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 mark_as_advanced(DART_ROOT)
13 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
14 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
15 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
17 # PROJECT_VERSION should have the following structure:
18 # VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
20 # The "-dev" suffix is important to keep because it makes possible to distinguish
21 # between a build from official release and a build from git release branch on a
22 # machine with no git.
24 # NOTE: when releasing the "-dev" suffix needs to be stripped off!
25 set(PROJECT_VERSION "5.0-dev")
26 # The version number of the regressiontest tarball against which this
27 # git branch can be tested. Normally, this will be the version of the
28 # last patch release. Comment the next line out for branches leading
29 # to a major/minor release.
30 set(REGRESSIONTEST_VERSION "4.6.1")
31 set(CUSTOM_VERSION_STRING ""
32 CACHE STRING "Custom version string (if empty, use hard-coded default)")
33 mark_as_advanced(CUSTOM_VERSION_STRING)
34 if (CUSTOM_VERSION_STRING)
35 set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
36 endif (CUSTOM_VERSION_STRING)
38 # It is a bit irritating, but this has to be set separately for now!
39 SET(CPACK_PACKAGE_VERSION_MAJOR "5")
40 SET(CPACK_PACKAGE_VERSION_MINOR "0")
41 #SET(CPACK_PACKAGE_VERSION_PATCH "0")
43 # The numerical gromacs version. It is 40600 for 4.6.0.
44 # The #define GMX_VERSION in gmx_header_config_h is set to this value.
46 "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
47 if(CPACK_PACKAGE_VERSION_PATCH)
49 "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
52 # The API version tracks the numerical Gromacs version (for now).
53 # It is potentially different from the Gromacs version in the future, if
54 # the programs/libraries diverge from the presumably more stable API.
55 # The #define GMX_API_VERSION in version.h is set to this value to
56 # provide backward compatibility of software written against the Gromacs API.
57 set(API_VERSION ${NUM_VERSION})
59 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
60 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
63 set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
64 mark_as_advanced(GMX_INSTALL_PREFIX)
66 include(gmxBuildTypeReference)
68 if(NOT CMAKE_BUILD_TYPE)
69 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference." FORCE)
70 endif(NOT CMAKE_BUILD_TYPE)
75 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
76 set(CPACK_PACKAGE_VENDOR "gromacs.org")
77 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
78 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
79 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
80 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
81 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
82 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$")
83 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
84 SET(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/man;man")
85 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
87 #must come after all cpack settings!
90 set(SOURCE_IS_GIT_REPOSITORY OFF)
91 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
92 set(SOURCE_IS_GIT_REPOSITORY ON)
95 ########################################################################
96 # Check and warn if cache generated on a different host is being reused
97 ########################################################################
99 execute_process(COMMAND hostname
100 OUTPUT_VARIABLE TMP_HOSTNAME
101 OUTPUT_STRIP_TRAILING_WHITESPACE)
102 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
104 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
105 is being reused! This could lead to inconsitencies; therefore, it is
106 recommended to regenerate the cache!")
108 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
109 "Hostname of the machine where the cache was generated.")
112 ########################################################################
113 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
114 mark_as_advanced(GMX_COOL_QUOTES)
116 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
117 # User input options #
118 ########################################################################
119 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
120 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
121 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
122 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
123 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
124 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
125 mark_as_advanced(GMX_FAHCORE)
127 # decide on GPU settings based on user-settings and GPU/CUDA detection
128 include(gmxManageGPU)
130 # TODO: move OpenMM to contrib
131 option(GMX_OPENMM "Accelerated execution on GPUs through the OpenMM library (rerun cmake after changing to see relevant options)" OFF)
132 mark_as_advanced(GMX_OPENMM)
134 include(gmxDetectAcceleration)
135 if(NOT DEFINED GMX_CPU_ACCELERATION)
136 if(CMAKE_CROSSCOMPILING)
137 if("${CMAKE_SYSTEM_NAME}" MATCHES "BlueGeneQ")
138 set(GMX_SUGGESTED_CPU_ACCELERATION "IBM_QPX")
140 set(GMX_SUGGESTED_CPU_ACCELERATION "None")
142 else(CMAKE_CROSSCOMPILING)
143 gmx_detect_acceleration(GMX_SUGGESTED_CPU_ACCELERATION)
144 endif(CMAKE_CROSSCOMPILING)
145 endif(NOT DEFINED GMX_CPU_ACCELERATION)
147 set(GMX_CPU_ACCELERATION "@GMX_SUGGESTED_CPU_ACCELERATION@"
148 CACHE STRING "Accelerated CPU kernels. Pick one of: None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX")
150 set(GMX_FFT_LIBRARY "fftw3"
151 CACHE STRING "FFT library choices: fftw3,mkl,fftpack[built-in]")
152 option(GMX_BUILD_OWN_FFTW "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack." OFF)
153 mark_as_advanced(GMX_BUILD_OWN_FFTW)
154 option(GMX_DISABLE_FFTW_MEASURE
155 "Do not optimize FFTW setups (not needed with SSE)" OFF)
156 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
157 set(GMX_QMMM_PROGRAM "none"
158 CACHE STRING "QM package choices: none,gaussian,mopac,gamess,orca")
159 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
160 mark_as_advanced(GMX_BROKEN_CALLOC)
161 option(GMX_MPI_IN_PLACE "Enable MPI_IN_PLACE for MPIs that have it defined" ON)
162 mark_as_advanced(GMX_MPI_IN_PLACE)
163 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
164 mark_as_advanced(GMX_LOAD_PLUGINS)
166 option(GMX_GPU "Enable GPU acceleration" ON)
167 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
169 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
170 mark_as_advanced(GMX_GIT_VERSION_INFO)
172 option(GMX_DEFAULT_SUFFIX "Use default suffixes for GROMACS binaries and libs (_d for double, _mpi for MPI; rerun cmake after changing to see relevant options)" ON)
174 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
178 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static archives (not available on non-*nix platforms and it will only work if static versions of external dependencies are available and found)!" OFF)
179 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
182 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
183 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
185 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
186 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
188 ######################################################################
190 # These need to be done early (before further tests).
