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 "4.6.2")
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 include(gmxDetectAcceleration)
131 if(NOT DEFINED GMX_CPU_ACCELERATION)
132 if(CMAKE_CROSSCOMPILING)
133 if("${CMAKE_SYSTEM_NAME}" MATCHES "BlueGeneQ")
134 set(GMX_SUGGESTED_CPU_ACCELERATION "IBM_QPX")
136 set(GMX_SUGGESTED_CPU_ACCELERATION "None")
138 else(CMAKE_CROSSCOMPILING)
139 gmx_detect_acceleration(GMX_SUGGESTED_CPU_ACCELERATION)
140 endif(CMAKE_CROSSCOMPILING)
141 endif(NOT DEFINED GMX_CPU_ACCELERATION)
143 set(GMX_CPU_ACCELERATION "@GMX_SUGGESTED_CPU_ACCELERATION@"
144 CACHE STRING "Accelerated CPU kernels. Pick one of: None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX, Sparc64_HPC_ACE")
146 set(GMX_FFT_LIBRARY "fftw3"
147 CACHE STRING "FFT library choices: fftw3,mkl,fftpack[built-in]")
148 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)
149 mark_as_advanced(GMX_BUILD_OWN_FFTW)
150 option(GMX_DISABLE_FFTW_MEASURE
151 "Do not optimize FFTW setups (not needed with SSE)" OFF)
152 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
153 set(GMX_QMMM_PROGRAM "none"
154 CACHE STRING "QM package choices: none,gaussian,mopac,gamess,orca")
155 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
156 mark_as_advanced(GMX_BROKEN_CALLOC)
157 option(GMX_MPI_IN_PLACE "Enable MPI_IN_PLACE for MPIs that have it defined" ON)
158 mark_as_advanced(GMX_MPI_IN_PLACE)
159 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
160 mark_as_advanced(GMX_LOAD_PLUGINS)
162 option(GMX_GPU "Enable GPU acceleration" ON)
163 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
165 option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
166 mark_as_advanced(GMX_GIT_VERSION_INFO)
168 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)
170 option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
174 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)
175 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
178 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
179 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
181 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
182 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
184 option(GMX_BUILD_FOR_COVERAGE
185 "Tune build for better code coverage metrics (e.g., disable asserts)"
187 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
189 ######################################################################
191 # These need to be done early (before further tests).
192 #####################################################################
194 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
195 # are used with permission from CMake v2.8.9 so that GROMACS can detect
196 # invalid options with the Intel Compilers.
197 # These files should be removed from the source tree when a CMake version that
198 # includes the features in question becomes required for building GROMACS.
199 include(CheckCCompilerFlag)
200 include(CheckCXXCompilerFlag)
202 # Get compiler version information, needs to be done early as check that depend
203 # on compiler verison follow below.
204 include(gmxGetCompilerInfo)
205 get_compiler_version()
207 # First exclude compilers known to not work with OpenMP although claim to support it:
208 # gcc 4.2.1 and gcc-llvm 4.2.1 (also claims to be 4.2.1) on Mac OS X
209 # This fixes redmine 900 and needs to run before OpenMP flags are set below.
210 if (CMAKE_SYSTEM_NAME STREQUAL "Darwin" AND
211 (CMAKE_COMPILER_IS_GNUCC AND C_COMPILER_VERSION AND C_COMPILER_VERSION VERSION_LESS 4.3))
212 message(STATUS "OpenMP multithreading not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled")
213 set(GMX_OPENMP OFF CACHE BOOL
214 "OpenMP multithreading not not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled!" FORCE)
217 # OpenMP check must come before other CFLAGS!
221 # CMake on Windows doesn't support linker flags passed to target_link_libraries
222 # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
223 if(NOT (WIN32 AND NOT CYGWIN))
224 if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP AND NOT APPLE)
225 set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
226 set(OpenMP_SHARED_LINKER_FLAGS "")
228 # Only set a linker flag if the user didn't set them manually
229 if(NOT DEFINED OpenMP_LINKER_FLAGS)
230 set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
232 if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
233 set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
239 "The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. For now, we are proceeding by turning off OpenMP.")
