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 # Set the possible values of build type for cmake-gui
69 set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
70 "MinSizeRel" "RelWithDebInfo")
71 endif(NOT CMAKE_BUILD_TYPE)
76 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
77 set(CPACK_PACKAGE_VENDOR "gromacs.org")
78 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
79 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
80 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
81 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
82 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
83 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$")
84 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
85 set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/share/man;share/man")
86 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
88 #must come after all cpack settings!
91 # Set a default valgrind suppression file.
92 # This unfortunately needs to duplicate information from CTest to work as
94 set(MEMORYCHECK_SUPPRESSIONS_FILE
95 "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
97 "File that contains suppressions for the memory checker")
100 set(SOURCE_IS_GIT_REPOSITORY OFF)
101 set(SOURCE_IS_SOURCE_DISTRIBUTION OFF)
102 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
103 set(SOURCE_IS_GIT_REPOSITORY ON)
105 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
106 set(SOURCE_IS_SOURCE_DISTRIBUTION ON)
109 ########################################################################
110 # Check and warn if cache generated on a different host is being reused
111 ########################################################################
113 execute_process(COMMAND hostname
114 OUTPUT_VARIABLE TMP_HOSTNAME
115 OUTPUT_STRIP_TRAILING_WHITESPACE)
116 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
118 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
119 is being reused! This could lead to inconsitencies; therefore, it is
120 recommended to regenerate the cache!")
122 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
123 "Hostname of the machine where the cache was generated.")
126 ########################################################################
127 # User input options #
128 ########################################################################
129 include(gmxOptionUtilities)
131 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
133 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
134 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
135 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
136 gmx_dependent_option(
138 "Enable MPI_IN_PLACE for MPIs that have it defined"
141 mark_as_advanced(GMX_MPI_IN_PLACE)
142 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
143 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
144 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
145 mark_as_advanced(GMX_FAHCORE)
147 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
148 mark_as_advanced(GMX_COOL_QUOTES)
149 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
151 # decide on GPU settings based on user-settings and GPU/CUDA detection
152 include(gmxManageGPU)
154 # Detect the architecture the compiler is targetting, detect
155 # acceleration possibilities on that hardware, suggest an acceleration
156 # to use if none is specified, and populate the cache option for CPU
158 include(gmxDetectTargetArchitecture)
159 gmx_detect_target_architecture()
160 include(gmxDetectAcceleration)
161 gmx_detect_acceleration(GMX_SUGGESTED_CPU_ACCELERATION)
163 gmx_option_multichoice(
165 "Acceleration for CPU kernels and compiler optimization"
166 "${GMX_SUGGESTED_CPU_ACCELERATION}"
167 None SSE2 SSE4.1 AVX_128_FMA AVX_256 IBM_QPX Sparc64_HPC_ACE)
169 gmx_option_multichoice(
173 fftw3 mkl "fftpack[built-in]")
174 gmx_dependent_option(
176 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
178 "GMX_FFT_LIBRARY STREQUAL FFTW3")
179 gmx_dependent_option(
180 GMX_DISABLE_FFTW_MEASURE
181 "Do not optimize FFTW setups (not needed with SSE)"
183 "GMX_FFT_LIBRARY STREQUAL FFTW3")
184 mark_as_advanced(GMX_BUILD_OWN_FFTW)
185 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
187 gmx_option_multichoice(
189 "QM package for QM/MM"
191 none gaussian mopac gamess orca)
193 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
194 mark_as_advanced(GMX_BROKEN_CALLOC)
195 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
196 mark_as_advanced(GMX_LOAD_PLUGINS)
198 option(GMX_GPU "Enable GPU acceleration" ON)
199 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
201 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
202 mark_as_advanced(GMX_GIT_VERSION_INFO)
205 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
207 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
209 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
210 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
212 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
213 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
215 option(GMX_BUILD_FOR_COVERAGE
216 "Tune build for better code coverage metrics (e.g., disable asserts)"
218 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
220 ######################################################################
222 # These need to be done early (before further tests).
223 #####################################################################
225 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
226 # are used with permission from CMake v2.8.9 so that GROMACS can detect
227 # invalid options with the Intel Compilers.
228 # These files should be removed from the source tree when a CMake version that
229 # includes the features in question becomes required for building GROMACS.
230 include(CheckCCompilerFlag)
231 include(CheckCXXCompilerFlag)
233 # Get compiler version information, needs to be done early as check that depend
234 # on compiler verison follow below.
235 include(gmxGetCompilerInfo)
236 get_compiler_version()
238 # First exclude compilers known to not work with OpenMP although claim to support it:
239 # gcc 4.2.1 and gcc-llvm 4.2.1 (also claims to be 4.2.1) on Mac OS X
240 # This fixes redmine 900 and needs to run before OpenMP flags are set below.