191 #####################################################################
193 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
194 # are used with permission from CMake v2.8.9 so that GROMACS can detect
195 # invalid options with the Intel Compilers.
196 # These files should be removed from the source tree when a CMake version that
197 # includes the features in question becomes required for building GROMACS.
198 include(CheckCCompilerFlag)
199 include(CheckCXXCompilerFlag)
201 # Get compiler version information, needs to be done early as check that depend
202 # on compiler verison follow below.
203 include(gmxGetCompilerInfo)
204 get_compiler_version()
206 # First exclude compilers known to not work with OpenMP although claim to support it:
207 # gcc 4.2.1 and gcc-llvm 4.2.1 (also claims to be 4.2.1) on Mac OS X
208 # This fixes redmine 900 and needs to run before OpenMP flags are set below.
209 if (CMAKE_SYSTEM_NAME STREQUAL "Darwin" AND
210 (CMAKE_COMPILER_IS_GNUCC AND C_COMPILER_VERSION AND C_COMPILER_VERSION VERSION_LESS 4.3))
211 message(STATUS "OpenMP multithreading not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled")
212 set(GMX_OPENMP OFF CACHE BOOL
213 "OpenMP multithreading not not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled!" FORCE)
216 # OpenMP check must come before other CFLAGS!
220 # CMake on Windows doesn't support linker flags passed to target_link_libraries
221 # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
222 if(NOT (WIN32 AND NOT CYGWIN))
223 if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE)
224 set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
225 set(OpenMP_SHARED_LINKER_FLAGS "")
227 # Only set a linker flag if the user didn't set them manually
228 if(NOT DEFINED OpenMP_LINKER_FLAGS)
229 set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
231 if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
232 set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
238 "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.")
239 set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
247 # gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
248 # Detect here whether applying a workaround is needed and will apply it later
249 # on the affected files.
250 include(gmxGCC44O3BugWorkaround)
251 gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
253 # clang 3.0 is buggy for some unknown reason detected during adding
254 # the SSE2 group kernels for GROMACS 4.6. If we ever work out what
255 # that is, we should replace these tests with a compiler feature test,
256 # update GROMACS Redmine task #1039 and perhaps report a clang bug.
258 # In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
259 # the compiler version for us. So we need a manual check for clang 3.0.
260 include(gmxDetectClang30)
261 gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
262 if(COMPILER_IS_CLANG_3_0)
263 message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
266 if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
267 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.")
270 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_LESS "12.0.0")
271 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.")
274 ########################################################################
275 # Set up binary and library suffixing
276 ########################################################################
277 set(GMX_BINARY_SUFFIX "" CACHE STRING "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
278 set(GMX_LIBS_SUFFIX ""
279 CACHE STRING "Suffix for GROMACS libs (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
280 if (GMX_DEFAULT_SUFFIX)
281 set(GMX_BINARY_SUFFIX "")
282 set(GMX_LIBS_SUFFIX "")
284 set(GMX_BINARY_SUFFIX "_mpi")
285 set(GMX_LIBS_SUFFIX "_mpi")
288 set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
289 set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
291 mark_as_advanced(FORCE GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
292 if (NOT SUFFIX_QUIETLY)
293 message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
294 message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
295 endif (NOT SUFFIX_QUIETLY)
296 else(GMX_DEFAULT_SUFFIX)
297 mark_as_advanced(CLEAR GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
298 if (NOT SUFFIX_QUIETLY)
299 message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
300 message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
301 endif (NOT SUFFIX_QUIETLY)
302 endif(GMX_DEFAULT_SUFFIX)
303 set(SUFFIX_QUIETLY TRUE CACHE INTERNAL "")
307 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
309 if(GMX_SOFTWARE_INVSQRT)
310 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
311 endif(GMX_SOFTWARE_INVSQRT)
315 ########################################################################
316 # Basic system tests (standard libraries, headers, functions, types) #
317 ########################################################################
318 include(CheckIncludeFiles)
319 include(CheckIncludeFileCXX)
320 check_include_files(unistd.h HAVE_UNISTD_H)
321 check_include_files(pwd.h HAVE_PWD_H)
322 check_include_files(pthread.h HAVE_PTHREAD_H)
323 check_include_files(dirent.h HAVE_DIRENT_H)
324 check_include_files(sys/time.h HAVE_SYS_TIME_H)
325 check_include_files(io.h HAVE_IO_H)
326 check_include_files(sched.h HAVE_SCHED_H)
328 check_include_files(regex.h HAVE_POSIX_REGEX)
329 check_include_file_cxx(regex HAVE_CXX11_REGEX)
330 # TODO: It could be nice to inform the user if no regex support is found,
331 # as selections won't be fully functional.
