly faster (no need to rewrite the
877 # RPATHs), and makes the binaries in the build tree relocatable.
878 if(GMX_LIB_INSTALL_DIR STREQUAL "lib")
879 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
881 # Set the RPATH as relative to the executable location to make the
882 # binaries relocatable.
883 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
884 set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
886 set(CMAKE_INSTALL_RPATH "@executable_path/../${GMX_LIB_INSTALL_DIR}")
888 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
889 set(CMAKE_MACOSX_RPATH 1)
891 # We are on Darwin/OSX, and CMake cannot handle RPATHs automatically.
892 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0)
893 # Set the RPATH options manually.
894 set(CMAKE_INSTALL_NAME_DIR "@rpath")
895 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../${GMX_LIB_INSTALL_DIR}")
897 # Use the old INSTALL_NAME_DIR mechanism if RPATH is not supported.
898 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
902 #COPYING file: Only necessary for binary distributions.
903 #Simpler to always install.
904 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
906 if(GMX_EXTERNAL_BOOST)
907 include_directories(${Boost_INCLUDE_DIRS})
908 set(PKG_CFLAGS "${PKG_CFLAGS} -I${Boost_INCLUDE_DIRS}")
910 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/boost)
911 # typeid not supported for minimal internal version
912 # (would add significant amount of code)
913 add_definitions(-DBOOST_NO_TYPEID)
914 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
915 # (from share/template/)
916 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${CMAKE_INSTALL_PREFIX}/${INCL_INSTALL_DIR}/gromacs/external/boost")
917 if (NOT GMX_BUILD_MDRUN_ONLY)
918 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
919 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
920 COMPONENT development)
924 if (GMX_BUILD_FOR_COVERAGE)
925 # Code heavy with asserts makes conditional coverage close to useless metric,
926 # as by design most of the false branches are impossible to trigger in
927 # correctly functioning code. And the benefit of testing those that could
928 # be triggered by using an API against its specification isn't usually
930 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
934 # "tests" target builds all the separate test binaries.
935 add_custom_target(tests)
936 # "run-ctest" is an internal target that actually runs the tests.
937 # This is necessary to be able to add separate targets that execute as part
938 # of 'make check', but are ensured to be executed after the actual tests.
939 add_custom_target(run-ctest
940 COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
941 COMMENT "Running all tests"
943 add_dependencies(run-ctest tests)
944 # "check" target builds and runs all tests.
945 add_custom_target(check DEPENDS run-ctest)
948 if (NOT GMX_BUILD_MDRUN_ONLY)
949 add_subdirectory(docs)
950 add_subdirectory(share)
951 add_subdirectory(scripts)
953 add_subdirectory(src)
956 add_subdirectory(tests)
959 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
960 # Don't bother the user after the first configure pass.
961 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
962 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
964 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
966 #######################
968 #######################
969 CONFIGURE_FILE( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
970 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
972 ###########################
973 ADD_CUSTOM_TARGET(uninstall
974 "${CMAKE_COMMAND}" -P
975 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
976 ###########################
977 set_directory_properties(PROPERTIES
978 ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")