2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2009,2010,2011,2012,2013, 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)
37 # CMake modules/macros are in a subdirectory to keep this file cleaner
38 # This needs to be set before project() in order to pick up toolchain files
39 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
43 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
44 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
45 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
47 # PROJECT_VERSION should have the following structure:
48 # VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
50 # The "-dev" suffix is important to keep because it makes possible to distinguish
51 # between a build from official release and a build from git release branch on a
52 # machine with no git.
54 # NOTE: when releasing the "-dev" suffix needs to be stripped off!
55 set(PROJECT_VERSION "5.0-beta2-dev")
56 # The version number of the regressiontest tarball against which this
57 # git branch can be tested. Normally, this will be the version of the
58 # last patch release. Comment the next line out for branches leading
59 # to a major/minor release.
60 set(REGRESSIONTEST_VERSION "5.0-beta1")
61 set(CUSTOM_VERSION_STRING ""
62 CACHE STRING "Custom version string (if empty, use hard-coded default)")
63 mark_as_advanced(CUSTOM_VERSION_STRING)
64 if (CUSTOM_VERSION_STRING)
65 set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
66 endif (CUSTOM_VERSION_STRING)
68 # It is a bit irritating, but this has to be set separately for now!
69 SET(CPACK_PACKAGE_VERSION_MAJOR "5")
70 SET(CPACK_PACKAGE_VERSION_MINOR "0")
71 #SET(CPACK_PACKAGE_VERSION_PATCH "0")
73 # The numerical gromacs version. It is 40600 for 4.6.0.
74 # The #define GMX_VERSION in gmx_header_config_h is set to this value.
76 "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
77 if(CPACK_PACKAGE_VERSION_PATCH)
79 "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
82 # The API version tracks the numerical Gromacs version (for now).
83 # It is potentially different from the Gromacs version in the future, if
84 # the programs/libraries diverge from the presumably more stable API.
85 # The #define GMX_API_VERSION in version.h is set to this value to
86 # provide backward compatibility of software written against the Gromacs API.
87 set(API_VERSION ${NUM_VERSION})
89 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
90 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
93 set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
94 mark_as_advanced(GMX_INSTALL_PREFIX)
96 include(gmxBuildTypeReference)
98 if(NOT CMAKE_BUILD_TYPE)
99 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference." FORCE)
100 # Set the possible values of build type for cmake-gui
101 set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
102 "MinSizeRel" "RelWithDebInfo")
103 endif(NOT CMAKE_BUILD_TYPE)
108 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
109 set(CPACK_PACKAGE_VENDOR "gromacs.org")
110 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
111 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
112 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
113 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
114 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
115 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$")
116 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
117 set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/share/man/man1;share/man/man1;${CMAKE_BINARY_DIR}/share/man/man7;share/man/man7;${CMAKE_BINARY_DIR}/share/html/final;share/html")
118 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
120 #must come after all cpack settings!
123 # Set a default valgrind suppression file.
124 # This unfortunately needs to duplicate information from CTest to work as
126 set(MEMORYCHECK_SUPPRESSIONS_FILE
127 "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
129 "File that contains suppressions for the memory checker")
132 set(SOURCE_IS_GIT_REPOSITORY OFF)
133 set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
134 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
135 set(SOURCE_IS_GIT_REPOSITORY ON)
137 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
138 set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
141 ########################################################################
142 # Check and warn if cache generated on a different host is being reused
143 ########################################################################
145 execute_process(COMMAND hostname
146 OUTPUT_VARIABLE TMP_HOSTNAME
147 OUTPUT_STRIP_TRAILING_WHITESPACE)
148 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
150 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
151 is being reused! This could lead to inconsitencies; therefore, it is
152 recommended to regenerate the cache!")
154 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
155 "Hostname of the machine where the cache was generated.")
