1 cmake_minimum_required(VERSION 2.8)
2 # Keep CMake suitably quiet on Cygwin
3 set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
5 # CMake modules/macros are in a subdirectory to keep this file cleaner
6 # This needs to be set before project() in order to pick up toolchain files
7 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
11 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
12 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
13 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
15 # PROJECT_VERSION should have the following structure:
16 # VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
18 # The "-dev" suffix is important to keep because it makes possible to distinguish
19 # between a build from official release and a build from git release branch on a
20 # machine with no git.
22 # NOTE: when releasing the "-dev" suffix needs to be stripped off!
23 set(PROJECT_VERSION "5.0-dev")
24 # The version number of the regressiontest tarball against which this
25 # git branch can be tested. Normally, this will be the version of the
26 # last patch release. Comment the next line out for branches leading
27 # to a major/minor release.
28 set(REGRESSIONTEST_VERSION "4.6.2")
29 set(CUSTOM_VERSION_STRING ""
30 CACHE STRING "Custom version string (if empty, use hard-coded default)")
31 mark_as_advanced(CUSTOM_VERSION_STRING)
32 if (CUSTOM_VERSION_STRING)
33 set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
34 endif (CUSTOM_VERSION_STRING)
36 # It is a bit irritating, but this has to be set separately for now!
37 SET(CPACK_PACKAGE_VERSION_MAJOR "5")
38 SET(CPACK_PACKAGE_VERSION_MINOR "0")
39 #SET(CPACK_PACKAGE_VERSION_PATCH "0")
41 # The numerical gromacs version. It is 40600 for 4.6.0.
42 # The #define GMX_VERSION in gmx_header_config_h is set to this value.
44 "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
45 if(CPACK_PACKAGE_VERSION_PATCH)
47 "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
50 # The API version tracks the numerical Gromacs version (for now).
51 # It is potentially different from the Gromacs version in the future, if
52 # the programs/libraries diverge from the presumably more stable API.
53 # The #define GMX_API_VERSION in version.h is set to this value to
54 # provide backward compatibility of software written against the Gromacs API.
55 set(API_VERSION ${NUM_VERSION})
57 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
58 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
61 set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
62 mark_as_advanced(GMX_INSTALL_PREFIX)
64 include(gmxBuildTypeReference)
66 if(NOT CMAKE_BUILD_TYPE)
67 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference." FORCE)
68 endif(NOT CMAKE_BUILD_TYPE)
73 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
74 set(CPACK_PACKAGE_VENDOR "gromacs.org")
75 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
76 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
77 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
78 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
79 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
80 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$")
81 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
82 set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/share/man;share/man")
83 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
85 #must come after all cpack settings!
88 # Set a default valgrind suppression file.
89 # This unfortunately needs to duplicate information from CTest to work as
91 set(MEMORYCHECK_SUPPRESSIONS_FILE
92 "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
94 "File that contains suppressions for the memory checker")
97 set(SOURCE_IS_GIT_REPOSITORY OFF)
98 set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
99 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
100 set(SOURCE_IS_GIT_REPOSITORY ON)
102 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
103 set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
106 ########################################################################
107 # Check and warn if cache generated on a different host is being reused
108 ########################################################################
110 execute_process(COMMAND hostname
111 OUTPUT_VARIABLE TMP_HOSTNAME
112 OUTPUT_STRIP_TRAILING_WHITESPACE)
113 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
115 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
116 is being reused! This could lead to inconsitencies; therefore, it is
117 recommended to regenerate the cache!")
119 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
120 "Hostname of the machine where the cache was generated.")
123 ########################################################################
124 # User input options #
125 ########################################################################
126 include(gmxOptionUtilities)
128 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
130 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
131 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
132 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
133 gmx_dependent_option(
135 "Enable MPI_IN_PLACE for MPIs that have it defined"
138 mark_as_advanced(GMX_MPI_IN_PLACE)
139 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
140 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
141 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
142 mark_as_advanced(GMX_FAHCORE)
144 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
145 mark_as_advanced(GMX_COOL_QUOTES)
146 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
148 # decide on GPU settings based on user-settings and GPU/CUDA detection
149 include(gmxManageGPU)
151 # Detect the architecture the compiler is targetting, detect
152 # acceleration possibilities on that hardware, suggest an acceleration
153 # to use if none is specified, and populate the cache option for CPU
155 include(gmxDetectTargetArchitecture)
156 gmx_detect_target_architecture()
157 include(gmxDetectAcceleration)
158 gmx_detect_acceleration(GMX_SUGGESTED_CPU_ACCELERATION)
160 gmx_option_multichoice(
162 "Acceleration for CPU kernels and compiler optimization"
163 "${GMX_SUGGESTED_CPU_ACCELERATION}"
164 None SSE2 SSE4.1 AVX_128_FMA AVX_256 IBM_QPX Sparc64_HPC_ACE)
166 gmx_option_multichoice(
170 fftw3 mkl "fftpack[built-in]")
171 gmx_dependent_option(
173 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
175 "GMX_FFT_LIBRARY STREQUAL FFTW3")
176 gmx_dependent_option(
177 GMX_DISABLE_FFTW_MEASURE
178 "Do not optimize FFTW setups (not needed with SSE)"
180 "GMX_FFT_LIBRARY STREQUAL FFTW3")
181 mark_as_advanced(GMX_BUILD_OWN_FFTW)
182 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
184 gmx_option_multichoice(
186 "QM package for QM/MM"
188 none gaussian mopac gamess orca)
190 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
191 mark_as_advanced(GMX_BROKEN_CALLOC)
192 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
193 mark_as_advanced(GMX_LOAD_PLUGINS)
195 option(GMX_GPU "Enable GPU acceleration" ON)
196 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
198 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
199 mark_as_advanced(GMX_GIT_VERSION_INFO)
202 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
204 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
206 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
207 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
209 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
210 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
212 option(GMX_BUILD_FOR_COVERAGE
213 "Tune build for better code coverage metrics (e.g., disable asserts)"
215 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
217 ######################################################################
219 # These need to be done early (before further tests).
