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 "5.0.6-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 "5.0.6-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 "c3258e8c3162ce851718d1649e33e565")
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 "${GMX_SUGGESTED_SIMD}"
266 None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 IBM_QPX Sparc64_HPC_ACE Reference)
269 set(GMX_FFT_LIBRARY_DEFAULT "mkl")
271 set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
274 gmx_option_multichoice(
277 "${GMX_FFT_LIBRARY_DEFAULT}"
278 fftw3 mkl "fftpack[built-in]")
279 gmx_dependent_option(
281 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
283 "GMX_FFT_LIBRARY STREQUAL FFTW3")
284 gmx_dependent_option(
285 GMX_DISABLE_FFTW_MEASURE
286 "Do not optimize FFTW setups (not needed with SSE)"
288 "GMX_FFT_LIBRARY STREQUAL FFTW3")
289 mark_as_advanced(GMX_BUILD_OWN_FFTW)
290 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
292 gmx_option_multichoice(
294 "QM package for QM/MM"
296 none gaussian mopac gamess orca)
298 gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
299 gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
301 # This should be moved to a separate NBNXN cmake module when that code is cleaned up and modularized
303 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
304 mark_as_advanced(GMX_BROKEN_CALLOC)
305 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
306 mark_as_advanced(GMX_LOAD_PLUGINS)
308 option(GMX_GPU "Enable GPU acceleration" ON)
309 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
311 option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
313 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
314 mark_as_advanced(GMX_GIT_VERSION_INFO)
317 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
319 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
321 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
322 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
324 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
325 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
327 option(GMX_BUILD_FOR_COVERAGE
328 "Tune build for better code coverage metrics (e.g., disable asserts)"
330 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
332 option(GMX_DEVELOPER_BUILD
333 "Enable Developer convenience features: always build unit-tests"
335 mark_as_advanced(GMX_DEVELOPER_BUILD)
337 option(GMX_BUILD_SHARED_EXE
338 "Build exectuables as shared binaries. If not set, this disables rpath and dynamic linker flags in an attempt to build a static binary, but this may require setting up the toolchain properly and making appropriate libraries available."
340 mark_as_advanced(GMX_BUILD_SHARED_EXE)
342 ######################################################################
343 # Detect OpenMP support
344 ######################################################################
345 # The OpenMP detection _must_ come before tests for other CFLAGS.
346 include(gmxManageOpenMP)
350 ######################################################################
352 # These need to be done early (before further tests).
353 #####################################################################
355 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
356 # are used with permission from CMake v3.0.0 so that GROMACS can detect
357 # invalid options with the Intel Compilers, and we have added a line
358 # to detect warnings with the Fujitsu compilers on K computer and ICC.
359 # CMake-3.0 also has a bug where the FAIL_REGEX pattern for AIX contains
360 # a semicolon. Since this is also used as a separator in lists inside CMake,
361 # that string ends up being split into two separate patterns, and the last
362 # part is just a single word that also matches other messages. We solved this
363 # by replacing the semicolon with a period that matches any character.
365 # These files should be removed from the source tree when a CMake version that
366 # includes the features in question becomes required for building GROMACS.
367 include(CheckCCompilerFlag)
368 include(CheckCXXCompilerFlag)
373 # This variable should be used for additional compiler flags which are not
374 # generated in gmxCFlags nor are SIMD or MPI related.
375 set(EXTRA_C_FLAGS "")
376 set(EXTRA_CXX_FLAGS "")
378 # Run through a number of tests for buggy compilers and other issues
379 include(gmxTestCompilerProblems)
380 gmx_test_compiler_problems()
381 # GMX_SIMD will not be set automatically until the second
382 # pass (which is not strictly guaranteed to occur), so putting this
383 # check here among logically-related tests is inefficient, but the
384 # potential loss is likely zero.