158 ########################################################################
159 # User input options #
160 ########################################################################
161 include(gmxOptionUtilities)
163 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
165 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
166 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
167 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
168 gmx_dependent_option(
170 "Enable MPI_IN_PLACE for MPIs that have it defined"
173 mark_as_advanced(GMX_MPI_IN_PLACE)
174 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
175 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
176 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
177 mark_as_advanced(GMX_FAHCORE)
179 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
180 mark_as_advanced(GMX_COOL_QUOTES)
181 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
183 # decide on GPU settings based on user-settings and GPU/CUDA detection
184 include(gmxManageGPU)
186 # Detect the architecture the compiler is targetting, detect
187 # acceleration possibilities on that hardware, suggest an acceleration
188 # to use if none is specified, and populate the cache option for CPU
190 include(gmxDetectTargetArchitecture)
191 gmx_detect_target_architecture()
192 include(gmxDetectAcceleration)
193 gmx_detect_acceleration(GMX_SUGGESTED_CPU_ACCELERATION)
195 gmx_option_multichoice(
197 "Acceleration for CPU kernels and compiler optimization"
198 "${GMX_SUGGESTED_CPU_ACCELERATION}"
199 None SSE2 SSE4.1 AVX_128_FMA AVX_256 IBM_QPX Sparc64_HPC_ACE)
201 gmx_option_multichoice(
205 fftw3 mkl "fftpack[built-in]")
206 gmx_dependent_option(
208 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
210 "GMX_FFT_LIBRARY STREQUAL FFTW3")
211 gmx_dependent_option(
212 GMX_DISABLE_FFTW_MEASURE
213 "Do not optimize FFTW setups (not needed with SSE)"
215 "GMX_FFT_LIBRARY STREQUAL FFTW3")
216 mark_as_advanced(GMX_BUILD_OWN_FFTW)
217 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
219 gmx_option_multichoice(
221 "QM package for QM/MM"
223 none gaussian mopac gamess orca)
225 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
226 mark_as_advanced(GMX_BROKEN_CALLOC)
227 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
228 mark_as_advanced(GMX_LOAD_PLUGINS)
230 option(GMX_GPU "Enable GPU acceleration" ON)
231 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
233 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
234 mark_as_advanced(GMX_GIT_VERSION_INFO)
237 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
239 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
241 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
242 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
244 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
245 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
247 option(GMX_BUILD_FOR_COVERAGE
248 "Tune build for better code coverage metrics (e.g., disable asserts)"
250 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
253 ######################################################################
254 # Detect OpenMP support
255 ######################################################################
256 # The OpenMP detection _must_ come before tests for other CFLAGS.
257 include(gmxManageOpenMP)
261 ######################################################################
263 # These need to be done early (before further tests).
264 #####################################################################
266 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
267 # are used with permission from CMake v2.8.9 so that GROMACS can detect
268 # invalid options with the Intel Compilers.
269 # These files should be removed from the source tree when a CMake version that
270 # includes the features in question becomes required for building GROMACS.
271 include(CheckCCompilerFlag)
272 include(CheckCXXCompilerFlag)
278 # This variable should be used for additional compiler flags which are not
279 # generated in gmxCFlags nor are acceleration or MPI related.
280 set(EXTRA_C_FLAGS "")
281 set(EXTRA_CXX_FLAGS "")
283 # Run through a number of tests for buggy compilers and other issues
284 include(gmxTestCompilerProblems)
285 gmx_test_compiler_problems()
290 add_definitions(-DGMX_DOUBLE)
291 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
293 if(GMX_SOFTWARE_INVSQRT)
294 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
295 endif(GMX_SOFTWARE_INVSQRT)
299 ########################################################################
300 # Basic system tests (standard libraries, headers, functions, types) #
301 ########################################################################
302 include(CheckIncludeFiles)
303 include(CheckIncludeFileCXX)
304 check_include_files(unistd.h HAVE_UNISTD_H)
305 check_include_files(pwd.h HAVE_PWD_H)
306 check_include_files(dirent.h HAVE_DIRENT_H)
307 check_include_files(time.h HAVE_TIME_H)
308 check_include_files(sys/time.h HAVE_SYS_TIME_H)
309 check_include_files(io.h HAVE_IO_H)
310 check_include_files(sched.h HAVE_SCHED_H)
312 check_include_files(regex.h HAVE_POSIX_REGEX)
313 check_include_file_cxx(regex HAVE_CXX11_REGEX)
314 # TODO: It could be nice to inform the user if no regex support is found,
315 # as selections won't be fully functional.
317 include(CheckFunctionExists)
318 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
319 check_function_exists(memalign HAVE_MEMALIGN)
320 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
321 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
322 check_function_exists(fsync HAVE_FSYNC)
323 check_function_exists(_fileno HAVE__FILENO)
324 check_function_exists(fileno HAVE_FILENO)
325 check_function_exists(_commit HAVE__COMMIT)
326 check_function_exists(sigaction HAVE_SIGACTION)
327 check_function_exists(sysconf HAVE_SYSCONF)
328 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
329 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
330 check_function_exists(rsqrt HAVE_RSQRT)
331 check_function_exists(rsqrtf HAVE_RSQRTF)
332 check_function_exists(sqrtf HAVE_SQRTF)
334 include(CheckLibraryExists)
335 check_library_exists(m sqrt "" HAVE_LIBM)
336 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
339 include(CheckTypeSize)
341 check_type_size("int" SIZEOF_INT)
342 check_type_size("long int" SIZEOF_LONG_INT)
343 check_type_size("long long int" SIZEOF_LONG_LONG_INT)
344 check_type_size("off_t" SIZEOF_OFF_T)
345 check_type_size("void *" SIZEOF_VOIDP)
347 include(TestBigEndian)
348 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
350 # Management of GROMACS options for specific toolchains should go
351 # here. Because the initial settings for some of the main options have
352 # already happened, but things like library detection and MPI compiler
353 # feature detection have not, the docstrings for any over-rides of
354 # GROMACS defaults or user settings will make sense. Also, any
355 # toolchain-related reasons for choosing whether to detect various
356 # things can be sorted out now, before the detection takes place.