241 if (CMAKE_SYSTEM_NAME STREQUAL "Darwin" AND
242 (CMAKE_COMPILER_IS_GNUCC AND C_COMPILER_VERSION AND C_COMPILER_VERSION VERSION_LESS 4.3))
243 message(STATUS "OpenMP multithreading not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled")
244 set(GMX_OPENMP OFF CACHE BOOL
245 "OpenMP multithreading not not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled!" FORCE)
248 # OpenMP check must come before other CFLAGS!
252 # CMake on Windows doesn't support linker flags passed to target_link_libraries
253 # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
254 if(NOT (WIN32 AND NOT CYGWIN))
255 if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE)
256 set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
257 set(OpenMP_SHARED_LINKER_FLAGS "")
259 # Only set a linker flag if the user didn't set them manually
260 if(NOT DEFINED OpenMP_LINKER_FLAGS)
261 set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
263 if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
264 set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
270 "The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. For now, we are proceeding by turning off OpenMP.")
271 set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
279 # This variable should be used for additional compiler flags which are not
280 # generated in gmxCFlags nor are acceleration or MPI related.
281 set(EXTRA_C_FLAGS "")
282 set(EXTRA_CXX_FLAGS "")
284 # gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
285 # Detect here whether applying a workaround is needed and will apply it later
286 # on the affected files.
287 include(gmxGCC44O3BugWorkaround)
288 gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
290 # clang 3.0 is buggy for some unknown reason detected during adding
291 # the SSE2 group kernels for GROMACS 4.6. If we ever work out what
292 # that is, we should replace these tests with a compiler feature test,
293 # update GROMACS Redmine task #1039 and perhaps report a clang bug.
295 # In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
296 # the compiler version for us. So we need a manual check for clang 3.0.
297 include(gmxDetectClang30)
298 gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
299 if(COMPILER_IS_CLANG_3_0)
300 message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
303 # clang <=3.2 contains a bug that causes incorrect code to be generated for the
304 # vfmaddps instruction and therefore the bug is triggered with AVX_128_FMA.
305 # (see: http://llvm.org/bugs/show_bug.cgi?id=15040).
306 # We can work around this by not using the integrated assembler (except on OS X
307 # which has an outdated assembler that does not support AVX instructions).
308 if (${CMAKE_C_COMPILER_ID} MATCHES "Clang" AND C_COMPILER_VERSION VERSION_LESS "3.3")
309 set(GMX_USE_CLANG_C_FMA_BUG_WORKAROUND TRUE)
311 if (${CMAKE_CXX_COMPILER_ID} MATCHES "Clang" AND CXX_COMPILER_VERSION VERSION_LESS "3.3")
312 set(GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND TRUE)
315 if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
316 message(WARNING "All tested PGI compiler versions (up to 12.9.0) generate binaries which produce incorrect results, or even fail to compile Gromacs. Highly recommended to use a different compiler. If you choose to use PGI, make sure to run the regressiontests.")
319 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_LESS "12.0.0")
320 message(WARNING "Intel compilers before 12.0.0 are not routinely tested, so there may be problems. Version 11.1 with SSE4.1 is known to produce incorrect results. It is highly recommended to use a more up-to-date compiler. If you choose to use this version, make sure you run the regressiontests.")
325 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
327 if(GMX_SOFTWARE_INVSQRT)
328 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
329 endif(GMX_SOFTWARE_INVSQRT)
333 ########################################################################
334 # Basic system tests (standard libraries, headers, functions, types) #
335 ########################################################################
336 include(CheckIncludeFiles)
337 include(CheckIncludeFileCXX)
338 check_include_files(unistd.h HAVE_UNISTD_H)
339 check_include_files(pwd.h HAVE_PWD_H)
340 check_include_files(dirent.h HAVE_DIRENT_H)
341 check_include_files(time.h HAVE_TIME_H)
342 check_include_files(sys/time.h HAVE_SYS_TIME_H)
343 check_include_files(io.h HAVE_IO_H)
344 check_include_files(sched.h HAVE_SCHED_H)
346 check_include_files(regex.h HAVE_POSIX_REGEX)
347 check_include_file_cxx(regex HAVE_CXX11_REGEX)
348 # TODO: It could be nice to inform the user if no regex support is found,
349 # as selections won't be fully functional.