333 include(CheckFunctionExists)
334 check_function_exists(strdup HAVE_STRDUP)
335 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
336 check_function_exists(memalign HAVE_MEMALIGN)
337 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
338 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
339 check_function_exists(fsync HAVE_FSYNC)
340 check_function_exists(_fileno HAVE__FILENO)
341 check_function_exists(fileno HAVE_FILENO)
342 check_function_exists(_commit HAVE__COMMIT)
343 check_function_exists(sigaction HAVE_SIGACTION)
344 check_function_exists(sysconf HAVE_SYSCONF)
345 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
346 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
347 check_function_exists(rsqrt HAVE_RSQRT)
348 check_function_exists(rsqrtf HAVE_RSQRTF)
349 check_function_exists(sqrtf HAVE_SQRTF)
351 include(CheckLibraryExists)
352 check_library_exists(m sqrt "" HAVE_LIBM)
353 check_library_exists(m cbrt "" HAVE_CBRT)
356 include(CheckTypeSize)
358 check_type_size("int" SIZEOF_INT)
359 check_type_size("long int" SIZEOF_LONG_INT)
360 check_type_size("long long int" SIZEOF_LONG_LONG_INT)
361 check_type_size("off_t" SIZEOF_OFF_T)
362 check_type_size("void *" SIZEOF_VOIDP)
364 if (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
366 else (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
367 set(GMX_64_BIT FALSE)
368 endif (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
370 include(TestBigEndian)
371 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
374 if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
375 # Maybe Solaris should be here? Patch this if you know!
376 SET(SHARED_LIBS_DEFAULT ON)
377 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
378 # Support for shared libs on native Windows is a bit new. Its
379 # default might change later if/when we sort things out. Also,
380 # Cray should go here. What variable value can detect it?
381 SET(SHARED_LIBS_DEFAULT OFF)
383 message(STATUS "Defaulting to building static libraries")
384 SET(SHARED_LIBS_DEFAULT OFF)
387 # Management of GROMACS options for specific toolchains should go
388 # here. Because the initial settings for some of the main options have
389 # already happened, but things like library detection and MPI compiler
390 # feature detection have not, the docstrings for any over-rides of
391 # GROMACS defaults or user settings will make sense. Also, any
392 # toolchain-related reasons for choosing whether to detect various
393 # things can be sorted out now, before the detection takes place.
394 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
395 include(gmxManageBlueGene)
398 if(UNIX AND GMX_PREFER_STATIC_LIBS AND SHARED_LIBS_DEFAULT)
399 if(BUILD_SHARED_LIBS)
400 # Warn the user about the combination. But don't overwrite the request.
401 message(WARNING "Searching for static libraries requested, and building shared Gromacs libraries requested. This might cause problems linking later.")
402 elseif(NOT DEFINED BUILD_SHARED_LIBS)
403 # Change default to OFF. Don't warn if it's already off.
404 message(WARNING "Searching for static libraries requested, so the GROMACS libraries will also be built statically (BUILD_SHARED_LIBS=OFF)")
405 set(SHARED_LIBS_DEFAULT OFF)
409 # By now, all tool chains should have spoken up if they care about
410 # the setting of SHARED_LIBS_DEFAULT.
411 option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic e.g. with MPI, or on some HPC systems)" ${SHARED_LIBS_DEFAULT})
413 ########################################################################
414 #Process MPI settings
415 ########################################################################
416 include(gmxManageMPI)
418 ########################################################################
419 # Find external packages #
420 ########################################################################
421 if(UNIX AND GMX_PREFER_STATIC_LIBS)
422 # On Linux .a is the static library suffix, on Mac OS X .lib can also
423 # be used, so we'll add both to the preference list.
424 SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
427 IF( WIN32 AND NOT CYGWIN)
428 # This makes windows.h not declare min/max as macros that would break
429 # C++ code using std::min/std::max.
430 add_definitions(-DNOMINMAX)
432 if (NOT BUILD_SHARED_LIBS)
433 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" ON)
434 if(NOT GMX_PREFER_STATIC_LIBS)
435 message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
438 message(FATAL_ERROR "BUILD_SHARED_LIBS not yet working for Windows in the master branch")
439 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" OFF)
440 if(GMX_PREFER_STATIC_LIBS)
441 #this combination segfaults (illigal passing of file handles)
442 message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
444 add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
445 set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
447 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
449 IF (GMX_PREFER_STATIC_LIBS)
450 #Only setting Debug and Release flags. Others configurations are current not used.