220 #####################################################################
222 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
223 # are used with permission from CMake v2.8.9 so that GROMACS can detect
224 # invalid options with the Intel Compilers.
225 # These files should be removed from the source tree when a CMake version that
226 # includes the features in question becomes required for building GROMACS.
227 include(CheckCCompilerFlag)
228 include(CheckCXXCompilerFlag)
230 # Get compiler version information, needs to be done early as check that depend
231 # on compiler verison follow below.
232 include(gmxGetCompilerInfo)
233 get_compiler_version()
235 # First exclude compilers known to not work with OpenMP although claim to support it:
236 # gcc 4.2.1 and gcc-llvm 4.2.1 (also claims to be 4.2.1) on Mac OS X
237 # This fixes redmine 900 and needs to run before OpenMP flags are set below.
238 if (CMAKE_SYSTEM_NAME STREQUAL "Darwin" AND
239 (CMAKE_COMPILER_IS_GNUCC AND C_COMPILER_VERSION AND C_COMPILER_VERSION VERSION_LESS 4.3))
240 message(STATUS "OpenMP multithreading not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled")
241 set(GMX_OPENMP OFF CACHE BOOL
242 "OpenMP multithreading not not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled!" FORCE)
245 # OpenMP check must come before other CFLAGS!
249 # CMake on Windows doesn't support linker flags passed to target_link_libraries
250 # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
251 if(NOT (WIN32 AND NOT CYGWIN))
252 if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE)
253 set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
254 set(OpenMP_SHARED_LINKER_FLAGS "")
256 # Only set a linker flag if the user didn't set them manually
257 if(NOT DEFINED OpenMP_LINKER_FLAGS)
258 set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
260 if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
261 set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
267 "The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. For now, we are proceeding by turning off OpenMP.")
268 set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
276 # This variable should be used for additional compiler flags which are not
277 # generated in gmxCFlags nor are acceleration or MPI related.
278 set(EXTRA_C_FLAGS "")
279 set(EXTRA_CXX_FLAGS "")
281 # gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
282 # Detect here whether applying a workaround is needed and will apply it later
283 # on the affected files.
284 include(gmxGCC44O3BugWorkaround)
285 gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
287 # clang 3.0 is buggy for some unknown reason detected during adding
288 # the SSE2 group kernels for GROMACS 4.6. If we ever work out what
289 # that is, we should replace these tests with a compiler feature test,
290 # update GROMACS Redmine task #1039 and perhaps report a clang bug.
292 # In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
293 # the compiler version for us. So we need a manual check for clang 3.0.
294 include(gmxDetectClang30)
295 gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
296 if(COMPILER_IS_CLANG_3_0)
297 message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
300 # clang <=3.2 contains a bug that causes incorrect code to be generated for the
301 # vfmaddps instruction and therefore the bug is triggered with AVX_128_FMA.
302 # (see: http://llvm.org/bugs/show_bug.cgi?id=15040).
303 # We can work around this by not using the integrated assembler (except on OS X
304 # which has an outdated assembler that does not support AVX instructions).
305 if (${CMAKE_C_COMPILER_ID} MATCHES "Clang" AND C_COMPILER_VERSION VERSION_LESS "3.3")
306 set(GMX_USE_CLANG_C_FMA_BUG_WORKAROUND TRUE)
308 if (${CMAKE_CXX_COMPILER_ID} MATCHES "Clang" AND CXX_COMPILER_VERSION VERSION_LESS "3.3")
309 set(GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND TRUE)
312 if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
313 message(WARNING "All tested PGI compiler versions (up to 12.9.0) generate binaries which produce incorrect results, or even fail to compile Gromacs. Highly recommended to use a different compiler. If you choose to use PGI, make sure to run the regressiontests.")
316 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_LESS "12.0.0")
317 message(WARNING "Intel compilers before 12.0.0 are not routinely tested, so there may be problems. Version 11.1 with SSE4.1 is known to produce incorrect results. It is highly recommended to use a more up-to-date compiler. If you choose to use this version, make sure you run the regressiontests.")