351 include(CheckFunctionExists)
352 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
353 check_function_exists(memalign HAVE_MEMALIGN)
354 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
355 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
356 check_function_exists(fsync HAVE_FSYNC)
357 check_function_exists(_fileno HAVE__FILENO)
358 check_function_exists(fileno HAVE_FILENO)
359 check_function_exists(_commit HAVE__COMMIT)
360 check_function_exists(sigaction HAVE_SIGACTION)
361 check_function_exists(sysconf HAVE_SYSCONF)
362 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
363 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
364 check_function_exists(rsqrt HAVE_RSQRT)
365 check_function_exists(rsqrtf HAVE_RSQRTF)
366 check_function_exists(sqrtf HAVE_SQRTF)
368 include(CheckLibraryExists)
369 check_library_exists(m sqrt "" HAVE_LIBM)
370 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
373 include(CheckTypeSize)
375 check_type_size("int" SIZEOF_INT)
376 check_type_size("long int" SIZEOF_LONG_INT)
377 check_type_size("long long int" SIZEOF_LONG_LONG_INT)
378 check_type_size("off_t" SIZEOF_OFF_T)
379 check_type_size("void *" SIZEOF_VOIDP)
381 include(TestBigEndian)
382 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
384 # Management of GROMACS options for specific toolchains should go
385 # here. Because the initial settings for some of the main options have
386 # already happened, but things like library detection and MPI compiler
387 # feature detection have not, the docstrings for any over-rides of
388 # GROMACS defaults or user settings will make sense. Also, any
389 # toolchain-related reasons for choosing whether to detect various
390 # things can be sorted out now, before the detection takes place.
391 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
392 include(gmxManageBlueGene)
395 ########################################################################
396 #Process MPI settings
397 ########################################################################
398 include(gmxManageMPI)
400 ########################################################################
401 # Shared/static library settings
402 ########################################################################
403 # Determine the defaults (this block has no effect if the variables have
405 if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
406 # Maybe Solaris should be here? Patch this if you know!
407 SET(SHARED_LIBS_DEFAULT ON)
408 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
409 # Support for shared libs on native Windows is a bit new. Its
410 # default might change later if/when we sort things out. Also,
411 # Cray should go here. What variable value can detect it?
412 SET(SHARED_LIBS_DEFAULT OFF)
414 if (NOT DEFINED BUILD_SHARED_LIBS)
415 message(STATUS "Defaulting to building static libraries")
417 SET(SHARED_LIBS_DEFAULT OFF)
419 if (GMX_PREFER_STATIC_LIBS)
420 if (NOT DEFINED BUILD_SHARED_LIBS AND SHARED_LIBS_DEFAULT)
421 message("Searching for static libraries requested, so the GROMACS libraries will also be built statically (BUILD_SHARED_LIBS=OFF)")
423 set(SHARED_LIBS_DEFAULT OFF)
425 set(GMX_PREFER_STATIC_LIBS_DEFAULT OFF)
426 if (WIN32 AND NOT CYGWIN AND NOT BUILD_SHARED_LIBS)
427 set(GMX_PREFER_STATIC_LIBS_DEFAULT ON)
430 # Declare the user-visible options
431 option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic e.g. with MPI, or on some HPC systems)" ${SHARED_LIBS_DEFAULT})
433 set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
434 "When finding libraries prefer static archives (it will only work if static versions of external dependencies are available and found)")
435 elseif (WIN32 AND NOT CYGWIN)
436 set(GMX_PREFER_STATIC_LIBS_DESCRIPTION
437 "When finding libraries prefer static system libraries (MT instead of MD)")
439 option(GMX_PREFER_STATIC_LIBS "${GMX_PREFER_STATIC_LIBS_DESCRIPTION}"
440 ${GMX_PREFER_STATIC_LIBS_DEFAULT})
441 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
443 # Act on the set values
444 if (UNIX AND GMX_PREFER_STATIC_LIBS)
445 if(BUILD_SHARED_LIBS)
446 # Warn the user about the combination. But don't overwrite the request.
447 message(WARNING "Searching for static libraries requested, and building shared Gromacs libraries requested. This might cause problems linking later.")
449 # On Linux .a is the static library suffix, on Mac OS X .lib can also
450 # be used, so we'll add both to the preference list.
451 SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
453 IF( WIN32 AND NOT CYGWIN)
454 if (NOT BUILD_SHARED_LIBS)
455 if(NOT GMX_PREFER_STATIC_LIBS)
456 message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
459 message(FATAL_ERROR "BUILD_SHARED_LIBS=ON not yet working for Windows in the master branch")
460 if(GMX_PREFER_STATIC_LIBS)
461 #this combination segfaults (illegal passing of file handles)
462 message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
464 add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
465 set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
468 IF (GMX_PREFER_STATIC_LIBS)
469 #Only setting Debug and Release flags. Others configurations are current not used.
470 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
471 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
472 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
473 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
475 IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
476 if(BUILD_SHARED_LIBS) #not sure why incremental building with shared libs doesn't work
477 STRING(REPLACE "/INCREMENTAL:YES" "" CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS})
482 ########################################################################
483 # Find external packages #
484 ########################################################################
486 # Unconditionally find the package, as it is also required for unit tests
487 find_package(LibXml2)
488 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${LIBXML2_FOUND})
490 mark_as_advanced(GMX_XML)
491 # Don't actually do anything, since libxml2 is currently not used by libgromacs
492 #if(GMX_XML AND NOT LIBXML2_FOUND)
493 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
496 # include_directories(${LIBXML2_INCLUDE_DIR})
497 # set(PKG_XML libxml-2.0)
498 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
501 option(GMX_GSL "Add support for gsl" OFF)
506 include_directories(${GSL_INCLUDE_DIR})
512 option(GMX_X11 "Use X window system" OFF)
515 # X11 includes/libraries are only set in the ngmx subdirectory!