385 if(GMX_SIMD STREQUAL "AVX_256"
386 AND CMAKE_COMPILER_IS_GNUCC
387 AND (C_COMPILER_VERSION VERSION_EQUAL "4.6.1"
388 OR CXX_COMPILER_VERSION VERSION_EQUAL "4.6.1"))
389 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")
390 # See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002
397 add_definitions(-DGMX_DOUBLE)
398 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
399 if(GMX_RELAXED_DOUBLE_PRECISION)
400 add_definitions(-DGMX_RELAXED_DOUBLE_PRECISION)
403 if(GMX_SOFTWARE_INVSQRT)
404 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
407 if(WIN32 AND NOT CYGWIN)
408 list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
409 add_definitions(-DGMX_HAVE_WINSOCK)
414 ########################################################################
415 # Basic system tests (standard libraries, headers, functions, types) #
416 ########################################################################
417 include(CheckIncludeFiles)
418 include(CheckIncludeFileCXX)
419 check_include_files(unistd.h HAVE_UNISTD_H)
420 check_include_files(pwd.h HAVE_PWD_H)
421 check_include_files(dirent.h HAVE_DIRENT_H)
422 check_include_files(time.h HAVE_TIME_H)
423 check_include_files(sys/time.h HAVE_SYS_TIME_H)
424 check_include_files(io.h HAVE_IO_H)
425 check_include_files(sched.h HAVE_SCHED_H)
427 check_include_files(regex.h HAVE_POSIX_REGEX)
428 # TODO: It could be nice to inform the user if no regex support is found,
429 # as selections won't be fully functional.
431 include(CheckFunctionExists)
432 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
433 check_function_exists(memalign HAVE_MEMALIGN)
434 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
435 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
436 check_function_exists(fsync HAVE_FSYNC)
437 check_function_exists(_fileno HAVE__FILENO)
438 check_function_exists(fileno HAVE_FILENO)
439 check_function_exists(_commit HAVE__COMMIT)
440 check_function_exists(sigaction HAVE_SIGACTION)
441 check_function_exists(sysconf HAVE_SYSCONF)
442 check_function_exists(rsqrt HAVE_RSQRT)
443 check_function_exists(rsqrtf HAVE_RSQRTF)
444 check_function_exists(sqrtf HAVE_SQRTF)
446 include(CheckLibraryExists)
447 check_library_exists(m sqrt "" HAVE_LIBM)
448 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
450 include(TestSchedAffinity)
451 test_sched_affinity(HAVE_SCHED_AFFINITY)
453 include(TestBigEndian)
454 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
456 # Management of GROMACS options for specific toolchains should go
457 # here. Because the initial settings for some of the main options have
458 # already happened, but things like library detection and MPI compiler
459 # feature detection have not, the docstrings for any over-rides of
460 # GROMACS defaults or user settings will make sense. Also, any
461 # toolchain-related reasons for choosing whether to detect various
462 # things can be sorted out now, before the detection takes place.
463 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
464 include(gmxManageBlueGene)
467 if(GMX_TARGET_FUJITSU_SPARC64)
468 include(gmxManageFujitsuSparc64)
471 ########################################################################
472 #Process MPI settings
473 ########################################################################
474 include(gmxManageMPI)
477 ########################################################################
478 #Process shared/static library settings
479 ########################################################################
480 include(gmxManageSharedLibraries)
483 ########################################################################
484 # Find external packages #
485 ########################################################################
487 # TNG wants zlib if it is available. And static libxml2 might have a dependency
488 find_package(ZLIB QUIET)
490 gmx_test_zlib(HAVE_ZLIB)
492 # Unconditionally find the package, as it is also required for unit
493 # tests. This exports LIBXML2_FOUND, which we should not use because
494 # it does not tell us that linking will succeed. Instead, we test that
496 if(DEFINED LIBXML2_LIBRARIES)
497 set(LibXml2_FIND_QUIETLY TRUE)
499 find_package(LibXml2)
500 include(gmxTestLibXml2)
501 gmx_test_libxml2(HAVE_LIBXML2)
502 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${HAVE_LIBXML2})
504 mark_as_advanced(GMX_XML)
505 # Don't actually do anything, since libxml2 is currently not used by libgromacs
506 #if(GMX_XML AND NOT HAVE_LIBXML2)
507 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
510 # include_directories(${LIBXML2_INCLUDE_DIR})
511 # set(PKG_XML libxml-2.0)
512 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
515 option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
516 mark_as_advanced(GMX_EXTRAE)
521 include_directories(${EXTRAE_INCLUDE_DIR})
524 message(FATAL_ERROR "EXTRAE library was not found. Please add the correct path to CMAKE_PREFIX_PATH")
528 option(GMX_X11 "Use X window system" OFF)
531 # X11 includes/libraries are only set in the ngmx subdirectory!