357 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
358 include(gmxManageBlueGene)
361 ########################################################################
362 #Process MPI settings
363 ########################################################################
364 include(gmxManageMPI)
366 ########################################################################
367 # Shared/static library settings
368 ########################################################################
369 # Determine the defaults (this block has no effect if the variables have
371 if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
372 # Maybe Solaris should be here? Patch this if you know!
373 SET(SHARED_LIBS_DEFAULT ON)
374 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
375 # Support for shared libs on native Windows is a bit new. Its
376 # default might change later if/when we sort things out. Also,
377 # Cray should go here. What variable value can detect it?
378 SET(SHARED_LIBS_DEFAULT OFF)
380 if (NOT DEFINED BUILD_SHARED_LIBS)
381 message(STATUS "Defaulting to building static libraries")
383 SET(SHARED_LIBS_DEFAULT OFF)
385 if (GMX_PREFER_STATIC_LIBS)
386 if (NOT DEFINED BUILD_SHARED_LIBS AND SHARED_LIBS_DEFAULT)
387 message("Searching for static libraries requested, so the GROMACS libraries will also be built statically (BUILD_SHARED_LIBS=OFF)")
389 set(SHARED_LIBS_DEFAULT OFF)
391 set(GMX_PREFER_STATIC_LIBS_DEFAULT OFF)
392 if (WIN32 AND NOT CYGWIN AND NOT BUILD_SHARED_LIBS)
393 set(GMX_PREFER_STATIC_LIBS_DEFAULT ON)
396 # Declare the user-visible options
397 option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic e.g. with MPI, or on some HPC systems)" ${SHARED_LIBS_DEFAULT})
399 set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
400 "When finding libraries prefer static archives (it will only work if static versions of external dependencies are available and found)")
401 elseif (WIN32 AND NOT CYGWIN)
402 set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
403 "When finding libraries prefer static system libraries (MT instead of MD)")
405 option(GMX_PREFER_STATIC_LIBS "${GMX_PREFER_STATIC_LIBS_DESCRIPTION}"
406 ${GMX_PREFER_STATIC_LIBS_DEFAULT})
407 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
409 # Act on the set values
410 if (UNIX AND GMX_PREFER_STATIC_LIBS)
411 if(BUILD_SHARED_LIBS)
412 # Warn the user about the combination. But don't overwrite the request.
413 message(WARNING "Searching for static libraries requested, and building shared Gromacs libraries requested. This might cause problems linking later.")
415 # On Linux .a is the static library suffix, on Mac OS X .lib can also
416 # be used, so we'll add both to the preference list.
417 SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
419 IF( WIN32 AND NOT CYGWIN)
420 if (NOT BUILD_SHARED_LIBS)
421 if(NOT GMX_PREFER_STATIC_LIBS)
422 message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
425 message(FATAL_ERROR "BUILD_SHARED_LIBS=ON not yet working for Windows in the master branch")
426 if(GMX_PREFER_STATIC_LIBS)
427 #this combination segfaults (illegal passing of file handles)
428 message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
430 add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
431 set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
434 IF (GMX_PREFER_STATIC_LIBS)
435 #Only setting Debug and Release flags. Others configurations are current not used.
436 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
437 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
438 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
439 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
441 IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
442 if(BUILD_SHARED_LIBS) #not sure why incremental building with shared libs doesn't work
443 STRING(REPLACE "/INCREMENTAL:YES" "" CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS})
448 ########################################################################
449 # Find external packages #
450 ########################################################################
452 # Unconditionally find the package, as it is also required for unit tests
453 find_package(LibXml2)
454 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${LIBXML2_FOUND})
456 mark_as_advanced(GMX_XML)
457 # Don't actually do anything, since libxml2 is currently not used by libgromacs
458 #if(GMX_XML AND NOT LIBXML2_FOUND)
459 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
462 # include_directories(${LIBXML2_INCLUDE_DIR})
463 # set(PKG_XML libxml-2.0)
464 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
467 option(GMX_GSL "Add support for gsl" OFF)
472 include_directories(${GSL_INCLUDE_DIR})
478 option(GMX_X11 "Use X window system" OFF)
481 # X11 includes/libraries are only set in the ngmx subdirectory!
484 "X11 include files and/or libraries were not found. "
485 "Set GMX_X11=OFF to compile without X11 support. "
486 "gmx view will not be available.")