517 message(WARNING "X11 include files and/or libraries were not found. Will not build the GROMACS X11-binaries, such as ngmx")
520 include_directories(${X11_INCLUDE_DIR})
525 set(THREAD_MPI_LIB thread_mpi)
526 # Enable core threading facilities
527 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders")
528 # Enable tMPI C++ support
531 # enable MPI functions
533 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
535 endif(GMX_THREAD_MPI)
536 tmpi_get_source_list(THREAD_MPI_SRC)
539 # now that we have detected the dependencies, do the second configure pass
547 if(WIN32 AND NOT CYGWIN)
548 set(GMX_NATIVE_WINDOWS 1)
549 # This makes windows.h not declare min/max as macros that would break
550 # C++ code using std::min/std::max.
551 add_definitions(-DNOMINMAX)
554 # only bother with finding git and using version.h if the source is a git repo
555 if(GMX_GIT_VERSION_INFO)
556 if (NOT SOURCE_IS_GIT_REPOSITORY)
558 "Cannot generate git version information from source tree not under git. "
559 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
561 # We need at least git v1.5.3 be able to parse git's date output. If not
562 # found or the version is too small, we can't generate version information.
565 # Find out the git version
566 if(GIT_FOUND AND NOT GIT_VERSION)
567 execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
568 OUTPUT_VARIABLE _exec_out
569 OUTPUT_STRIP_TRAILING_WHITESPACE)
570 string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
571 set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
572 mark_as_advanced(GIT_VERSION)
575 if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
577 "No compatible git version found (>= 1.5.3 required). "
578 "Won't be able to generate development version information. "
579 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
583 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
584 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
585 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
586 find_package(Boost 1.44.0)
587 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
588 set(Boost_FOUND FALSE)
590 # Print the notification only on first run, when determining the default
591 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
592 message("Boost >= 1.44 not found. Using minimal internal version. "
593 "This may cause trouble if you plan on compiling/linking other "
594 "software that uses Boost against Gromacs.")
597 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
599 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
601 "Boost >= 1.44 not found. "
602 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
603 "version of Boost included with Gromacs.")
606 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${LIBXML2_FOUND})
607 mark_as_advanced(GMX_BUILD_UNITTESTS)
608 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
609 if (GMX_BUILD_UNITTESTS AND NOT LIBXML2_FOUND)
611 "Cannot build unit tests without libxml2. "
612 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find libxml2.")
615 ########################################################################
616 # Generate development version info for cache
617 ########################################################################
618 # set(GEN_VERSION_INFO_INTERNAL "ON")
619 # include(gmxGenerateVersionString)
621 ########################################################################
622 # Our own GROMACS tests
623 ########################################################################
625 add_definitions( -DHAVE_CONFIG_H )
626 include_directories(${CMAKE_SOURCE_DIR}/src)
627 # Required for config.h, maybe should only be set in src/CMakeLists.txt
628 include_directories(${CMAKE_BINARY_DIR}/src)
629 # Required for gmx_header_config_gen.h to be found before installation
630 include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
631 # Required for now to make old code compile
632 include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
634 include(gmxTestInlineASM)
635 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
637 include(gmxSetBuildInformation)
638 gmx_set_build_information()
639 if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
641 endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
643 include(gmxTestFloatFormat)
644 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
645 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
646 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
648 include(gmxTestLargeFiles)
649 gmx_test_large_files(GMX_LARGEFILES)
651 include(gmxTestSignal)
652 gmx_test_sigusr1(HAVE_SIGUSR1)
654 include(gmxTestInline)
655 gmx_test_inline(INLINE_KEYWORD)
657 include(gmxTestRestrict)
658 gmx_test_restrict(RESTRICT_KEYWORD)
660 include(gmxTestPipes)
661 gmx_test_pipes(HAVE_PIPES)
663 include(gmxTestIsfinite)
664 gmx_test_isfinite(HAVE_ISFINITE)
665 gmx_test__isfinite(HAVE__ISFINITE)
666 gmx_test__finite(HAVE__FINITE)
668 include(gmxTestCXX11)
669 gmx_test_cxx11(GMX_CXX11 GMX_CXX11_FLAGS)
670 if(CXX11_FLAG AND GMX_GPU)
671 #FIXME: add proper solution for progate all but cxx11 flag
672 set(CUDA_PROPAGATE_HOST_FLAGS no)
673 message(WARNING "Please manually add compiler flags to CUDA_NVCC_FLAGS. Automatic propogation temporary not working.")