240 set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
248 # This variable should be used for additional compiler flags which are not
249 # generated in gmxCFlags nor are acceleration or MPI related.
250 set(EXTRA_C_FLAGS "")
251 set(EXTRA_CXX_FLAGS "")
253 # gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
254 # Detect here whether applying a workaround is needed and will apply it later
255 # on the affected files.
256 include(gmxGCC44O3BugWorkaround)
257 gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
259 # clang 3.0 is buggy for some unknown reason detected during adding
260 # the SSE2 group kernels for GROMACS 4.6. If we ever work out what
261 # that is, we should replace these tests with a compiler feature test,
262 # update GROMACS Redmine task #1039 and perhaps report a clang bug.
264 # In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
265 # the compiler version for us. So we need a manual check for clang 3.0.
266 include(gmxDetectClang30)
267 gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
268 if(COMPILER_IS_CLANG_3_0)
269 message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
272 # clang <=3.2 contains a bug that causes incorrect code to be generated for the
273 # vfmaddps instruction and therefore the bug is triggered with AVX_128_FMA.
274 # (see: http://llvm.org/bugs/show_bug.cgi?id=15040).
275 # We can work around this by not using the integrated assembler (except on OS X
276 # which has an outdated assembler that does not support AVX instructions).
277 if (${CMAKE_C_COMPILER_ID} MATCHES "Clang" AND C_COMPILER_VERSION VERSION_LESS "3.3")
278 set(GMX_USE_CLANG_C_FMA_BUG_WORKAROUND TRUE)
280 if (${CMAKE_CXX_COMPILER_ID} MATCHES "Clang" AND CXX_COMPILER_VERSION VERSION_LESS "3.3")
281 set(GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND TRUE)
284 if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
285 message(WARNING "All tested PGI compiler versions (up to 12.9.0) generate binaries which produce incorrect results, or even fail to compile Gromacs. Highly recommended to use a different compiler. If you choose to use PGI, make sure to run the regressiontests.")
288 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_LESS "12.0.0")
289 message(WARNING "Intel compilers before 12.0.0 are not routinely tested, so there may be problems. Version 11.1 with SSE4.1 is known to produce incorrect results. It is highly recommended to use a more up-to-date compiler. If you choose to use this version, make sure you run the regressiontests.")
292 ########################################################################
293 # Set up binary and library suffixing
294 ########################################################################
295 set(GMX_BINARY_SUFFIX "" CACHE STRING "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
296 set(GMX_LIBS_SUFFIX ""
297 CACHE STRING "Suffix for GROMACS libs (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
298 if (GMX_DEFAULT_SUFFIX)
299 set(GMX_BINARY_SUFFIX "")
300 set(GMX_LIBS_SUFFIX "")
302 set(GMX_BINARY_SUFFIX "_mpi")
303 set(GMX_LIBS_SUFFIX "_mpi")
306 set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
307 set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
309 mark_as_advanced(FORCE GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
310 if (NOT SUFFIX_QUIETLY)
311 message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
312 message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
313 endif (NOT SUFFIX_QUIETLY)
314 else(GMX_DEFAULT_SUFFIX)
315 mark_as_advanced(CLEAR GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
316 if (NOT SUFFIX_QUIETLY)
317 message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
318 message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
319 endif (NOT SUFFIX_QUIETLY)
320 endif(GMX_DEFAULT_SUFFIX)
321 set(SUFFIX_QUIETLY TRUE CACHE INTERNAL "")
325 set(PKG_CFLAGS "${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(pthread.h HAVE_PTHREAD_H)
341 check_include_files(dirent.h HAVE_DIRENT_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(strdup HAVE_STRDUP)
353 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
354 check_function_exists(memalign HAVE_MEMALIGN)
355 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
356 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
357 check_function_exists(fsync HAVE_FSYNC)
358 check_function_exists(_fileno HAVE__FILENO)
359 check_function_exists(fileno HAVE_FILENO)
360 check_function_exists(_commit HAVE__COMMIT)
361 check_function_exists(sigaction HAVE_SIGACTION)
362 check_function_exists(sysconf HAVE_SYSCONF)
363 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
364 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
365 check_function_exists(rsqrt HAVE_RSQRT)
366 check_function_exists(rsqrtf HAVE_RSQRTF)
367 check_function_exists(sqrtf HAVE_SQRTF)
369 include(CheckLibraryExists)
370 check_library_exists(m sqrt "" HAVE_LIBM)
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 if (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
383 else (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
384 set(GMX_64_BIT FALSE)
385 endif (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
387 include(TestBigEndian)
388 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
391 if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
392 # Maybe Solaris should be here? Patch this if you know!