451 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
452 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
453 if(CMAKE_CXX_COMPILER_LOADED)
454 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
455 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
458 IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
459 if(BUILD_SHARED_LIBS) #not sure why incremental building with shared libs doesn't work
460 STRING(REPLACE "/INCREMENTAL:YES" "" CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS})
465 # Unconditionally find the package, as it is also required for unit tests
466 find_package(LibXml2)
467 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${LIBXML2_FOUND})
469 mark_as_advanced(GMX_XML)
470 # Don't actually do anything, since libxml2 is currently not used by libgromacs
471 #if(GMX_XML AND NOT LIBXML2_FOUND)
472 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
475 # include_directories(${LIBXML2_INCLUDE_DIR})
476 # set(PKG_XML libxml-2.0)
477 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
480 option(GMX_GSL "Add support for gsl" OFF)
485 include_directories(${GSL_INCLUDE_DIR})
491 option(GMX_X11 "Use X window system" OFF)
494 # X11 includes/libraries are only set in the ngmx subdirectory!
496 message(WARNING "X11 include files and/or libraries were not found. Will not build the GROMACS X11-binaries, such as ngmx")
501 set(THREAD_MPI_LIB thread_mpi)
503 tmpi_get_source_list(THREAD_MPI_SRC CXX)
504 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
507 tmpi_get_source_list(THREAD_MPI_SRC CXX NOMPI)
508 endif(GMX_THREAD_MPI)
511 # now that we have detected the dependencies, do the second configure pass
516 find_library(ACCELERATE_FRAMEWORK Accelerate)
517 list(APPEND GMX_EXTRA_LIBRARIES ${ACCELERATE_FRAMEWORK})
524 if(WIN32 AND NOT CYGWIN)
525 set(GMX_NATIVE_WINDOWS 1)
528 # only bother with finding git and using version.h if the source is a git repo
529 if(GMX_GIT_VERSION_INFO)
530 if (NOT SOURCE_IS_GIT_REPOSITORY)
532 "Cannot generate git version information from source tree not under git. "
533 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
535 # We need at least git v1.5.3 be able to parse git's date output. If not
536 # found or the version is too small, we can't generate version information.
539 # Find out the git version
540 if(GIT_FOUND AND NOT GIT_VERSION)
541 execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
542 OUTPUT_VARIABLE _exec_out
543 OUTPUT_STRIP_TRAILING_WHITESPACE)
544 string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
545 set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
546 mark_as_advanced(GIT_VERSION)
549 if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
551 "No compatible git version found (>= 1.5.3 required). "
552 "Won't be able to generate development version information. "
553 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
557 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
558 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
559 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
560 find_package(Boost 1.44.0)
561 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
562 set(Boost_FOUND FALSE)
564 # Print the notification only on first run, when determining the default
565 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
566 message("Boost >= 1.44 not found. Using minimal internal version. "
567 "This may cause trouble if you plan on compiling/linking other "
568 "software that uses Boost against Gromacs.")
571 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
573 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
575 "Boost >= 1.44 not found. "
576 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
577 "version of Boost included with Gromacs.")
580 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${LIBXML2_FOUND})
581 mark_as_advanced(GMX_BUILD_UNITTESTS)
582 if (GMX_BUILD_UNITTESTS AND NOT LIBXML2_FOUND)
584 "Cannot build unit tests without libxml2. "
585 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find libxml2.")
587 set(MEMORYCHECK_SUPPRESSIONS_FILE ${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp)
589 ########################################################################
590 # Generate development version info for cache
591 ########################################################################
592 # set(GEN_VERSION_INFO_INTERNAL "ON")
593 # include(gmxGenerateVersionString)
595 ########################################################################
596 # Our own GROMACS tests
597 ########################################################################
599 add_definitions( -DHAVE_CONFIG_H )
600 include_directories(${CMAKE_SOURCE_DIR}/src)
601 # Required for config.h, maybe should only be set in src/CMakeLists.txt
602 include_directories(${CMAKE_BINARY_DIR}/src)
603 # Required for gmx_header_config_gen.h to be found before installation
604 include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
605 # Required for now to make old code compile
606 include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
608 include(gmxTestInlineASM)
609 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
611 include(gmxSetBuildInformation)
612 gmx_set_build_information()
613 if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
614 # The timestep counter headers do not include config.h
615 add_definitions(-DHAVE_RDTSCP)
616 endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
618 include(gmxTestFloatFormat)
619 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
620 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
621 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
623 include(gmxTestLargeFiles)
624 gmx_test_large_files(GMX_LARGEFILES)
626 include(gmxTestSignal)
627 gmx_test_sigusr1(HAVE_SIGUSR1)
629 include(gmxTestInline)
630 gmx_test_inline(INLINE_KEYWORD)
632 include(gmxTestRestrict)
633 gmx_test_restrict(RESTRICT_KEYWORD)
635 include(gmxTestPipes)
636 gmx_test_pipes(HAVE_PIPES)
638 include(gmxTestIsfinite)
639 gmx_test_isfinite(HAVE_ISFINITE)
640 gmx_test__isfinite(HAVE__ISFINITE)
641 gmx_test__finite(HAVE__FINITE)
643 include(gmxTestCXX11)
644 gmx_test_cxx11(GMX_CXX11 GMX_CXX11_FLAGS)
645 if(CXX11_FLAG AND GMX_GPU)
646 #FIXME: add proper solution for progate all but cxx11 flag
647 set(CUDA_PROPAGATE_HOST_FLAGS no)
648 message(WARNING "Please manually add compiler flags to CUDA_NVCC_FLAGS. Automatic propogation temporary not working.")