677 gmx_test_xdr(GMX_SYSTEM_XDR)
678 if(NOT GMX_SYSTEM_XDR)
679 set(GMX_INTERNAL_XDR 1)
680 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_INTERNAL_XDR")
681 endif(NOT GMX_SYSTEM_XDR)
683 # include avx test source, used if the AVX flags are set below
684 include(gmxTestAVXMaskload)
686 # Process nonbonded accelerated kernels settings
688 # Note that for the backward-compatible x86 SIMD architectures, the
689 # GMX_CPU_ACCELERATION determines the maximum level of the instruction
690 # set used (e.g. GMX_CPU_ACCLERATION=SSE4.1 implies
691 # SSE2). Accordingly, there are a set of CMake variables
692 # GMX_<arch>_<feature-set> that are exported to the C code to specify
693 # CPU features that should be used. This means that the logic for
694 # requiring such backward compatibility is all located here.
695 if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
697 set(ACCELERATION_STATUS_MESSAGE "CPU acceleration disabled")
699 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
701 GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" ACCELERATION_C_FLAGS)
702 if(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
703 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
704 endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
706 GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
707 if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
708 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
709 endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
711 # We dont warn for lacking SSE2 flag support, since that is probably standard today.
713 # Only test the include after we have tried to add the correct flag for SSE2 support
714 check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${ACCELERATION_C_FLAGS})
716 if(NOT HAVE_EMMINTRIN_H)
717 message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
718 endif(NOT HAVE_EMMINTRIN_H)
720 set(GMX_CPU_ACCELERATION_X86_SSE2 1)
721 # The user should not be able to set this orthogonally to the acceleration
723 set(ACCELERATION_STATUS_MESSAGE
724 "Enabling SSE2 Gromacs acceleration")
726 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
728 GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" ACCELERATION_C_FLAGS)
729 if (NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
730 GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" ACCELERATION_C_FLAGS)
731 endif(NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
732 if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
733 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
734 # intrinsics when SSE2 support is enabled, so we try that instead first.
735 if (GMX_NATIVE_WINDOWS)
736 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
737 message(WARNING "Neither SSE4.1 or SSE2 seems to be supported by your Windows compiler. Something is likely broken.")
739 message(WARNING "No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance")
741 endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
743 GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
744 if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
745 GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
746 endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
747 if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
748 message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
749 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
750 # intrinsics when SSE2 support is enabled, so we try that instead.
751 if (GMX_NATIVE_WINDOWS)
752 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
754 endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
756 # This must come after we have added the -msse4.1 flag on some platforms.
757 check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
759 if(NOT HAVE_SMMINTRIN_H)
760 message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
761 endif(NOT HAVE_SMMINTRIN_H)
763 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_EQUAL "11.1")
764 message(FATAL_ERROR "You are using Intel compiler version 11.1, and that compiler is known to produce incorrect results with SSE4.1 acceleration. You need to use another compiler (e.g. icc 12 or newer) or different acceleration (probably slower simulations).")
767 set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
768 # The user should not be able to set this orthogonally to the acceleration
769 set(GMX_X86_SSE4_1 1)
771 set(ACCELERATION_STATUS_MESSAGE
772 "Enabling SSE4.1 Gromacs acceleration")
774 elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
776 # Set the AVX compiler flag for both these choices!
778 GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" ACCELERATION_C_FLAGS)
779 if (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
780 GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" ACCELERATION_C_FLAGS)
781 endif (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
782 if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
783 message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance) giving the -DGMX_CPU_ACCELERATION=SSE4.1 to cmake.")
784 endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
786 GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
787 if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
788 GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
789 endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
790 if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
791 message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance) giving the -DGMX_CPU_ACCELERATION=SSE4.1 to cmake.")
792 endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
794 # Set the FMA4 flags (MSVC doesn't require any)
795 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
796 GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
797 if (NOT GNU_FMA_CFLAG)
798 message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
799 endif(NOT GNU_FMA_CFLAG)
800 GMX_TEST_CFLAG(GNU_XOP_CFLAG "-mxop" ACCELERATION_C_FLAGS)
801 # No big deal if we do not have xop, so no point yelling warnings about it.
802 GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" ACCELERATION_CXX_FLAGS)
803 if (NOT GNU_FMA_CXXFLAG)
804 message(WARNING "No C++ FMA flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
805 endif (NOT GNU_FMA_CXXFLAG)
806 GMX_TEST_CXXFLAG(GNU_XOP_CXXFLAG "-mxop" ACCELERATION_CXX_FLAGS)
807 # No big deal if we do not have xop, so no point yelling warnings about it.
810 # Only test the header after we have tried to add the flag for AVX support
811 check_include_file(immintrin.h HAVE_IMMINTRIN_H ${ACCELERATION_C_FLAGS})
813 if(NOT HAVE_IMMINTRIN_H)
814 message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
815 endif(NOT HAVE_IMMINTRIN_H)
817 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
818 try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
819 "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
820 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
822 message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
826 # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
827 check_include_file(x86intrin.h HAVE_X86INTRIN_H ${ACCELERATION_C_FLAGS})
828 check_include_file(intrin.h HAVE_INTRIN_H ${ACCELERATION_C_FLAGS})
830 # The user should not be able to set this orthogonally to the acceleration
831 set(GMX_X86_SSE4_1 1)
834 # But just enable one of the choices internally...