322 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
324 if(GMX_SOFTWARE_INVSQRT)
325 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
326 endif(GMX_SOFTWARE_INVSQRT)
330 ########################################################################
331 # Basic system tests (standard libraries, headers, functions, types) #
332 ########################################################################
333 include(CheckIncludeFiles)
334 include(CheckIncludeFileCXX)
335 check_include_files(unistd.h HAVE_UNISTD_H)
336 check_include_files(pwd.h HAVE_PWD_H)
337 check_include_files(dirent.h HAVE_DIRENT_H)
338 check_include_files(time.h HAVE_TIME_H)
339 check_include_files(sys/time.h HAVE_SYS_TIME_H)
340 check_include_files(io.h HAVE_IO_H)
341 check_include_files(sched.h HAVE_SCHED_H)
343 check_include_files(regex.h HAVE_POSIX_REGEX)
344 check_include_file_cxx(regex HAVE_CXX11_REGEX)
345 # TODO: It could be nice to inform the user if no regex support is found,
346 # as selections won't be fully functional.
348 include(CheckFunctionExists)
349 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
350 check_function_exists(memalign HAVE_MEMALIGN)
351 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
352 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
353 check_function_exists(fsync HAVE_FSYNC)
354 check_function_exists(_fileno HAVE__FILENO)
355 check_function_exists(fileno HAVE_FILENO)
356 check_function_exists(_commit HAVE__COMMIT)
357 check_function_exists(sigaction HAVE_SIGACTION)
358 check_function_exists(sysconf HAVE_SYSCONF)
359 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
360 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
361 check_function_exists(rsqrt HAVE_RSQRT)
362 check_function_exists(rsqrtf HAVE_RSQRTF)
363 check_function_exists(sqrtf HAVE_SQRTF)
365 include(CheckLibraryExists)
366 check_library_exists(m sqrt "" HAVE_LIBM)
367 check_library_exists(rt clock_gettime "" HAVE_LIBRT)
370 include(CheckTypeSize)
372 check_type_size("int" SIZEOF_INT)
373 check_type_size("long int" SIZEOF_LONG_INT)
374 check_type_size("long long int" SIZEOF_LONG_LONG_INT)
375 check_type_size("off_t" SIZEOF_OFF_T)
376 check_type_size("void *" SIZEOF_VOIDP)
378 include(TestBigEndian)
379 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
381 # Management of GROMACS options for specific toolchains should go
382 # here. Because the initial settings for some of the main options have
383 # already happened, but things like library detection and MPI compiler
384 # feature detection have not, the docstrings for any over-rides of
385 # GROMACS defaults or user settings will make sense. Also, any
386 # toolchain-related reasons for choosing whether to detect various
387 # things can be sorted out now, before the detection takes place.
388 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
389 include(gmxManageBlueGene)
392 ########################################################################
393 #Process MPI settings
394 ########################################################################
395 include(gmxManageMPI)
397 ########################################################################
398 # Shared/static library settings
399 ########################################################################
400 # Determine the defaults (this block has no effect if the variables have
402 if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
403 # Maybe Solaris should be here? Patch this if you know!
404 SET(SHARED_LIBS_DEFAULT ON)
405 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
406 # Support for shared libs on native Windows is a bit new. Its
407 # default might change later if/when we sort things out. Also,
408 # Cray should go here. What variable value can detect it?
409 SET(SHARED_LIBS_DEFAULT OFF)
411 if (NOT DEFINED BUILD_SHARED_LIBS)
412 message(STATUS "Defaulting to building static libraries")
414 SET(SHARED_LIBS_DEFAULT OFF)
416 if (GMX_PREFER_STATIC_LIBS)
417 if (NOT DEFINED BUILD_SHARED_LIBS AND SHARED_LIBS_DEFAULT)
418 message("Searching for static libraries requested, so the GROMACS libraries will also be built statically (BUILD_SHARED_LIBS=OFF)")
420 set(SHARED_LIBS_DEFAULT OFF)
422 set(GMX_PREFER_STATIC_LIBS_DEFAULT OFF)
423 if (WIN32 AND NOT CYGWIN AND NOT BUILD_SHARED_LIBS)
424 set(GMX_PREFER_STATIC_LIBS_DEFAULT ON)
427 # Declare the user-visible options
428 option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic e.g. with MPI, or on some HPC systems)" ${SHARED_LIBS_DEFAULT})
430 set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
431 "When finding libraries prefer static archives (it will only work if static versions of external dependencies are available and found)")
432 elseif (WIN32 and NOT CYGWIN)
433 set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
434 "When finding libraries prefer static system libraries (MT instead of MD)")
436 option(GMX_PREFER_STATIC_LIBS "${GMX_PREFER_STATIC_LIBS_DESCRIPTION}"
437 ${GMX_PREFER_STATIC_LIBS_DEFAULT})
438 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
440 # Act on the set values
441 if (UNIX AND GMX_PREFER_STATIC_LIBS)
442 if(BUILD_SHARED_LIBS)
443 # Warn the user about the combination. But don't overwrite the request.
444 message(WARNING "Searching for static libraries requested, and building shared Gromacs libraries requested. This might cause problems linking later.")
446 # On Linux .a is the static library suffix, on Mac OS X .lib can also
447 # be used, so we'll add both to the preference list.