488 include_directories(${X11_INCLUDE_DIR})
492 set(THREAD_MPI_LIB thread_mpi)
493 # Enable core threading facilities
494 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders")
495 # Enable tMPI C++ support
498 # enable MPI functions
500 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
502 set(MPI_IN_PLACE_EXISTS 1)
503 endif(GMX_THREAD_MPI)
504 tmpi_get_source_list(THREAD_MPI_SRC)
507 # now that we have detected the dependencies, do the second configure pass
515 if(WIN32 AND NOT CYGWIN)
516 set(GMX_NATIVE_WINDOWS 1)
517 # This makes windows.h not declare min/max as macros that would break
518 # C++ code using std::min/std::max.
519 add_definitions(-DNOMINMAX)
522 # only bother with finding git and using version.h if the source is a git repo
523 if(GMX_GIT_VERSION_INFO)
524 if (NOT SOURCE_IS_GIT_REPOSITORY)
526 "Cannot generate git version information from source tree not under git. "
527 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
529 # We need at least git v1.5.3 be able to parse git's date output. If not
530 # found or the version is too small, we can't generate version information.
533 if(NOT GIT_FOUND OR GIT_VERSION_STRING VERSION_LESS "1.5.3")
535 "No compatible git version found (>= 1.5.3 required). "
536 "Won't be able to generate development version information. "
537 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
541 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
542 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
543 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
544 find_package(Boost 1.44.0)
545 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
546 set(Boost_FOUND FALSE)
548 # Print the notification only on first run, when determining the default
549 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
550 message("Boost >= 1.44 not found. Using minimal internal version. "
551 "This may cause trouble if you plan on compiling/linking other "
552 "software that uses Boost against Gromacs.")
555 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
557 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
559 "Boost >= 1.44 not found. "
560 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
561 "version of Boost included with Gromacs.")
564 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${LIBXML2_FOUND})
565 mark_as_advanced(GMX_BUILD_UNITTESTS)
566 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
567 if (GMX_BUILD_UNITTESTS AND NOT LIBXML2_FOUND)
569 "Cannot build unit tests without libxml2. "
570 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find libxml2.")
573 ########################################################################
574 # Generate development version info for cache
575 ########################################################################
576 # set(GEN_VERSION_INFO_INTERNAL "ON")
577 # include(gmxGenerateVersionString)
579 ########################################################################
580 # Our own GROMACS tests
581 ########################################################################
583 add_definitions( -DHAVE_CONFIG_H )
584 include_directories(${CMAKE_SOURCE_DIR}/src)
585 # Required for config.h, maybe should only be set in src/CMakeLists.txt
586 include_directories(${CMAKE_BINARY_DIR}/src)
587 # Required for gmx_header_config_gen.h to be found before installation
588 include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
589 # Required for now to make old code compile
590 include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
592 include(gmxTestInlineASM)
593 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
595 include(gmxSetBuildInformation)
596 gmx_set_build_information()
597 if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
599 endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
601 include(gmxTestFloatFormat)
602 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
603 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
604 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
606 include(gmxTestLargeFiles)
607 gmx_test_large_files(GMX_LARGEFILES)
609 include(gmxTestSignal)
610 gmx_test_sigusr1(HAVE_SIGUSR1)
612 include(gmxTestInline)
613 gmx_test_inline(INLINE_KEYWORD)
615 include(gmxTestRestrict)
616 gmx_test_restrict(RESTRICT_KEYWORD)
618 include(gmxTestPipes)
619 gmx_test_pipes(HAVE_PIPES)
621 include(gmxTestIsfinite)
622 gmx_test_isfinite(HAVE_ISFINITE)
623 gmx_test__isfinite(HAVE__ISFINITE)
624 gmx_test__finite(HAVE__FINITE)
626 include(gmxTestCXX11)
627 gmx_test_cxx11(GMX_CXX11 GMX_CXX11_FLAGS)
628 if(CXX11_FLAG AND GMX_GPU)
629 #FIXME: add proper solution for progate all but cxx11 flag
630 set(CUDA_PROPAGATE_HOST_FLAGS no)
631 message(WARNING "Please manually add compiler flags to CUDA_NVCC_FLAGS. Automatic propogation temporary not working.")
635 gmx_test_xdr(GMX_SYSTEM_XDR)
636 if(NOT GMX_SYSTEM_XDR)
637 set(GMX_INTERNAL_XDR 1)
638 endif(NOT GMX_SYSTEM_XDR)
640 # include avx test source, used if the AVX flags are set below
641 include(gmxTestAVXMaskload)
643 # Process nonbonded accelerated kernels settings
645 # Note that for the backward-compatible x86 SIMD architectures, the
646 # GMX_CPU_ACCELERATION determines the maximum level of the instruction
647 # set used (e.g. GMX_CPU_ACCLERATION=SSE4.1 implies
648 # SSE2). Accordingly, there are a set of CMake variables
649 # GMX_<arch>_<feature-set> that are exported to the C code to specify
650 # CPU features that should be used. This means that the logic for
651 # requiring such backward compatibility is all located here.