652 gmx_test_xdr(GMX_SYSTEM_XDR)
653 if(NOT GMX_SYSTEM_XDR)
654 set(GMX_INTERNAL_XDR 1)
655 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_INTERNAL_XDR")
656 endif(NOT GMX_SYSTEM_XDR)
658 # include avx test source, used if the AVX flags are set below
659 include(gmxTestAVXMaskload)
661 # Process nonbonded accelerated kernels settings
663 # Note that for the backward-compatible x86 SIMD architectures, the
664 # GMX_CPU_ACCELERATION determines the maximum level of the instruction
665 # set used (e.g. GMX_CPU_ACCLERATION=SSE4.1 implies
666 # SSE2). Accordingly, there are a set of CMake variables
667 # GMX_<arch>_<feature-set> that are exported to the C code to specify
668 # CPU features that should be used. This means that the logic for
669 # requiring such backward compatibility is all located here.
670 string(TOUPPER ${GMX_CPU_ACCELERATION} GMX_CPU_ACCELERATION)
671 if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
673 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
675 GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" ACCELERATION_C_FLAGS)
676 if(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
677 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
678 endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
680 GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
681 if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
682 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
683 endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
685 # We dont warn for lacking SSE2 flag support, since that is probably standard today.
687 # Only test the include after we have tried to add the correct flag for SSE2 support
688 check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${ACCELERATION_C_FLAGS})
690 if(NOT HAVE_EMMINTRIN_H)
691 message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
692 endif(NOT HAVE_EMMINTRIN_H)
694 set(GMX_CPU_ACCELERATION_X86_SSE2 1)
695 # The user should not be able to set this orthogonally to the acceleration
697 if (NOT ACCELERATION_QUIETLY)
698 message(STATUS "Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.")
701 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
703 GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" ACCELERATION_C_FLAGS)
704 if (NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
705 GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" ACCELERATION_C_FLAGS)
706 endif(NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
707 if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
708 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
709 # intrinsics when SSE2 support is enabled, so we try that instead first.
710 if (GMX_NATIVE_WINDOWS)
711 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
712 message(WARNING "Neither SSE4.1 or SSE2 seems to be supported by your Windows compiler. Something is likely broken.")
714 message(WARNING "No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance")
716 endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
718 GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
719 if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
720 GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
721 endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
722 if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
723 message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
724 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
725 # intrinsics when SSE2 support is enabled, so we try that instead.
726 if (GMX_NATIVE_WINDOWS)
727 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
729 endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
731 # This must come after we have added the -msse4.1 flag on some platforms.
732 check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
734 if(NOT HAVE_SMMINTRIN_H)
735 message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
736 endif(NOT HAVE_SMMINTRIN_H)
738 set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
739 # The user should not be able to set this orthogonally to the acceleration
740 set(GMX_X86_SSE4_1 1)
742 if (NOT ACCELERATION_QUIETLY)
743 message(STATUS "Enabling SSE4.1 Gromacs acceleration, and it will help compiler optimization.")
746 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_EQUAL "11.1")
747 message(FATAL_ERROR "You are using Intel compiler version 11.1, and that compiler is known to produce incorrect results with SSE4.1 acceleration. You need to use another compiler (e.g. icc 12 or newer) or different acceleration (probably slower simulations).")
749 elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
751 # Set the AVX compiler flag for both these choices!
753 GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" ACCELERATION_C_FLAGS)
754 if (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
755 GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" ACCELERATION_C_FLAGS)
756 endif (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
757 if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
758 message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
759 endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
761 GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
762 if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
763 GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
764 endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
765 if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
766 message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
767 endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
769 # Set the FMA4 flags (MSVC doesn't require any)
770 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
771 if (${CMAKE_COMPILER_ID} MATCHES "Clang")
772 message(FATAL_ERROR "Clang up to at least version 3.2 produces incorrect code for AVX_128_FMA. Sorry, but you will have to select a different compiler or acceleration.")
774 GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
775 if (NOT GNU_FMA_CFLAG)
776 message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
777 endif(NOT GNU_FMA_CFLAG)
778 GMX_TEST_CFLAG(GNU_XOP_CFLAG "-mxop" ACCELERATION_C_FLAGS)
779 # No big deal if we do not have xop, so no point yelling warnings about it.