448 SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
450 IF( WIN32 AND NOT CYGWIN)
451 if (NOT BUILD_SHARED_LIBS)
452 if(NOT GMX_PREFER_STATIC_LIBS)
453 message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
456 message(FATAL_ERROR "BUILD_SHARED_LIBS=ON not yet working for Windows in the master branch")
457 if(GMX_PREFER_STATIC_LIBS)
458 #this combination segfaults (illegal passing of file handles)
459 message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
461 add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
462 set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
465 IF (GMX_PREFER_STATIC_LIBS)
466 #Only setting Debug and Release flags. Others configurations are current not used.
467 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
468 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
469 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
470 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
472 IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
473 if(BUILD_SHARED_LIBS) #not sure why incremental building with shared libs doesn't work
474 STRING(REPLACE "/INCREMENTAL:YES" "" CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS})
479 ########################################################################
480 # Find external packages #
481 ########################################################################
483 # Unconditionally find the package, as it is also required for unit tests
484 find_package(LibXml2)
485 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${LIBXML2_FOUND})
487 mark_as_advanced(GMX_XML)
488 # Don't actually do anything, since libxml2 is currently not used by libgromacs
489 #if(GMX_XML AND NOT LIBXML2_FOUND)
490 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
493 # include_directories(${LIBXML2_INCLUDE_DIR})
494 # set(PKG_XML libxml-2.0)
495 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
498 option(GMX_GSL "Add support for gsl" OFF)
503 include_directories(${GSL_INCLUDE_DIR})
509 option(GMX_X11 "Use X window system" OFF)
512 # X11 includes/libraries are only set in the ngmx subdirectory!
514 message(WARNING "X11 include files and/or libraries were not found. Will not build the GROMACS X11-binaries, such as ngmx")
517 include_directories(${X11_INCLUDE_DIR})
522 set(THREAD_MPI_LIB thread_mpi)
523 # Enable core threading facilities
524 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders")
525 # Enable tMPI C++ support
528 # enable MPI functions
530 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
532 endif(GMX_THREAD_MPI)
533 tmpi_get_source_list(THREAD_MPI_SRC)
536 # now that we have detected the dependencies, do the second configure pass
544 if(WIN32 AND NOT CYGWIN)
545 set(GMX_NATIVE_WINDOWS 1)
546 # This makes windows.h not declare min/max as macros that would break
547 # C++ code using std::min/std::max.
548 add_definitions(-DNOMINMAX)
551 # only bother with finding git and using version.h if the source is a git repo
552 if(GMX_GIT_VERSION_INFO)
553 if (NOT SOURCE_IS_GIT_REPOSITORY)
555 "Cannot generate git version information from source tree not under git. "
556 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
558 # We need at least git v1.5.3 be able to parse git's date output. If not
559 # found or the version is too small, we can't generate version information.
562 # Find out the git version
563 if(GIT_FOUND AND NOT GIT_VERSION)
564 execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
565 OUTPUT_VARIABLE _exec_out
566 OUTPUT_STRIP_TRAILING_WHITESPACE)
567 string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
568 set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
569 mark_as_advanced(GIT_VERSION)
572 if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
574 "No compatible git version found (>= 1.5.3 required). "
575 "Won't be able to generate development version information. "
576 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
580 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
581 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
582 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
583 find_package(Boost 1.44.0)
584 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
585 set(Boost_FOUND FALSE)
587 # Print the notification only on first run, when determining the default
588 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
589 message("Boost >= 1.44 not found. Using minimal internal version. "
590 "This may cause trouble if you plan on compiling/linking other "
591 "software that uses Boost against Gromacs.")
594 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
596 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
598 "Boost >= 1.44 not found. "
599 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
600 "version of Boost included with Gromacs.")
603 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${LIBXML2_FOUND})
604 mark_as_advanced(GMX_BUILD_UNITTESTS)
605 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
606 if (GMX_BUILD_UNITTESTS AND NOT LIBXML2_FOUND)
608 "Cannot build unit tests without libxml2. "
609 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find libxml2.")
612 ########################################################################
613 # Generate development version info for cache
614 ########################################################################
615 # set(GEN_VERSION_INFO_INTERNAL "ON")
616 # include(gmxGenerateVersionString)
618 ########################################################################
619 # Our own GROMACS tests
620 ########################################################################
622 add_definitions( -DHAVE_CONFIG_H )
623 include_directories(${CMAKE_SOURCE_DIR}/src)
624 # Required for config.h, maybe should only be set in src/CMakeLists.txt
625 include_directories(${CMAKE_BINARY_DIR}/src)
626 # Required for gmx_header_config_gen.h to be found before installation
627 include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
628 # Required for now to make old code compile
629 include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
631 include(gmxTestInlineASM)
632 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
634 include(gmxSetBuildInformation)
635 gmx_set_build_information()
636 if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
637 # The timestep counter headers do not include config.h
638 add_definitions(-DHAVE_RDTSCP)
639 endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
641 include(gmxTestFloatFormat)
642 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
643 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
644 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
646 include(gmxTestLargeFiles)
647 gmx_test_large_files(GMX_LARGEFILES)
649 include(gmxTestSignal)
650 gmx_test_sigusr1(HAVE_SIGUSR1)
652 include(gmxTestInline)
653 gmx_test_inline(INLINE_KEYWORD)
655 include(gmxTestRestrict)
656 gmx_test_restrict(RESTRICT_KEYWORD)
658 include(gmxTestPipes)
659 gmx_test_pipes(HAVE_PIPES)
661 include(gmxTestIsfinite)
662 gmx_test_isfinite(HAVE_ISFINITE)
663 gmx_test__isfinite(HAVE__ISFINITE)
664 gmx_test__finite(HAVE__FINITE)
666 include(gmxTestCXX11)
667 gmx_test_cxx11(GMX_CXX11 GMX_CXX11_FLAGS)
668 if(CXX11_FLAG AND GMX_GPU)
669 #FIXME: add proper solution for progate all but cxx11 flag
670 set(CUDA_PROPAGATE_HOST_FLAGS no)
671 message(WARNING "Please manually add compiler flags to CUDA_NVCC_FLAGS. Automatic propogation temporary not working.")