652 if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
654 set(ACCELERATION_STATUS_MESSAGE "CPU acceleration disabled")
656 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
658 GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" ACCELERATION_C_FLAGS)
659 if(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
660 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
661 endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
663 GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
664 if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
665 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
666 endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
668 # We dont warn for lacking SSE2 flag support, since that is probably standard today.
670 # Only test the include after we have tried to add the correct flag for SSE2 support
671 check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${ACCELERATION_C_FLAGS})
673 if(NOT HAVE_EMMINTRIN_H)
674 message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
675 endif(NOT HAVE_EMMINTRIN_H)
677 set(GMX_CPU_ACCELERATION_X86_SSE2 1)
678 # The user should not be able to set this orthogonally to the acceleration
680 set(ACCELERATION_STATUS_MESSAGE
681 "Enabling SSE2 Gromacs acceleration")
683 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
685 GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" ACCELERATION_C_FLAGS)
686 if (NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
687 GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" ACCELERATION_C_FLAGS)
688 endif(NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
689 if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
690 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
691 # intrinsics when SSE2 support is enabled, so we try that instead first.
692 if (GMX_NATIVE_WINDOWS)
693 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
694 message(WARNING "Neither SSE4.1 or SSE2 seems to be supported by your Windows compiler. Something is likely broken.")
696 message(WARNING "No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance")
698 endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
700 GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
701 if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
702 GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
703 endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
704 if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
705 message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
706 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
707 # intrinsics when SSE2 support is enabled, so we try that instead.
708 if (GMX_NATIVE_WINDOWS)
709 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
711 endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
713 # This must come after we have added the -msse4.1 flag on some platforms.
714 check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
716 if(NOT HAVE_SMMINTRIN_H)
717 message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
718 endif(NOT HAVE_SMMINTRIN_H)
720 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND CMAKE_C_COMPILER_VERSION VERSION_EQUAL "11.1")
721 message(FATAL_ERROR "You are using Intel compiler version 11.1, and that compiler is known to produce incorrect results with SSE4.1 acceleration. You need to use another compiler (e.g. icc 12 or newer) or different acceleration (probably slower simulations).")
724 set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
725 # The user should not be able to set this orthogonally to the acceleration
726 set(GMX_X86_SSE4_1 1)
728 set(ACCELERATION_STATUS_MESSAGE
729 "Enabling SSE4.1 Gromacs acceleration")
731 elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
733 # Set the AVX compiler flag for both these choices!
735 GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" ACCELERATION_C_FLAGS)
736 if (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
737 GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" ACCELERATION_C_FLAGS)
738 endif (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
739 if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
740 message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance) giving the -DGMX_CPU_ACCELERATION=SSE4.1 to cmake.")
741 endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
743 GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
744 if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
745 GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
746 endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
747 if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
748 message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance) giving the -DGMX_CPU_ACCELERATION=SSE4.1 to cmake.")
749 endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
751 # Set the FMA4 flags (MSVC doesn't require any)
752 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
753 GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
754 if (NOT GNU_FMA_CFLAG)
755 message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
756 endif(NOT GNU_FMA_CFLAG)
757 GMX_TEST_CFLAG(GNU_XOP_CFLAG "-mxop" ACCELERATION_C_FLAGS)
758 # No big deal if we do not have xop, so no point yelling warnings about it.
759 GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" ACCELERATION_CXX_FLAGS)
760 if (NOT GNU_FMA_CXXFLAG)
761 message(WARNING "No C++ FMA flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
762 endif (NOT GNU_FMA_CXXFLAG)
763 GMX_TEST_CXXFLAG(GNU_XOP_CXXFLAG "-mxop" ACCELERATION_CXX_FLAGS)
764 # No big deal if we do not have xop, so no point yelling warnings about it.
767 # Only test the header after we have tried to add the flag for AVX support
768 check_include_file(immintrin.h HAVE_IMMINTRIN_H ${ACCELERATION_C_FLAGS})
770 if(NOT HAVE_IMMINTRIN_H)
771 message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
772 endif(NOT HAVE_IMMINTRIN_H)
774 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
775 try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
776 "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
777 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
779 message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
783 # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
784 check_include_file(x86intrin.h HAVE_X86INTRIN_H ${ACCELERATION_C_FLAGS})
785 check_include_file(intrin.h HAVE_INTRIN_H ${ACCELERATION_C_FLAGS})
787 # The user should not be able to set this orthogonally to the acceleration
788 set(GMX_X86_SSE4_1 1)
791 # But just enable one of the choices internally...
792 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
793 # We don't have the full compiler version string yet (BUILD_C_COMPILER),
794 # so we can't distinguish vanilla and Apple clang, but catering for AMD
795 # hackintoshes is not worth the effort.