780 if (CMAKE_CXX_COMPILER_LOADED)
781 GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" ACCELERATION_CXX_FLAGS)
782 if (NOT GNU_FMA_CXXFLAG)
783 message(WARNING "No C++ FMA flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
784 endif (NOT GNU_FMA_CXXFLAG)
785 GMX_TEST_CXXFLAG(GNU_XOP_CXXFLAG "-mxop" ACCELERATION_CXX_FLAGS)
786 # No big deal if we do not have xop, so no point yelling warnings about it.
790 # Only test the header after we have tried to add the flag for AVX support
791 check_include_file(immintrin.h HAVE_IMMINTRIN_H ${ACCELERATION_C_FLAGS})
793 if(NOT HAVE_IMMINTRIN_H)
794 message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
795 endif(NOT HAVE_IMMINTRIN_H)
797 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
798 try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
799 "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
800 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
802 message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
806 # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
807 check_include_file(x86intrin.h HAVE_X86INTRIN_H ${ACCELERATION_C_FLAGS})
808 check_include_file(intrin.h HAVE_INTRIN_H ${ACCELERATION_C_FLAGS})
810 # The user should not be able to set this orthogonally to the acceleration
811 set(GMX_X86_SSE4_1 1)
814 # But just enable one of the choices internally...
815 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
816 set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
817 set(GMX_X86_AVX_128_FMA 1)
818 if (NOT ACCELERATION_QUIETLY)
819 message(STATUS "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add), and it will help compiler optimization.")
822 # If we are not doing AVX_128, it must be AVX_256...
823 set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
824 set(GMX_X86_AVX_256 1)
825 if (NOT ACCELERATION_QUIETLY)
826 message(STATUS "Enabling 256-bit AVX Gromacs acceleration, and it will help compiler optimization.")
830 # Unfortunately gcc-4.5.2 and gcc-4.6.0 has a bug where they use the wrong datatype for the formal
831 # parameter of the mask for maskload/maskstore arguments. Check if this is present, since we can work around it.
832 gmx_test_avx_gcc_maskload_bug(${ACCELERATION_C_FLAGS} GMX_X86_AVX_GCC_MASKLOAD_BUG)
834 elseif(${GMX_CPU_ACCELERATION} STREQUAL "IBM_QPX")
836 if (CMAKE_C_COMPILER_ID MATCHES "XL")
837 GMX_TEST_CFLAG(XLC_BLUEGENEQ_CFLAG "-qarch=qp -qtune=qp" ACCELERATION_C_FLAGS)
838 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
839 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c"
840 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
842 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
845 if (CMAKE_CXX_COMPILER_ID MATCHES "XL" AND CMAKE_CXX_COMPILER_LOADED)
846 GMX_TEST_CXXFLAG(XLC_BLUEGENEQ_CXXFLAG "-qarch=qp -qtune=qp" ACCELERATION_CXX_FLAGS)
847 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
849 COMPILE_DEFINITIONS "${ACCELERATION_CXX_FLAGS")
851 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
856 message(WARNING "IBM QPX acceleration was selected and could be compiled, but the accelerated kernels are not yet available.")
857 set(GMX_CPU_ACCELERATION_IBM_QPX 1)
859 message(FATAL_ERROR "Cannot compile IBM QPX intrinsics without the XL compiler. If you are compiling for BlueGene/Q, use 'cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C' to set up the tool chain.")
862 else(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
863 MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_CPU_ACCELERATION}. Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX")
864 endif(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
865 set(ACCELERATION_QUIETLY TRUE CACHE INTERNAL "")
867 # Process QM/MM Settings
868 string(TOUPPER ${GMX_QMMM_PROGRAM} GMX_QMMM_PROGRAM)
869 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
870 set(GMX_QMMM_GAUSSIAN 1)
871 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
872 set(GMX_QMMM_MOPAC 1)
873 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
874 set(GMX_QMMM_GAMESS 1)
875 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
877 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
879 else(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
880 MESSAGE(FATAL_ERROR "Invalid QM/MM program option: ${GMX_QMMM_PROGRAM}. Choose one of: Gaussian, Mopac, Gamess, Orca, None")
881 endif(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
883 # Process FFT library settings
884 string(TOUPPER ${GMX_FFT_LIBRARY} GMX_FFT_LIBRARY)
887 set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
888 set(MKL_LIBRARIES "" CACHE STRING "List of libraries for linking to MKL. Only used with GMX_FFT_LIBRARY=mkl. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
889 set(MKL_INCLUDE_DIR "" CACHE PATH "Path to mkl.h (non-inclusive). Only used with GMX_FFT_LIBRARY=mkl.")
890 mark_as_advanced(FORCE MKL_LIBRARIES)
891 mark_as_advanced(FORCE MKL_INCLUDE_DIR)
892 if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
899 if(GMX_BUILD_OWN_FFTW)
900 add_subdirectory(src/contrib/fftw)
902 find_package(FFTW COMPONENTS ${FFTW})
905 string(TOUPPER "${FFTW}" FFTW)
906 set(PKG_FFT "${${FFTW}_PKG}")
907 include_directories(${${FFTW}_INCLUDE_DIRS})
908 set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
909 if(NOT ${FFTW}_FOUND)
910 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, enable the advanced option to let GROMACS build FFTW 3 for you, or use the really slow GROMACS built-in fftpack library.")