675 gmx_test_xdr(GMX_SYSTEM_XDR)
676 if(NOT GMX_SYSTEM_XDR)
677 set(GMX_INTERNAL_XDR 1)
678 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_INTERNAL_XDR")
679 endif(NOT GMX_SYSTEM_XDR)
681 # include avx test source, used if the AVX flags are set below
682 include(gmxTestAVXMaskload)
684 # Process nonbonded accelerated kernels settings
686 # Note that for the backward-compatible x86 SIMD architectures, the
687 # GMX_CPU_ACCELERATION determines the maximum level of the instruction
688 # set used (e.g. GMX_CPU_ACCLERATION=SSE4.1 implies
689 # SSE2). Accordingly, there are a set of CMake variables
690 # GMX_<arch>_<feature-set> that are exported to the C code to specify
691 # CPU features that should be used. This means that the logic for
692 # requiring such backward compatibility is all located here.
693 if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
695 set(ACCELERATION_STATUS_MESSAGE "CPU acceleration disabled")
697 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
699 GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" ACCELERATION_C_FLAGS)
700 if(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
701 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
702 endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
704 GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
705 if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
706 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
707 endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
709 # We dont warn for lacking SSE2 flag support, since that is probably standard today.
711 # Only test the include after we have tried to add the correct flag for SSE2 support
712 check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${ACCELERATION_C_FLAGS})
714 if(NOT HAVE_EMMINTRIN_H)
715 message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
716 endif(NOT HAVE_EMMINTRIN_H)
718 set(GMX_CPU_ACCELERATION_X86_SSE2 1)
719 # The user should not be able to set this orthogonally to the acceleration
721 set(ACCELERATION_STATUS_MESSAGE
722 "Enabling SSE2 Gromacs acceleration")
724 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
726 GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" ACCELERATION_C_FLAGS)
727 if (NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
728 GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" ACCELERATION_C_FLAGS)
729 endif(NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
730 if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
731 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
732 # intrinsics when SSE2 support is enabled, so we try that instead first.
733 if (GMX_NATIVE_WINDOWS)
734 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
735 message(WARNING "Neither SSE4.1 or SSE2 seems to be supported by your Windows compiler. Something is likely broken.")
737 message(WARNING "No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance")
739 endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
741 GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
742 if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
743 GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
744 endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
745 if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
746 message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
747 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
748 # intrinsics when SSE2 support is enabled, so we try that instead.
749 if (GMX_NATIVE_WINDOWS)
750 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
752 endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
754 # This must come after we have added the -msse4.1 flag on some platforms.
755 check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
757 if(NOT HAVE_SMMINTRIN_H)
758 message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
759 endif(NOT HAVE_SMMINTRIN_H)
761 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_EQUAL "11.1")
762 message(FATAL_ERROR "You are using Intel compiler version 11.1, and that compiler is known to produce incorrect results with SSE4.1 acceleration. You need to use another compiler (e.g. icc 12 or newer) or different acceleration (probably slower simulations).")
765 set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
766 # The user should not be able to set this orthogonally to the acceleration
767 set(GMX_X86_SSE4_1 1)
769 set(ACCELERATION_STATUS_MESSAGE
770 "Enabling SSE4.1 Gromacs acceleration")
772 elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
774 # Set the AVX compiler flag for both these choices!
776 GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" ACCELERATION_C_FLAGS)
777 if (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
778 GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" ACCELERATION_C_FLAGS)
779 endif (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
780 if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
781 message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance) giving the -DGMX_CPU_ACCELERATION=SSE4.1 to cmake.")
782 endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
784 GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
785 if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
786 GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
787 endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
788 if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
789 message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance) giving the -DGMX_CPU_ACCELERATION=SSE4.1 to cmake.")
790 endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
792 # Set the FMA4 flags (MSVC doesn't require any)
793 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
794 GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
795 if (NOT GNU_FMA_CFLAG)
796 message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
797 endif(NOT GNU_FMA_CFLAG)
798 GMX_TEST_CFLAG(GNU_XOP_CFLAG "-mxop" ACCELERATION_C_FLAGS)
799 # No big deal if we do not have xop, so no point yelling warnings about it.