796 if (APPLE AND (${CMAKE_C_COMPILER_ID} STREQUAL "Clang" OR
797 ${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
798 message(WARNING "Due to a known compiler bug, Clang up to version 3.2 (and Apple Clang up to version 4.1) produces incorrect code with AVX_128_FMA acceleration. As we can not work around this bug on OS X, you will have to select a different compiler or CPU acceleration.")
801 if (GMX_USE_CLANG_C_FMA_BUG_WORKAROUND)
802 # we assume that we have an external assembler that supports AVX
803 message(STATUS "Clang ${CMAKE_C_COMPILER_VERSION} detected, enabling FMA bug workaround")
804 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} -no-integrated-as")
806 if (GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND)
807 # we assume that we have an external assembler that supports AVX
808 message(STATUS "Clang ${CMAKE_CXX_COMPILER_VERSION} detected, enabling FMA bug workaround")
809 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} -no-integrated-as")
812 set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
813 set(GMX_X86_AVX_128_FMA 1)
814 set(ACCELERATION_STATUS_MESSAGE
815 "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add)")
818 # If we are not doing AVX_128, it must be AVX_256...
819 set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
820 set(GMX_X86_AVX_256 1)
821 set(ACCELERATION_STATUS_MESSAGE
822 "Enabling 256-bit AVX Gromacs acceleration")
825 # Unfortunately gcc-4.5.2 and gcc-4.6.0 has a bug where they use the wrong datatype for the formal
826 # parameter of the mask for maskload/maskstore arguments. Check if this is present, since we can work around it.
827 gmx_test_avx_gcc_maskload_bug(${ACCELERATION_C_FLAGS} GMX_X86_AVX_GCC_MASKLOAD_BUG)
829 elseif(${GMX_CPU_ACCELERATION} STREQUAL "IBM_QPX")
830 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
831 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c")
834 message(WARNING "IBM QPX acceleration was selected. This will work, but SIMD-accelerated kernels are only available for the Verlet cut-off scheme. The plain C kernels that are used for the group cut-off scheme kernels will be slow, so please consider using the Verlet cut-off scheme.")
835 set(GMX_CPU_ACCELERATION_IBM_QPX 1)
837 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics. If you are compiling for BlueGene/Q with the XL compilers, use 'cmake .. -DCMAKE_TOOLCHAIN_FILE=Platform/BlueGeneQ-static-XL-C' to set up the tool chain.")
839 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SPARC64_HPC_ACE")
840 set(GMX_CPU_ACCELERATION_SPARC64_HPC_ACE 1)
842 gmx_invalid_option_value(GMX_CPU_ACCELERATION)
844 gmx_check_if_changed(ACCELERATION_CHANGED GMX_CPU_ACCELERATION)
845 if (ACCELERATION_CHANGED AND DEFINED ACCELERATION_STATUS_MESSAGE)
846 message(STATUS "${ACCELERATION_STATUS_MESSAGE}")
849 # Process QM/MM Settings
850 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
851 set(GMX_QMMM_GAUSSIAN 1)
852 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
853 set(GMX_QMMM_MOPAC 1)
854 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
855 set(GMX_QMMM_GAMESS 1)
856 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
858 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
861 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
864 # Process FFT library settings
867 # Intel 11 and up makes life somewhat easy if you just want to use
868 # all their stuff. It's not easy if you only want some of their
870 set(MKL_MANUALLY FALSE)
871 if (GMX_FFT_LIBRARY STREQUAL "MKL" AND
872 NOT (CMAKE_C_COMPILER_ID MATCHES "Intel" AND CMAKE_C_COMPILER_VERSION VERSION_GREATER "11"))
873 # The user will have to provide the set of magic libraries in
874 # MKL_LIBRARIES (see below), which we cache (non-advanced), so that they
875 # don't have to keep specifying it, and can easily see that
876 # CMake is still using that information.
877 set(MKL_MANUALLY TRUE)
879 set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
880 gmx_dependent_cache_variable(
882 "List of libraries for linking to MKL. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}"
885 gmx_dependent_cache_variable(
887 "Path to mkl.h (non-inclusive)."
890 if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
897 if(GMX_BUILD_OWN_FFTW)
898 add_subdirectory(src/contrib/fftw)
900 find_package(FFTW COMPONENTS ${FFTW})
903 string(TOUPPER "${FFTW}" FFTW)
904 if(NOT ${FFTW}_FOUND)
905 MESSAGE(FATAL_ERROR "Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision GROMACS or libfftw3 for double-precision GROMACS). Either choose the right precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the advanced option to let GROMACS build FFTW 3 for you (-DGMX_BUILD_OWN_FFTW=ON) , or use the really slow GROMACS built-in fftpack library (-DGMX_FFT_LIBRARY=fftpack).")