835 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
836 # We don't have the full compiler version string yet (BUILD_C_COMPILER),
837 # so we can't distinguish vanilla and Apple clang, but catering for AMD
838 # hackintoshes is not worth the effort.
839 if (APPLE AND (${CMAKE_C_COMPILER_ID} STREQUAL "Clang" OR
840 ${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
841 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.")
844 if (GMX_USE_CLANG_C_FMA_BUG_WORKAROUND)
845 # we assume that we have an external assembler that supports AVX
846 message(STATUS "Clang ${C_COMPILER_VERSION} detected, enabling FMA bug workaround")
847 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} -no-integrated-as")
849 if (GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND)
850 # we assume that we have an external assembler that supports AVX
851 message(STATUS "Clang ${CXX_COMPILER_VERSION} detected, enabling FMA bug workaround")
852 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} -no-integrated-as")
855 set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
856 set(GMX_X86_AVX_128_FMA 1)
857 set(ACCELERATION_STATUS_MESSAGE
858 "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add)")
861 # If we are not doing AVX_128, it must be AVX_256...
862 set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
863 set(GMX_X86_AVX_256 1)
864 set(ACCELERATION_STATUS_MESSAGE
865 "Enabling 256-bit AVX Gromacs acceleration")
868 # Unfortunately gcc-4.5.2 and gcc-4.6.0 has a bug where they use the wrong datatype for the formal
869 # parameter of the mask for maskload/maskstore arguments. Check if this is present, since we can work around it.
870 gmx_test_avx_gcc_maskload_bug(${ACCELERATION_C_FLAGS} GMX_X86_AVX_GCC_MASKLOAD_BUG)
872 elseif(${GMX_CPU_ACCELERATION} STREQUAL "IBM_QPX")
873 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
874 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c")
877 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.")
878 set(GMX_CPU_ACCELERATION_IBM_QPX 1)
880 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.")
882 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SPARC64_HPC_ACE")
883 set(GMX_CPU_ACCELERATION_SPARC64_HPC_ACE 1)
885 gmx_invalid_option_value(GMX_CPU_ACCELERATION)
887 gmx_check_if_changed(ACCELERATION_CHANGED GMX_CPU_ACCELERATION)
888 if (ACCELERATION_CHANGED AND DEFINED ACCELERATION_STATUS_MESSAGE)
889 message(STATUS "${ACCELERATION_STATUS_MESSAGE}")
892 # Process QM/MM Settings
893 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
894 set(GMX_QMMM_GAUSSIAN 1)
895 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
896 set(GMX_QMMM_MOPAC 1)
897 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
898 set(GMX_QMMM_GAMESS 1)
899 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
901 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
904 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
907 # Process FFT library settings
910 # Intel 11 and up makes life somewhat easy if you just want to use
911 # all their stuff. It's not easy if you only want some of their
913 set(MKL_MANUALLY FALSE)
914 if (GMX_FFT_LIBRARY STREQUAL "MKL" AND
915 NOT (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11"))
916 # The user will have to provide the set of magic libraries in
917 # MKL_LIBRARIES (see below), which we cache (non-advanced), so that they
918 # don't have to keep specifying it, and can easily see that
919 # CMake is still using that information.
920 set(MKL_MANUALLY TRUE)
922 set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
923 gmx_dependent_cache_variable(
925 "List of libraries for linking to MKL. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}"
928 gmx_dependent_cache_variable(
930 "Path to mkl.h (non-inclusive)."
933 if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
940 if(GMX_BUILD_OWN_FFTW)
941 add_subdirectory(src/contrib/fftw)
943 find_package(FFTW COMPONENTS ${FFTW})
946 string(TOUPPER "${FFTW}" FFTW)
947 if(NOT ${FFTW}_FOUND)
948 MESSAGE(FATAL_ERROR "Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision GROMACS or libfftw3 for double-precision GROMACS). Either choose the right precision, choose another FFT(W) library (-DGMX_FFT_LIBRARY), enable the advanced option to let GROMACS build FFTW 3 for you (-DGMX_BUILD_OWN_FFTW=ON) , or use the really slow GROMACS built-in fftpack library (-DGMX_FFT_LIBRARY=fftpack).")
951 set(PKG_FFT "${${FFTW}_PKG}")
952 include_directories(${${FFTW}_INCLUDE_DIRS})
953 set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
956 if ((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
957 message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
960 if((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND ${FFTW}_HAVE_AVX)
961 # If we're not doing CPU acceleration, we don't care about FFTW performance on x86 either
962 message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
965 set(FFT_STATUS_MESSAGE "Using external FFT library - FFTW3")
966 elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
967 # Intel 11 and up makes life somewhat easy if you just want to use
968 # all their stuff. It's not easy if you only want some of their
970 if (NOT MKL_MANUALLY)
971 # The next line takes care of everything for MKL
973 set(FFT_LINKER_FLAGS "/Qmkl=sequential")
975 set(FFT_LINKER_FLAGS "-mkl=sequential")
977 # Some versions of icc require this in order that mkl.h can be
978 # found at compile time.