800 GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" ACCELERATION_CXX_FLAGS)
801 if (NOT GNU_FMA_CXXFLAG)
802 message(WARNING "No C++ FMA flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
803 endif (NOT GNU_FMA_CXXFLAG)
804 GMX_TEST_CXXFLAG(GNU_XOP_CXXFLAG "-mxop" ACCELERATION_CXX_FLAGS)
805 # No big deal if we do not have xop, so no point yelling warnings about it.
808 # Only test the header after we have tried to add the flag for AVX support
809 check_include_file(immintrin.h HAVE_IMMINTRIN_H ${ACCELERATION_C_FLAGS})
811 if(NOT HAVE_IMMINTRIN_H)
812 message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
813 endif(NOT HAVE_IMMINTRIN_H)
815 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
816 try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
817 "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
818 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
820 message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
824 # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
825 check_include_file(x86intrin.h HAVE_X86INTRIN_H ${ACCELERATION_C_FLAGS})
826 check_include_file(intrin.h HAVE_INTRIN_H ${ACCELERATION_C_FLAGS})
828 # The user should not be able to set this orthogonally to the acceleration
829 set(GMX_X86_SSE4_1 1)
832 # But just enable one of the choices internally...
833 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
834 # We don't have the full compiler version string yet (BUILD_C_COMPILER),
835 # so we can't distinguish vanilla and Apple clang, but catering for AMD
836 # hackintoshes is not worth the effort.
837 if (APPLE AND (${CMAKE_C_COMPILER_ID} STREQUAL "Clang" OR
838 ${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
839 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.")
842 if (GMX_USE_CLANG_C_FMA_BUG_WORKAROUND)
843 # we assume that we have an external assembler that supports AVX
844 message(STATUS "Clang ${C_COMPILER_VERSION} detected, enabling FMA bug workaround")
845 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} -no-integrated-as")
847 if (GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND)
848 # we assume that we have an external assembler that supports AVX
849 message(STATUS "Clang ${CXX_COMPILER_VERSION} detected, enabling FMA bug workaround")
850 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} -no-integrated-as")
853 set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
854 set(GMX_X86_AVX_128_FMA 1)
855 set(ACCELERATION_STATUS_MESSAGE
856 "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add)")
859 # If we are not doing AVX_128, it must be AVX_256...
860 set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
861 set(GMX_X86_AVX_256 1)
862 set(ACCELERATION_STATUS_MESSAGE
863 "Enabling 256-bit AVX Gromacs acceleration")
866 # Unfortunately gcc-4.5.2 and gcc-4.6.0 has a bug where they use the wrong datatype for the formal
867 # parameter of the mask for maskload/maskstore arguments. Check if this is present, since we can work around it.
868 gmx_test_avx_gcc_maskload_bug(${ACCELERATION_C_FLAGS} GMX_X86_AVX_GCC_MASKLOAD_BUG)
870 elseif(${GMX_CPU_ACCELERATION} STREQUAL "IBM_QPX")
871 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
872 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c")
875 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.")
876 set(GMX_CPU_ACCELERATION_IBM_QPX 1)
878 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.")
880 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SPARC64_HPC_ACE")
881 set(GMX_CPU_ACCELERATION_SPARC64_HPC_ACE 1)
883 gmx_invalid_option_value(GMX_CPU_ACCELERATION)
885 gmx_check_if_changed(ACCELERATION_CHANGED GMX_CPU_ACCELERATION)
886 if (ACCELERATION_CHANGED AND DEFINED ACCELERATION_STATUS_MESSAGE)
887 message(STATUS "${ACCELERATION_STATUS_MESSAGE}")
890 # Process QM/MM Settings
891 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
892 set(GMX_QMMM_GAUSSIAN 1)
893 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
894 set(GMX_QMMM_MOPAC 1)
895 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
896 set(GMX_QMMM_GAMESS 1)
897 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
899 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
902 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
905 # Process FFT library settings
908 # Intel 11 and up makes life somewhat easy if you just want to use
909 # all their stuff. It's not easy if you only want some of their
911 set(MKL_MANUALLY FALSE)
912 if (GMX_FFT_LIBRARY STREQUAL "MKL" AND
913 NOT (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11"))
914 # The user will have to provide the set of magic libraries in
915 # MKL_LIBRARIES (see below), which we cache (non-advanced), so that they
916 # don't have to keep specifying it, and can easily see that
917 # CMake is still using that information.
918 set(MKL_MANUALLY TRUE)
920 set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
921 gmx_dependent_cache_variable(
923 "List of libraries for linking to MKL. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}"
926 gmx_dependent_cache_variable(
928 "Path to mkl.h (non-inclusive)."
931 if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
938 if(GMX_BUILD_OWN_FFTW)
939 add_subdirectory(src/contrib/fftw)
941 find_package(FFTW COMPONENTS ${FFTW})
944 string(TOUPPER "${FFTW}" FFTW)
945 if(NOT ${FFTW}_FOUND)
946 MESSAGE(FATAL_ERROR "Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision GROMACS or libfftw3 for double-precision GROMACS). Either choose the right precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the advanced option to let GROMACS build FFTW 3 for you (-DGMX_BUILD_OWN_FFTW=ON) , or use the really slow GROMACS built-in fftpack library (-DGMX_FFT_LIBRARY=fftpack).")