393 SET(SHARED_LIBS_DEFAULT ON)
394 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
395 # Support for shared libs on native Windows is a bit new. Its
396 # default might change later if/when we sort things out. Also,
397 # Cray should go here. What variable value can detect it?
398 SET(SHARED_LIBS_DEFAULT OFF)
400 message(STATUS "Defaulting to building static libraries")
401 SET(SHARED_LIBS_DEFAULT OFF)
404 # Management of GROMACS options for specific toolchains should go
405 # here. Because the initial settings for some of the main options have
406 # already happened, but things like library detection and MPI compiler
407 # feature detection have not, the docstrings for any over-rides of
408 # GROMACS defaults or user settings will make sense. Also, any
409 # toolchain-related reasons for choosing whether to detect various
410 # things can be sorted out now, before the detection takes place.
411 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
412 include(gmxManageBlueGene)
415 if(UNIX AND GMX_PREFER_STATIC_LIBS AND SHARED_LIBS_DEFAULT)
416 if(BUILD_SHARED_LIBS)
417 # Warn the user about the combination. But don't overwrite the request.
418 message(WARNING "Searching for static libraries requested, and building shared Gromacs libraries requested. This might cause problems linking later.")
419 elseif(NOT DEFINED BUILD_SHARED_LIBS)
420 # Change default to OFF. Don't warn if it's already off.
421 message(WARNING "Searching for static libraries requested, so the GROMACS libraries will also be built statically (BUILD_SHARED_LIBS=OFF)")
422 set(SHARED_LIBS_DEFAULT OFF)
426 # By now, all tool chains should have spoken up if they care about
427 # the setting of SHARED_LIBS_DEFAULT.
428 option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic e.g. with MPI, or on some HPC systems)" ${SHARED_LIBS_DEFAULT})
430 ########################################################################
431 #Process MPI settings
432 ########################################################################
433 include(gmxManageMPI)
435 ########################################################################
436 # Find external packages #
437 ########################################################################
438 if(UNIX AND GMX_PREFER_STATIC_LIBS)
439 # On Linux .a is the static library suffix, on Mac OS X .lib can also
440 # be used, so we'll add both to the preference list.
441 SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
444 IF( WIN32 AND NOT CYGWIN)
445 # This makes windows.h not declare min/max as macros that would break
446 # C++ code using std::min/std::max.
447 add_definitions(-DNOMINMAX)
449 if (NOT BUILD_SHARED_LIBS)
450 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" ON)
451 if(NOT GMX_PREFER_STATIC_LIBS)
452 message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
455 message(FATAL_ERROR "BUILD_SHARED_LIBS not yet working for Windows in the master branch")
456 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" OFF)
457 if(GMX_PREFER_STATIC_LIBS)
458 #this combination segfaults (illigal passing of file handles)
459 message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
461 add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
462 set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
464 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
466 IF (GMX_PREFER_STATIC_LIBS)
467 #Only setting Debug and Release flags. Others configurations are current not used.