534 "X11 include files and/or libraries were not found. "
535 "Set GMX_X11=OFF to compile without X11 support. "
536 "gmx view will not be available.")
538 include_directories(${X11_INCLUDE_DIR})
542 # Enable core threading facilities
543 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include")
544 # Enable tMPI C++ support
547 # enable MPI functions
550 set(MPI_IN_PLACE_EXISTS 1)
552 # If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
553 if (TMPI_ATOMICS_DISABLED)
554 add_definitions(-DTMPI_ATOMICS_DISABLED)
558 # now that we have detected the dependencies, do the second configure pass
566 if(WIN32 AND NOT CYGWIN)
567 set(GMX_NATIVE_WINDOWS 1)
568 # This makes windows.h not declare min/max as macros that would break
569 # C++ code using std::min/std::max.
570 add_definitions(-DNOMINMAX)
573 # only bother with finding git and using version.h if the source is a git repo
574 if(GMX_GIT_VERSION_INFO)
575 if (NOT SOURCE_IS_GIT_REPOSITORY)
577 "Cannot generate git version information from source tree not under git. "
578 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
580 # We need at least git v1.5.3 be able to parse git's date output. If not
581 # found or the version is too small, we can't generate version information.
584 if(NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
586 "No compatible git version found (>= 1.5.3 required). "
587 "Won't be able to generate development version information. "
588 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
592 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
593 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
594 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
595 find_package(Boost 1.44.0)
596 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
597 set(Boost_FOUND FALSE)
599 # Print the notification only on first run, when determining the default
600 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
601 message("Boost >= 1.44 not found. Using minimal internal version. "
602 "This may cause trouble if you plan on compiling/linking other "
603 "software that uses Boost against Gromacs.")
606 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
608 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
610 "Boost >= 1.44 not found. "
611 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
612 "version of Boost included with Gromacs.")
615 if(NOT DEFINED GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
616 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.")
618 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${HAVE_LIBXML2})
619 mark_as_advanced(GMX_BUILD_UNITTESTS)
620 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
621 if (GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
623 "Cannot build unit tests without libxml2. "
624 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version of libxml2.")
627 ########################################################################
628 # Generate development version info for cache
629 ########################################################################
630 # set(GEN_VERSION_INFO_INTERNAL "ON")
631 # include(gmxGenerateVersionString)
633 ########################################################################
634 # Our own GROMACS tests
635 ########################################################################
637 add_definitions( -DHAVE_CONFIG_H )
638 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
639 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
640 # Required for config.h, maybe should only be set in src/CMakeLists.txt
641 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
642 # Required for gmx_header_config_gen.h to be found before installation
643 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src/gromacs/utility)
644 # Required for now to make old code compile
645 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
647 include(gmxTestInlineASM)
648 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
650 include(gmxSetBuildInformation)
651 gmx_set_build_information()
653 # - the build system's CPU supports it
654 # - the acceleration is set to AVX as all AVX-capable CPUs support AVX (which
655 # at this point means that the user set it).
656 # Note: it's better to not use the later set value of GMX_SIMD because
657 # it reflects the system's capability of both compiling and running AVX code.
658 # TODO: After merge with 5.0 one could implement a cache variable dependency
659 # such that GMX_USE_RDTSCP can change if GMX_SIMD is changed to AVX
660 # after the first cmake pass.
661 if (BUILD_CPU_FEATURES MATCHES "rdtscp" OR GMX_SIMD MATCHES "AVX")
662 set(GMX_USE_RDTSCP_DEFAULT_VALUE ON)
664 set(GMX_USE_RDTSCP_DEFAULT_VALUE OFF)
666 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)" ${GMX_USE_RDTSCP_DEFAULT_VALUE})
667 mark_as_advanced(GMX_USE_RDTSCP)
672 include(gmxTestFloatFormat)
673 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
674 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
675 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
677 include(gmxTestLargeFiles)
678 gmx_test_large_files(GMX_LARGEFILES)
680 include(gmxTestSignal)
681 gmx_test_sigusr1(HAVE_SIGUSR1)
683 include(gmxTestPipes)
684 gmx_test_pipes(HAVE_PIPES)
686 include(gmxTestIsfinite)
687 gmx_test_isfinite(HAVE_ISFINITE)
688 gmx_test__isfinite(HAVE__ISFINITE)
689 gmx_test__finite(HAVE__FINITE)
691 include(gmxTestCXX11)
692 gmx_test_cxx11(GMX_CXX11_SUPPORTED GMX_CXX11_FLAGS)
693 include(CMakeDependentOption)
694 # clang with some older versions of boost fail to work with C++11
695 if(CMAKE_CXX_COMPILER_ID MATCHES Clang AND
696 (Boost_VERSION VERSION_EQUAL 104601 OR Boost_VERSION VERSION_EQUAL 104700))
697 set(CLANG_AND_OLD_EXTERNAL_BOOST TRUE)
699 # nvcc does not support C++11 flags, so with GPUs we prefer to skip C++11 flags
700 # entirely to keep the compilation environment uniform.