949 set(PKG_FFT "${${FFTW}_PKG}")
950 include_directories(${${FFTW}_INCLUDE_DIRS})
951 set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
954 if ((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
955 message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
958 if((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND ${FFTW}_HAVE_AVX)
959 # If we're not doing CPU acceleration, we don't care about FFTW performance on x86 either
960 message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
963 set(FFT_STATUS_MESSAGE "Using external FFT library - FFTW3")
964 elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
965 # Intel 11 and up makes life somewhat easy if you just want to use
966 # all their stuff. It's not easy if you only want some of their
968 if (NOT MKL_MANUALLY)
969 # The next line takes care of everything for MKL
971 set(FFT_LINKER_FLAGS "/Qmkl=sequential")
973 set(FFT_LINKER_FLAGS "-mkl=sequential")
975 # Some versions of icc require this in order that mkl.h can be
976 # found at compile time.
977 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} ${FFT_LINKER_FLAGS}")
979 set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
981 include_directories(${MKL_INCLUDE_DIR})
982 set(FFT_LIBRARIES "${MKL_LIBRARIES}")
983 set(MKL_ERROR_MESSAGE "The include path to mkl.h in MKL_INCLUDE_DIR, and the link libraries in MKL_LIBRARIES=${MKL_LIBRARIES} need to match what the MKL documentation says you need for your system. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
984 # Convert the semi-colon separated list to a list of
985 # command-line linker arguments so that code using our
986 # pkgconfig setup can use it.
987 string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
990 # Check MKL works. If we were in a non-global scope, we wouldn't
991 # have to play nicely.
992 set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
993 set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
994 set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
995 set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
997 check_function_exists(DftiCreateDescriptor TEST_MKL)
999 set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
1000 set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
1003 # Hack to help the user vary MKL settings until they work.
1004 # TODO Make this logic more useful.
1005 unset(TEST_MKL CACHE)
1006 message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
1009 # Set variables to signal that we have MKL available and should use it for FFTs.
1013 set(FFT_STATUS_MESSAGE "Using external FFT library - Intel MKL")
1014 elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
1015 set(GMX_FFT_FFTPACK 1)
1016 set(FFT_STATUS_MESSAGE "Using internal FFT library - fftpack")
1017 else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1018 gmx_invalid_option_value(GMX_FFT_LIBRARY)
1019 endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1020 gmx_check_if_changed(FFT_CHANGED GMX_FFT_LIBRARY)
1022 message(STATUS "${FFT_STATUS_MESSAGE}")
1025 # enable threaded fftw3 if we've found it
1026 if(FFTW3_THREADS OR FFTW3F_THREADS)
1027 add_definitions(-DFFT5D_FFTW_THREADS)
1030 include(gmxManageLinearAlgebraLibraries)
1032 # Whether GROMACS will really try to compile support for VMD plugins
1033 set(GMX_USE_PLUGINS OFF)
1035 if(GMX_LOAD_PLUGINS)
1036 if(CYGWIN OR NOT WIN32)
1037 # Native Windows does not have, nor need dlopen
1038 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
1039 include(gmxTestdlopen)
1040 gmx_test_dlopen(HAVE_DLOPEN)
1043 # so, should we use plug-ins?
1044 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
1047 "Found the ability to use plug-ins when building shared libaries, "
1048 "so will compile to use plug-ins (e.g. to read VMD-supported file "
1051 if(NOT GMX_VMD_PLUGIN_PATH)
1054 set(GMX_USE_PLUGINS ON)
1055 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
1056 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
1060 endif(GMX_LOAD_PLUGINS)
1061 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
1063 # Link real-time library for POSIX timers
1064 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_LIBRT)
1065 list(APPEND GMX_EXTRA_LIBRARIES rt)
1068 # Math and thread libraries must often come after all others when linking...
1070 list(APPEND GMX_EXTRA_LIBRARIES m)
1072 if (${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
1073 check_library_exists(mass_simd atan2f4 "" HAVE_MASS_SIMD)
1075 list(APPEND GMX_EXTRA_LIBRARIES mass_simd)
1077 message(FATAL_ERROR "Could not link to the SIMD version of the IBM MASS library. Please adjust your CMAKE_PREFIX_PATH to contain it")
1082 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
1083 "Path to swindirect.h")
1084 include_directories(${COREWRAP_INCLUDE_DIR})
1087 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
1088 # these are set after everything else
1089 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
1090 set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
1091 set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
1092 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
1093 set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
1095 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
1096 message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
1097 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
1098 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
1099 message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
1100 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
1101 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
1102 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
1103 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
1107 #Unset all OpenMP flags in case OpenMP was disabled either by the user
1108 #or because it was only partially detected (e.g. only for C but not C++ compiler)
1109 unset(OpenMP_C_FLAGS CACHE)
1110 unset(OpenMP_CXX_FLAGS CACHE)
1112 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
1113 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
1115 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
1117 ######################################
1118 # Output compiler and CFLAGS used
1119 ######################################
1120 get_compiler_info(C BUILD_C_COMPILER BUILD_CFLAGS)
1121 get_compiler_info(CXX BUILD_CXX_COMPILER BUILD_CXXFLAGS)
1123 get_cuda_compiler_info(CUDA_NVCC_COMPILER_INFO CUDA_NVCC_COMPILER_FLAGS)
1126 ########################################################################
1127 # Specify install locations
1128 ########################################################################
1129 set(GMX_LIB_INSTALL_DIR lib CACHE STRING
1130 "Library installation directory (default: lib)")
1131 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
1132 "Data installation directory under share/ (default: gromacs)")
1133 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
1135 set(LIB_INSTALL_DIR ${GMX_INSTALL_PREFIX}${GMX_LIB_INSTALL_DIR})
1136 set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
1137 set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/${GMX_DATA_INSTALL_DIR})
1138 set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
1139 set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
1141 set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
1142 set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
1144 ########################################################################
1145 # Set up binary and library suffixing
1146 ########################################################################
1149 "Use default suffixes for GROMACS binaries and libs (_d for double, _mpi for MPI; rerun cmake after changing to see relevant options)"
1151 gmx_dependent_cache_variable(
1153 "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double)."