908 set(PKG_FFT "${${FFTW}_PKG}")
909 include_directories(${${FFTW}_INCLUDE_DIRS})
910 set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
913 if ((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
914 message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
917 if((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND ${FFTW}_HAVE_AVX)
918 # If we're not doing CPU acceleration, we don't care about FFTW performance on x86 either
919 message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
922 set(FFT_STATUS_MESSAGE "Using external FFT library - FFTW3")
923 elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
924 # Intel 11 and up makes life somewhat easy if you just want to use
925 # all their stuff. It's not easy if you only want some of their
927 if (NOT MKL_MANUALLY)
928 # The next line takes care of everything for MKL
930 set(FFT_LINKER_FLAGS "/Qmkl=sequential")
932 set(FFT_LINKER_FLAGS "-mkl=sequential")
934 # Some versions of icc require this in order that mkl.h can be
935 # found at compile time.
936 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} ${FFT_LINKER_FLAGS}")
938 set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
940 include_directories(${MKL_INCLUDE_DIR})
941 set(FFT_LIBRARIES "${MKL_LIBRARIES}")
942 set(MKL_ERROR_MESSAGE "The include path to mkl.h in MKL_INCLUDE_DIR, and the link libraries in MKL_LIBRARIES=${MKL_LIBRARIES} need to match what the MKL documentation says you need for your system. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
943 # Convert the semi-colon separated list to a list of
944 # command-line linker arguments so that code using our
945 # pkgconfig setup can use it.
946 string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
949 # Check MKL works. If we were in a non-global scope, we wouldn't
950 # have to play nicely.
951 set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
952 set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
953 set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
954 set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
956 check_function_exists(DftiCreateDescriptor TEST_MKL)
958 set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
959 set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
962 # Hack to help the user vary MKL settings until they work.
963 # TODO Make this logic more useful.
964 unset(TEST_MKL CACHE)
965 message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
968 # Set variables to signal that we have MKL available and should use it for FFTs.
972 set(FFT_STATUS_MESSAGE "Using external FFT library - Intel MKL")
973 elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
974 set(GMX_FFT_FFTPACK 1)
975 set(FFT_STATUS_MESSAGE "Using internal FFT library - fftpack")
976 else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
977 gmx_invalid_option_value(GMX_FFT_LIBRARY)
978 endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
979 gmx_check_if_changed(FFT_CHANGED GMX_FFT_LIBRARY)
981 message(STATUS "${FFT_STATUS_MESSAGE}")
984 # enable threaded fftw3 if we've found it
985 if(FFTW3_THREADS OR FFTW3F_THREADS)
986 add_definitions(-DFFT5D_FFTW_THREADS)
989 include(gmxManageLinearAlgebraLibraries)
991 # Whether GROMACS will really try to compile support for VMD plugins
992 set(GMX_USE_PLUGINS OFF)
995 if(CYGWIN OR NOT WIN32)
996 # Native Windows does not have, nor need dlopen
997 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
998 include(gmxTestdlopen)
999 gmx_test_dlopen(HAVE_DLOPEN)
1002 # so, should we use plug-ins?
1003 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
1006 "Found the ability to use plug-ins when building shared libaries, "
1007 "so will compile to use plug-ins (e.g. to read VMD-supported file "
1010 if(NOT GMX_VMD_PLUGIN_PATH)
1013 set(GMX_USE_PLUGINS ON)
1014 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
1015 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
1019 endif(GMX_LOAD_PLUGINS)
1020 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
1022 # Link real-time library for POSIX timers. The check for clock_gettime
1023 # confirms the linkability of rt.
1024 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
1025 list(APPEND GMX_EXTRA_LIBRARIES rt)
1028 # Math and thread libraries must often come after all others when linking...
1030 list(APPEND GMX_EXTRA_LIBRARIES m)
1032 if (${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
1033 check_library_exists(mass_simd atan2f4 "" HAVE_MASS_SIMD)
1035 list(APPEND GMX_EXTRA_LIBRARIES mass_simd)
1037 message(FATAL_ERROR "Could not link to the SIMD version of the IBM MASS library. Please adjust your CMAKE_PREFIX_PATH to contain it")
1042 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
1043 "Path to swindirect.h")
1044 include_directories(${COREWRAP_INCLUDE_DIR})
1047 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
1048 # these are set after everything else
1049 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
1050 set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
1051 set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
1052 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
1053 set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
1055 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
1056 message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
1057 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
1058 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
1059 message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
1060 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
1061 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
1062 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
1063 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
1067 #Unset all OpenMP flags in case OpenMP was disabled either by the user
1068 #or because it was only partially detected (e.g. only for C but not C++ compiler)
1069 unset(OpenMP_C_FLAGS CACHE)
1070 unset(OpenMP_CXX_FLAGS CACHE)
1072 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
1073 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
1075 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
1077 ########################################################################
1078 # Specify install locations
1079 ########################################################################
1080 set(GMX_LIB_INSTALL_DIR lib CACHE STRING
1081 "Library installation directory (default: lib)")
1082 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
1083 "Data installation directory under share/ (default: gromacs)")
1084 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
1086 set(LIB_INSTALL_DIR ${GMX_INSTALL_PREFIX}${GMX_LIB_INSTALL_DIR})
1087 set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
1088 set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/${GMX_DATA_INSTALL_DIR})
1089 set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
1090 set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
1092 set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
1093 set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
1095 ########################################################################
1096 # Set up binary and library suffixing
1097 ########################################################################
1100 "Use default suffixes for GROMACS binaries and libs (_d for double, _mpi for MPI; rerun cmake after changing to see relevant options)"
1102 gmx_dependent_cache_variable(
1104 "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double)."