915 if (NOT ${GMX_CPU_ACCELERATION} STREQUAL "NONE" AND NOT ${FFTW}_HAVE_SIMD)
916 message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
919 if(NOT ${GMX_CPU_ACCELERATION} STREQUAL "NONE" AND ${FFTW}_HAVE_AVX)
920 # If we're not doing CPU acceleration, we don't care about FFTW performance on x86 either
921 message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
924 elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
925 MESSAGE(STATUS "Using external FFT library - Intel MKL")
927 # Intel 11 and up makes life somewhat easy if you just want to use
928 # all their stuff. It's not easy if you only want some of their
930 if (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11")
931 # The next line takes care of everything for MKL
933 set(FFT_LINKER_FLAGS "/Qmkl=sequential")
935 set(FFT_LINKER_FLAGS "-mkl=sequential")
937 set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
939 # The user will have to provide the set of magic libraries in
940 # MKL_LIBRARIES, which we cache (non-advanced), so that they
941 # don't have to keep specifying it, and can easily see that
942 # CMake is still using that information.
943 set(MKL_LIBRARIES "${MKL_LIBRARIES}" CACHE STRING "User-specified libraries for linking to MKL")
944 mark_as_advanced(CLEAR MKL_LIBRARIES)
945 include_directories(${MKL_INCLUDE_DIR})
946 mark_as_advanced(CLEAR MKL_INCLUDE_DIR)
947 set(FFT_LIBRARIES "${MKL_LIBRARIES}")
948 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. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
949 # Convert the semi-colon separated list to a list of
950 # command-line linker arguments so that code using our
951 # pkgconfig setup can use it.
952 string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
955 # Check MKL works. If we were in a non-global scope, we wouldn't
956 # have to play nicely.
957 set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
958 set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
959 set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
960 set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
962 check_function_exists(DftiCreateDescriptor TEST_MKL)
964 set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
965 set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
968 # Hack to help the user vary MKL settings until they work.
969 # TODO Make this logic more useful.
970 unset(TEST_MKL CACHE)
971 message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
974 # Set variables to signal that we have MKL available and should use it for FFTs.
978 #elseif(${GMX_FFT_LIBRARY} STREQUAL "ACML")
979 # MESSAGE(STATUS "Using external FFT library - AMD core math library")
980 # set(GMX_FFT_ACML 1)
981 elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
982 MESSAGE(STATUS "Using internal FFT library - fftpack")
983 set(GMX_FFT_FFTPACK 1)
984 else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
985 MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, mkl, fftpack")
986 endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
988 # enable threaded fftw3 if we've found it
989 if(FFTW3_THREADS OR FFTW3F_THREADS)
990 add_definitions(-DFFT5D_FFTW_THREADS)
993 set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use external BLAS instead of built-in")
994 set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use external LAPACK instead of built-in")
995 # MKL has BLAS/LAPACK routines
996 if(NOT HAVE_LIBMKL AND NOT ACCELERATE_FRAMEWORK)
997 if(GMX_EXTERNAL_BLAS)
999 list(APPEND GMX_EXTRA_LIBRARIES ${GMX_BLAS_USER})
1001 set(BLAS_FIND_QUIETLY ON)
1004 list(APPEND GMX_EXTRA_LIBRARIES ${BLAS_LIBRARIES})
1006 MESSAGE(STATUS "Using internal BLAS library")
1007 set(GMX_EXTERNAL_BLAS FALSE CACHE BOOL "Use external BLAS instead of built-in" FORCE)
1009 endif(GMX_BLAS_USER)
1010 endif(GMX_EXTERNAL_BLAS)
1011 if(GMX_EXTERNAL_LAPACK)
1012 if (GMX_LAPACK_USER)
1013 list(APPEND GMX_EXTRA_LIBRARIES ${GMX_LAPACK_USER})
1014 else(GMX_LAPACK_USER)
1015 set(LAPACK_FIND_QUIETLY ON)
1016 find_package(LAPACK)
1018 list(APPEND GMX_EXTRA_LIBRARIES ${LAPACK_LIBRARIES})
1020 MESSAGE(STATUS "Using internal LAPACK library")
1021 set(GMX_EXTERNAL_LAPACK FALSE CACHE BOOL "Use external LAPACK instead of built-in" FORCE)
1023 endif(GMX_LAPACK_USER)
1024 endif(GMX_EXTERNAL_LAPACK)
1026 mark_as_advanced(GMX_EXTERNAL_LAPACK)
1027 mark_as_advanced(GMX_EXTERNAL_BLAS)
1029 set(GMX_USE_PLUGINS OFF CACHE INTERNAL "Whether GROMACS will really try to compile support for VMD plugins")
1031 if(GMX_LOAD_PLUGINS)
1032 if(CYGWIN OR NOT WIN32)
1033 # Native Windows does not have, nor need dlopen
1034 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
1035 include(gmxTestdlopen)
1036 gmx_test_dlopen(HAVE_DLOPEN)
1039 # so, should we use plug-ins?