1155 "NOT GMX_DEFAULT_SUFFIX")
1156 gmx_dependent_cache_variable(
1158 "Suffix for GROMACS libraries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double)."
1160 "NOT GMX_DEFAULT_SUFFIX")
1161 if (GMX_DEFAULT_SUFFIX)
1162 gmx_check_if_changed(SUFFIXES_CHANGED GMX_DEFAULT_SUFFIX)
1163 set(GMX_BINARY_SUFFIX "")
1164 set(GMX_LIBS_SUFFIX "")
1166 set(GMX_BINARY_SUFFIX "_mpi")
1167 set(GMX_LIBS_SUFFIX "_mpi")
1170 set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
1171 set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
1173 if (SUFFIXES_CHANGED)
1174 message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
1175 message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
1177 else(GMX_DEFAULT_SUFFIX)
1178 gmx_check_if_changed(SUFFIXES_CHANGED
1179 GMX_DEFAULT_SUFFIX GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
1180 if (SUFFIXES_CHANGED)
1181 message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
1182 message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
1184 endif(GMX_DEFAULT_SUFFIX)
1185 if (GMX_BUILD_MDRUN_ONLY)
1186 set(GMX_LIBS_SUFFIX "_mdrun${GMX_LIBS_SUFFIX}")
1189 ##################################################################
1190 # Shared library settings
1191 ##################################################################
1192 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
1193 set(CMAKE_SKIP_BUILD_RPATH FALSE)
1194 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
1195 set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
1196 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
1198 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) #rpath supported for >10.4
1199 set(CMAKE_INSTALL_NAME_DIR "@rpath")
1200 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../lib")
1202 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
1206 #COPYING file: Only necessary for binary distributions.
1207 #Simpler to always install.
1208 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
1210 if(GMX_EXTERNAL_BOOST)
1211 include_directories(${Boost_INCLUDE_DIRS})
1213 include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
1214 # typeid not supported for minimal internal version
1215 # (would add significant amount of code)
1216 add_definitions(-DBOOST_NO_TYPEID)
1217 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
1218 # (from share/template/)
1219 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${INCL_INSTALL_DIR}/gromacs/external/boost")
1220 if (NOT GMX_BUILD_MDRUN_ONLY)
1221 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
1222 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
1223 COMPONENT development)
1227 if (GMX_BUILD_FOR_COVERAGE)
1228 # Code heavy with asserts makes conditional coverage close to useless metric,
1229 # as by design most of the false branches are impossible to trigger in
1230 # correctly functioning code. And the benefit of testing those that could
1231 # be triggered by using an API against its specification isn't usually
1233 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
1236 if (NOT GMX_BUILD_MDRUN_ONLY)
1237 add_subdirectory(doxygen)
1238 add_subdirectory(share)
1239 add_subdirectory(scripts)
1241 add_subdirectory(src)
1243 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
1244 # Don't bother the user after the first configure pass.
1245 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1246 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
1248 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
1250 #######################
1252 #######################
1254 "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
1255 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
1257 ###########################
1258 ADD_CUSTOM_TARGET(uninstall
1259 "${CMAKE_COMMAND}" -P
1260 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
1261 ###########################
1263 ########################################################################
1265 ########################################################################
1269 #"check" target builds and runs all tests
1270 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
1271 add_dependencies(check tests)
1272 # TODO: This would be better within tests/CMakeLists.txt
1273 if (NOT GMX_BUILD_MDRUN_ONLY)
1274 #gmxtests target builds all binaries required for running gmxtest
1275 add_custom_target(gmxtests DEPENDS gmx links)
1276 add_dependencies(check gmxtests)
1277 add_subdirectory(tests)
1279 #TODO: Add warning if NOT REGRESSIONTEST_PATH OR NOT GMX_XML that regression/unit tests are not run.
1282 ########################################################################
1284 ########################################################################
1286 option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF)
1287 mark_as_advanced(GMX_BUILD_MANUAL)
1288 if(GMX_BUILD_MANUAL)
1289 # Make sure we only do detection of manual-building dependencies
1290 # when the user opted in for that.
1291 add_subdirectory(manual)