979 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} ${FFT_LINKER_FLAGS}")
981 set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
983 include_directories(${MKL_INCLUDE_DIR})
984 set(FFT_LIBRARIES "${MKL_LIBRARIES}")
985 set(MKL_ERROR_MESSAGE "The include path to mkl.h in MKL_INCLUDE_DIR, and the link libraries in MKL_LIBRARIES=${MKL_LIBRARIES} need to match what the MKL documentation says you need for your system. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
986 # Convert the semi-colon separated list to a list of
987 # command-line linker arguments so that code using our
988 # pkgconfig setup can use it.
989 string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
992 # Check MKL works. If we were in a non-global scope, we wouldn't
993 # have to play nicely.
994 set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
995 set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
996 set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
997 set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
999 check_function_exists(DftiCreateDescriptor TEST_MKL)
1001 set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
1002 set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
1005 # Hack to help the user vary MKL settings until they work.
1006 # TODO Make this logic more useful.
1007 unset(TEST_MKL CACHE)
1008 message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
1011 # Set variables to signal that we have MKL available and should use it for FFTs.
1015 set(FFT_STATUS_MESSAGE "Using external FFT library - Intel MKL")
1016 elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
1017 set(GMX_FFT_FFTPACK 1)
1018 set(FFT_STATUS_MESSAGE "Using internal FFT library - fftpack")
1019 else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1020 gmx_invalid_option_value(GMX_FFT_LIBRARY)
1021 endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1022 gmx_check_if_changed(FFT_CHANGED GMX_FFT_LIBRARY)
1024 message(STATUS "${FFT_STATUS_MESSAGE}")
1027 # enable threaded fftw3 if we've found it
1028 if(FFTW3_THREADS OR FFTW3F_THREADS)
1029 add_definitions(-DFFT5D_FFTW_THREADS)
1032 include(gmxManageLinearAlgebraLibraries)
1034 # Whether GROMACS will really try to compile support for VMD plugins
1035 set(GMX_USE_PLUGINS OFF)
1037 if(GMX_LOAD_PLUGINS)
1038 if(CYGWIN OR NOT WIN32)
1039 # Native Windows does not have, nor need dlopen
1040 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
1041 include(gmxTestdlopen)
1042 gmx_test_dlopen(HAVE_DLOPEN)
1045 # so, should we use plug-ins?
1046 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
1049 "Found the ability to use plug-ins when building shared libaries, "
1050 "so will compile to use plug-ins (e.g. to read VMD-supported file "
1053 if(NOT GMX_VMD_PLUGIN_PATH)
1056 set(GMX_USE_PLUGINS ON)
1057 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
1058 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
1062 endif(GMX_LOAD_PLUGINS)
1063 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
1065 # Link real-time library for POSIX timers. The check for clock_gettime
1066 # confirms the linkability of rt.
1067 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
1068 list(APPEND GMX_EXTRA_LIBRARIES rt)
1071 # Math and thread libraries must often come after all others when linking...
1073 list(APPEND GMX_EXTRA_LIBRARIES m)
1075 if (${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
1076 check_library_exists(mass_simd atan2f4 "" HAVE_MASS_SIMD)
1078 list(APPEND GMX_EXTRA_LIBRARIES mass_simd)
1080 message(FATAL_ERROR "Could not link to the SIMD version of the IBM MASS library. Please adjust your CMAKE_PREFIX_PATH to contain it")
1085 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
1086 "Path to swindirect.h")
1087 include_directories(${COREWRAP_INCLUDE_DIR})
1090 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
1091 # these are set after everything else
1092 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
1093 set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
1094 set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
1095 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
1096 set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
1098 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
1099 message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
1100 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
1101 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
1102 message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
1103 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
1104 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
1105 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
1106 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
1110 #Unset all OpenMP flags in case OpenMP was disabled either by the user
1111 #or because it was only partially detected (e.g. only for C but not C++ compiler)
1112 unset(OpenMP_C_FLAGS CACHE)
1113 unset(OpenMP_CXX_FLAGS CACHE)
1115 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
1116 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
1118 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
1120 ######################################
1121 # Output compiler and CFLAGS used
1122 ######################################
1123 get_compiler_info(C BUILD_C_COMPILER BUILD_CFLAGS)
1124 get_compiler_info(CXX BUILD_CXX_COMPILER BUILD_CXXFLAGS)
1126 get_cuda_compiler_info(CUDA_NVCC_COMPILER_INFO CUDA_NVCC_COMPILER_FLAGS)
1129 ########################################################################
1130 # Specify install locations
1131 ########################################################################
1132 set(GMX_LIB_INSTALL_DIR lib CACHE STRING
1133 "Library installation directory (default: lib)")
1134 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
1135 "Data installation directory under share/ (default: gromacs)")
1136 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
1138 set(LIB_INSTALL_DIR ${GMX_INSTALL_PREFIX}${GMX_LIB_INSTALL_DIR})
1139 set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
1140 set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/${GMX_DATA_INSTALL_DIR})
1141 set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
1142 set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
1144 set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
1145 set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
1147 ########################################################################
1148 # Set up binary and library suffixing
1149 ########################################################################
1152 "Use default suffixes for GROMACS binaries and libs (_d for double, _mpi for MPI; rerun cmake after changing to see relevant options)"
1154 gmx_dependent_cache_variable(
1156 "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double)."