701 cmake_dependent_option(GMX_CXX11
703 ON "GMX_CXX11_SUPPORTED AND NOT GMX_GPU AND NOT CLANG_AND_OLD_EXTERNAL_BOOST" OFF)
704 mark_as_advanced(GMX_CXX11)
706 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} ${GMX_CXX11_FLAGS}")
709 # Now we can test for CXX11_REGEX include file
710 check_include_file_cxx(regex HAVE_CXX11_REGEX)
713 gmx_test_xdr(GMX_SYSTEM_XDR)
714 if(NOT GMX_SYSTEM_XDR)
715 set(GMX_INTERNAL_XDR 1)
719 ##################################################
720 # Process SIMD instruction settings
721 ##################################################
722 # This checks what flags to add in order to
723 # support the SIMD instructions we need, and sets
724 # correct defines for the SIMD instructions supported.
729 # Process QM/MM Settings
730 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
731 set(GMX_QMMM_GAUSSIAN 1)
732 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
733 set(GMX_QMMM_MOPAC 1)
734 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
735 set(GMX_QMMM_GAMESS 1)
736 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
738 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
741 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
745 ##################################################
746 # Process FFT library settings
747 ##################################################
748 include(gmxManageFFTLibraries)
751 include(gmxManageLinearAlgebraLibraries)
753 # Whether GROMACS will really try to compile support for VMD plugins
754 set(GMX_USE_PLUGINS OFF)
757 if(CYGWIN OR NOT WIN32)
758 # Native Windows does not have, nor need dlopen
759 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
760 include(gmxTestdlopen)
761 gmx_test_dlopen(HAVE_DLOPEN)
764 # so, should we use plug-ins?
765 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
767 MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
769 if(NOT GMX_VMD_PLUGIN_PATH)
772 set(GMX_USE_PLUGINS ON)
773 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
774 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
779 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
781 # Link real-time library for POSIX timers. The check for clock_gettime
782 # confirms the linkability of rt.
783 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
784 list(APPEND GMX_EXTRA_LIBRARIES rt)
787 # Math and thread libraries must often come after all others when linking...
789 list(APPEND GMX_EXTRA_LIBRARIES m)
792 option(GMX_NACL "Configure for Native Client builds" OFF)
794 list(APPEND GMX_EXTRA_LIBRARIES nosys)
795 set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
799 mark_as_advanced(GMX_NACL)
802 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
803 "Path to swindirect.h")
804 include_directories(${COREWRAP_INCLUDE_DIR})
807 option(GMX_BUILD_HELP "Build man pages, HTML help, and completions automatically (requires that compiled binaries can be executed on the build host)" OFF)
808 mark_as_advanced(GMX_BUILD_HELP)
809 if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND
810 "${CMAKE_CURRENT_SOURCE_DIR}" STREQUAL "${CMAKE_CURRENT_BINARY_DIR}")
813 "Rebuilding HTML and man pages is not supported for in-source "
814 "builds from a source distribution. "
815 "Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
818 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
819 # these are set after everything else
820 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
821 set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
822 set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
823 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
824 set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
826 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
827 message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
828 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
829 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
830 message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
831 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
832 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
833 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
834 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
838 #Unset all OpenMP flags in case OpenMP was disabled either by the user
839 #or because it was only partially detected (e.g. only for C but not C++ compiler)
840 unset(OpenMP_C_FLAGS CACHE)
841 unset(OpenMP_CXX_FLAGS CACHE)
843 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
844 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
846 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
848 ########################################################################
849 # Specify install locations
850 ########################################################################
851 # Use GNUInstallDirs to set paths on multiarch systems.
852 include(GNUInstallDirs)
854 # Customization for the installation tree paths.