1040 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
1043 "Found the ability to use plug-ins when building shared libaries, "
1044 "so will compile to use plug-ins (e.g. to read VMD-supported file "
1047 if(NOT GMX_VMD_PLUGIN_PATH)
1050 set(GMX_USE_PLUGINS ON)
1051 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
1052 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
1056 endif(GMX_LOAD_PLUGINS)
1057 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
1059 if(EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
1060 if(NOT CMAKE_CROSSCOMPILING)
1061 option(GMX_BUILD_MANPAGES "Build man pages" ON)
1063 message(STATUS "Building the man pages is not available when "
1064 "cross-compiling the developer version from git")
1067 #make sure source package contains all man pages
1068 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/man/man1/ngmx.1")
1069 message(FATAL_ERROR "Man pages are missing from source package.")
1072 mark_as_advanced(GMX_BUILD_MANPAGES)
1074 # Math and thread libraries must often come after all others when linking...
1076 list(APPEND GMX_EXTRA_LIBRARIES m)
1080 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
1081 "Path to swindirect.h")
1082 include_directories(${COREWRAP_INCLUDE_DIR})
1083 set_property(CACHE GMX_COOL_QUOTES VALUE OFF)
1086 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
1087 # these are set after everything else
1088 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
1089 set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_C_FLAGS}")
1090 set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${CMAKE_CXX_FLAGS}")
1091 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
1092 set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
1094 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
1095 message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${GMXC_CFLAGS}")
1096 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
1097 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
1098 message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${GMXC_CXXFLAGS}")
1099 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
1100 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
1101 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
1102 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
1106 #Unset all OpenMP flags in case OpenMP was disabled either by the user
1107 #or because it was only partially detected (e.g. only for C but not C++ compiler)
1108 unset(OpenMP_C_FLAGS CACHE)
1109 unset(OpenMP_CXX_FLAGS CACHE)
1111 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
1112 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
1114 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
1116 ######################################
1117 # Output compiler and CFLAGS used
1118 ######################################
1119 get_compiler_info(C BUILD_C_COMPILER BUILD_CFLAGS)
1120 if (CMAKE_CXX_COMPILER_LOADED)
1121 get_compiler_info(CXX BUILD_CXX_COMPILER BUILD_CXXFLAGS)
1124 ########################################################################
1125 # Specify install locations
1126 ########################################################################
1127 if ( NOT DEFINED GMXLIB )
1130 set(LIB_INSTALL_DIR "${GMX_INSTALL_PREFIX}${GMXLIB}")
1131 set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
1132 set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/gromacs)
1133 set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
1134 set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
1136 set(GMXLIBDIR ${DATA_INSTALL_DIR}/top)
1138 ##################################################################
1139 # Shared library settings
1140 ##################################################################
1141 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
1142 set(CMAKE_SKIP_BUILD_RPATH FALSE)
1143 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
1144 set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
1145 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
1147 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) #rpath supported for >10.4
1148 set(CMAKE_INSTALL_NAME_DIR "@rpath")
1149 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../lib")
1151 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
1155 #COPYING file: Only necessary for binary distributions.
1156 #Simpler to always install.
1157 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
1159 if(GMX_EXTERNAL_BOOST)
1160 include_directories(${Boost_INCLUDE_DIRS})
1162 include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
1163 # typeid not supported for minimal internal version
1164 # (would add significant amount of code)
1165 add_definitions(-DBOOST_NO_TYPEID)
1166 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
1167 # (from share/template/)
1168 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${INCL_INSTALL_DIR}/gromacs/external/boost")
1169 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
1170 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
1171 COMPONENT development)
1174 add_subdirectory(doxygen)
1175 add_subdirectory(share)
1176 add_subdirectory(src)
1177 add_subdirectory(scripts)
1179 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
1180 # Don't bother the user after the first configure pass.
1181 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1182 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
1183 unset(CUDA_NOTFOUND_AUTO)
1184 unset(CUDA_NOTFOUND_MESSAGE)
1186 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
1188 #######################
1190 #######################
1192 "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
1193 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
1195 ###########################
1196 ADD_CUSTOM_TARGET(uninstall
1197 "${CMAKE_COMMAND}" -P
1198 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
1199 ###########################
1201 ########################################################################
1203 ########################################################################
1206 mark_as_advanced(BUILD_TESTING)
1207 #gmxtests target builds all binaries required for running gmxtest
1208 add_custom_target(gmxtests DEPENDS grompp mdrun pdb2gmx gmxcheck gmx links)
1211 add_subdirectory(tests)
1212 #"check" target builds and runs all tests
1213 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
1214 add_dependencies(check gmxtests tests)
1215 #TODO: Add warning if NOT REGRESSIONTEST_PATH OR NOT GMX_XML that regression/unit tests are not run.