1158 "NOT GMX_DEFAULT_SUFFIX")
1159 gmx_dependent_cache_variable(
1161 "Suffix for GROMACS libraries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double)."
1163 "NOT GMX_DEFAULT_SUFFIX")
1164 if (GMX_DEFAULT_SUFFIX)
1165 gmx_check_if_changed(SUFFIXES_CHANGED GMX_DEFAULT_SUFFIX)
1166 set(GMX_BINARY_SUFFIX "")
1167 set(GMX_LIBS_SUFFIX "")
1169 set(GMX_BINARY_SUFFIX "_mpi")
1170 set(GMX_LIBS_SUFFIX "_mpi")
1173 set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
1174 set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
1176 if (SUFFIXES_CHANGED)
1177 message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
1178 message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
1180 else(GMX_DEFAULT_SUFFIX)
1181 gmx_check_if_changed(SUFFIXES_CHANGED
1182 GMX_DEFAULT_SUFFIX GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
1183 if (SUFFIXES_CHANGED)
1184 message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
1185 message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
1187 endif(GMX_DEFAULT_SUFFIX)
1188 if (GMX_BUILD_MDRUN_ONLY)
1189 set(GMX_LIBS_SUFFIX "_mdrun${GMX_LIBS_SUFFIX}")
1192 ##################################################################
1193 # Shared library settings
1194 ##################################################################
1195 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
1196 set(CMAKE_SKIP_BUILD_RPATH FALSE)
1197 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
1198 set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
1199 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
1201 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) #rpath supported for >10.4
1202 set(CMAKE_INSTALL_NAME_DIR "@rpath")
1203 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../lib")
1205 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
1209 #COPYING file: Only necessary for binary distributions.
1210 #Simpler to always install.
1211 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
1213 if(GMX_EXTERNAL_BOOST)
1214 include_directories(${Boost_INCLUDE_DIRS})
1216 include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
1217 # typeid not supported for minimal internal version
1218 # (would add significant amount of code)
1219 add_definitions(-DBOOST_NO_TYPEID)
1220 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
1221 # (from share/template/)
1222 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${INCL_INSTALL_DIR}/gromacs/external/boost")
1223 if (NOT GMX_BUILD_MDRUN_ONLY)
1224 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
1225 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
1226 COMPONENT development)
1230 if (GMX_BUILD_FOR_COVERAGE)
1231 # Code heavy with asserts makes conditional coverage close to useless metric,
1232 # as by design most of the false branches are impossible to trigger in
1233 # correctly functioning code. And the benefit of testing those that could
1234 # be triggered by using an API against its specification isn't usually
1236 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
1239 if (NOT GMX_BUILD_MDRUN_ONLY)
1240 add_subdirectory(doxygen)
1241 add_subdirectory(share)
1242 add_subdirectory(scripts)
1244 add_subdirectory(src)
1246 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
1247 # Don't bother the user after the first configure pass.
1248 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1249 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
1251 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
1253 #######################
1255 #######################
1257 "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
1258 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
1260 ###########################
1261 ADD_CUSTOM_TARGET(uninstall
1262 "${CMAKE_COMMAND}" -P
1263 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
1264 ###########################
1266 ########################################################################
1268 ########################################################################
1272 #"check" target builds and runs all tests
1273 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
1274 add_dependencies(check tests)
1275 # TODO: This would be better within tests/CMakeLists.txt
1276 if (NOT GMX_BUILD_MDRUN_ONLY)
1277 #gmxtests target builds all binaries required for running gmxtest
1278 add_custom_target(gmxtests DEPENDS gmx links)
1279 add_dependencies(check gmxtests)
1280 add_subdirectory(tests)
1282 #TODO: Add warning if NOT REGRESSIONTEST_PATH OR NOT GMX_XML that regression/unit tests are not run.
1285 ########################################################################
1287 ########################################################################
1289 option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF)
1290 mark_as_advanced(GMX_BUILD_MANUAL)
1291 if(GMX_BUILD_MANUAL)
1292 # Make sure we only do detection of manual-building dependencies
1293 # when the user opted in for that.
1294 add_subdirectory(manual)