1106 "NOT GMX_DEFAULT_SUFFIX")
1107 gmx_dependent_cache_variable(
1109 "Suffix for GROMACS libraries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double)."
1111 "NOT GMX_DEFAULT_SUFFIX")
1112 if (GMX_DEFAULT_SUFFIX)
1113 gmx_check_if_changed(SUFFIXES_CHANGED GMX_DEFAULT_SUFFIX)
1114 set(GMX_BINARY_SUFFIX "")
1115 set(GMX_LIBS_SUFFIX "")
1117 set(GMX_BINARY_SUFFIX "_mpi")
1118 set(GMX_LIBS_SUFFIX "_mpi")
1121 set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
1122 set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
1124 if (SUFFIXES_CHANGED)
1125 message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
1126 message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
1128 else(GMX_DEFAULT_SUFFIX)
1129 gmx_check_if_changed(SUFFIXES_CHANGED
1130 GMX_DEFAULT_SUFFIX GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
1131 if (SUFFIXES_CHANGED)
1132 message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
1133 message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
1135 endif(GMX_DEFAULT_SUFFIX)
1136 if (GMX_BUILD_MDRUN_ONLY)
1137 set(GMX_LIBS_SUFFIX "_mdrun${GMX_LIBS_SUFFIX}")
1140 ##################################################################
1141 # Shared library settings
1142 ##################################################################
1143 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
1144 set(CMAKE_SKIP_BUILD_RPATH FALSE)
1145 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
1146 set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
1147 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
1149 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) #rpath supported for >10.4
1150 set(CMAKE_INSTALL_NAME_DIR "@rpath")
1151 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../lib")
1153 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
1157 #COPYING file: Only necessary for binary distributions.
1158 #Simpler to always install.
1159 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
1161 if(GMX_EXTERNAL_BOOST)
1162 include_directories(${Boost_INCLUDE_DIRS})
1164 include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
1165 # typeid not supported for minimal internal version
1166 # (would add significant amount of code)
1167 add_definitions(-DBOOST_NO_TYPEID)
1168 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
1169 # (from share/template/)
1170 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${INCL_INSTALL_DIR}/gromacs/external/boost")
1171 if (NOT GMX_BUILD_MDRUN_ONLY)
1172 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
1173 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
1174 COMPONENT development)
1178 if (GMX_BUILD_FOR_COVERAGE)
1179 # Code heavy with asserts makes conditional coverage close to useless metric,
1180 # as by design most of the false branches are impossible to trigger in
1181 # correctly functioning code. And the benefit of testing those that could
1182 # be triggered by using an API against its specification isn't usually
1184 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
1187 if (NOT GMX_BUILD_MDRUN_ONLY)
1188 add_subdirectory(doxygen)
1189 add_subdirectory(share)
1190 add_subdirectory(scripts)
1192 add_subdirectory(src)
1194 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
1195 # Don't bother the user after the first configure pass.
1196 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1197 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
1199 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
1201 #######################
1203 #######################
1205 "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
1206 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
1208 ###########################
1209 ADD_CUSTOM_TARGET(uninstall
1210 "${CMAKE_COMMAND}" -P
1211 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
1212 ###########################
1214 ########################################################################
1216 ########################################################################
1220 #"check" target builds and runs all tests
1221 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
1222 add_dependencies(check tests)
1223 # TODO: This would be better within tests/CMakeLists.txt
1224 if (NOT GMX_BUILD_MDRUN_ONLY)
1225 #gmxtests target builds all binaries required for running gmxtest
1226 add_custom_target(gmxtests DEPENDS gmx links)
1227 add_dependencies(check gmxtests)
1228 add_subdirectory(tests)
1230 #TODO: Add warning if NOT REGRESSIONTEST_PATH OR NOT GMX_XML that regression/unit tests are not run.
1233 ########################################################################
1235 ########################################################################
1237 option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF)
1238 mark_as_advanced(GMX_BUILD_MANUAL)
1239 if(GMX_BUILD_MANUAL)
1240 # Make sure we only do detection of manual-building dependencies
1241 # when the user opted in for that.
1242 add_subdirectory(manual)