855 set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
856 "Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
857 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
858 "Data installation directory under share/ (default: gromacs)")
859 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
861 # These variables are used internally to provide a central location for
862 # customizing the install locations.
863 set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
864 set(BIN_INSTALL_DIR bin)
865 set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
866 set(MAN_INSTALL_DIR share/man)
867 set(INCL_INSTALL_DIR include)
869 # These variables get written into config.h for use in finding the data
871 set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
872 set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
874 # Binary and library suffix options
875 include(gmxManageSuffixes)
877 ################################################################
878 # Shared library load path settings
879 ################################################################
880 # CMake supports RPATH on OS X only from 2.8.12 upwards.
881 # CMAKE_SYSTEM_VERSION > 8.0 matches OS X 10.5 and above, where RPATH support
884 if(NOT GMX_BUILD_SHARED_EXE)
886 set(CMAKE_SKIP_RPATH TRUE)
887 set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) # remove -Wl,-Bdynamic
888 set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
889 elseif((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR
890 ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (NOT CMAKE_VERSION VERSION_LESS 2.8.12)))
891 # The build folder always has bin/ and lib/; if we are also going to
892 # install to lib/, then the installation RPATH works also in the build
893 # tree. This makes installation slightly faster (no need to rewrite the
894 # RPATHs), and makes the binaries in the build tree relocatable.
895 if(GMX_LIB_INSTALL_DIR STREQUAL "lib")
896 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
898 # Set the RPATH as relative to the executable location to make the
899 # binaries relocatable.
900 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
901 set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
903 set(CMAKE_INSTALL_RPATH "@executable_path/../${GMX_LIB_INSTALL_DIR}")
905 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
906 set(CMAKE_MACOSX_RPATH 1)
908 # We are on Darwin/OSX, and CMake cannot handle RPATHs automatically.
909 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0)
910 # Set the RPATH options manually.
911 set(CMAKE_INSTALL_NAME_DIR "@rpath")
912 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../${GMX_LIB_INSTALL_DIR}")
914 # Use the old INSTALL_NAME_DIR mechanism if RPATH is not supported.
915 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
919 #COPYING file: Only necessary for binary distributions.
920 #Simpler to always install.
921 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
923 if(GMX_EXTERNAL_BOOST)
924 include_directories(${Boost_INCLUDE_DIRS})
925 set(PKG_CFLAGS "${PKG_CFLAGS} -I${Boost_INCLUDE_DIRS}")
927 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/boost)
928 # typeid not supported for minimal internal version
929 # (would add significant amount of code)
930 add_definitions(-DBOOST_NO_TYPEID)
931 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
932 # (from share/template/)
933 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${CMAKE_INSTALL_PREFIX}/${INCL_INSTALL_DIR}/gromacs/external/boost")
934 if (NOT GMX_BUILD_MDRUN_ONLY)
935 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
936 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
937 COMPONENT development)
941 if (GMX_BUILD_FOR_COVERAGE)
942 # Code heavy with asserts makes conditional coverage close to useless metric,
943 # as by design most of the false branches are impossible to trigger in
944 # correctly functioning code. And the benefit of testing those that could
945 # be triggered by using an API against its specification isn't usually
947 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
951 # "tests" target builds all the separate test binaries.
952 add_custom_target(tests)
953 # "run-ctest" is an internal target that actually runs the tests.
954 # This is necessary to be able to add separate targets that execute as part
955 # of 'make check', but are ensured to be executed after the actual tests.
956 add_custom_target(run-ctest
957 COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
958 COMMENT "Running all tests"
960 add_dependencies(run-ctest tests)
961 # "check" target builds and runs all tests.
962 add_custom_target(check DEPENDS run-ctest)
965 if (NOT GMX_BUILD_MDRUN_ONLY)
966 add_subdirectory(docs)
967 add_subdirectory(share)
968 add_subdirectory(scripts)
970 add_subdirectory(src)
973 add_subdirectory(tests)
976 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
977 # Don't bother the user after the first configure pass.
978 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
979 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
981 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
983 #######################
985 #######################
986 CONFIGURE_FILE( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
987 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
989 ###########################
990 ADD_CUSTOM_TARGET(uninstall
991 "${CMAKE_COMMAND}" -P
992 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
993 ###########################
994 set_directory_properties(PROPERTIES
995 ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")