468 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
469 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
470 if(CMAKE_CXX_COMPILER_LOADED)
471 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
472 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 # Unconditionally find the package, as it is also required for unit tests
483 find_package(LibXml2)
484 option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${LIBXML2_FOUND})
486 mark_as_advanced(GMX_XML)
487 # Don't actually do anything, since libxml2 is currently not used by libgromacs
488 #if(GMX_XML AND NOT LIBXML2_FOUND)
489 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
492 # include_directories(${LIBXML2_INCLUDE_DIR})
493 # set(PKG_XML libxml-2.0)
494 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
497 option(GMX_GSL "Add support for gsl" OFF)
502 include_directories(${GSL_INCLUDE_DIR})
508 option(GMX_X11 "Use X window system" OFF)
511 # X11 includes/libraries are only set in the ngmx subdirectory!
513 message(WARNING "X11 include files and/or libraries were not found. Will not build the GROMACS X11-binaries, such as ngmx")
518 set(THREAD_MPI_LIB thread_mpi)
519 # Enable core threading facilities
520 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders")
521 # Enable tMPI C++ support
524 # enable MPI functions
526 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
528 endif(GMX_THREAD_MPI)
529 tmpi_get_source_list(THREAD_MPI_SRC)
532 # now that we have detected the dependencies, do the second configure pass
540 if(WIN32 AND NOT CYGWIN)
541 set(GMX_NATIVE_WINDOWS 1)
544 # only bother with finding git and using version.h if the source is a git repo
545 if(GMX_GIT_VERSION_INFO)
546 if (NOT SOURCE_IS_GIT_REPOSITORY)
548 "Cannot generate git version information from source tree not under git. "
549 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
551 # We need at least git v1.5.3 be able to parse git's date output. If not
552 # found or the version is too small, we can't generate version information.
555 # Find out the git version
556 if(GIT_FOUND AND NOT GIT_VERSION)
557 execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
558 OUTPUT_VARIABLE _exec_out
559 OUTPUT_STRIP_TRAILING_WHITESPACE)
560 string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
561 set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
562 mark_as_advanced(GIT_VERSION)
565 if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
567 "No compatible git version found (>= 1.5.3 required). "
568 "Won't be able to generate development version information. "
569 "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
573 # Detect boost unless GMX_EXTERNAL_BOOST is explicitly OFF
574 # Used for default if GMX_EXTERNAL_BOOST is not defined (first CMake pass)
575 if(NOT DEFINED GMX_EXTERNAL_BOOST OR GMX_EXTERNAL_BOOST)
576 find_package(Boost 1.44.0)
577 if(Boost_FOUND AND Boost_VERSION VERSION_LESS "104400")
578 set(Boost_FOUND FALSE)
580 # Print the notification only on first run, when determining the default
581 if(NOT DEFINED GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
582 message("Boost >= 1.44 not found. Using minimal internal version. "
583 "This may cause trouble if you plan on compiling/linking other "
584 "software that uses Boost against Gromacs.")
587 option(GMX_EXTERNAL_BOOST "Use external Boost instead of minimal built-in version"
589 if(GMX_EXTERNAL_BOOST AND NOT Boost_FOUND)
591 "Boost >= 1.44 not found. "
592 "You can set GMX_EXTERNAL_BOOST=OFF to compile against minimal "
593 "version of Boost included with Gromacs.")
596 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${LIBXML2_FOUND})
597 mark_as_advanced(GMX_BUILD_UNITTESTS)
598 if (GMX_BUILD_UNITTESTS AND NOT LIBXML2_FOUND)
600 "Cannot build unit tests without libxml2. "
601 "Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find libxml2.")
603 set(MEMORYCHECK_SUPPRESSIONS_FILE ${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp)
605 ########################################################################
606 # Generate development version info for cache
607 ########################################################################
608 # set(GEN_VERSION_INFO_INTERNAL "ON")
609 # include(gmxGenerateVersionString)
611 ########################################################################
612 # Our own GROMACS tests
613 ########################################################################
615 add_definitions( -DHAVE_CONFIG_H )
616 include_directories(${CMAKE_SOURCE_DIR}/src)
617 # Required for config.h, maybe should only be set in src/CMakeLists.txt
618 include_directories(${CMAKE_BINARY_DIR}/src)
619 # Required for gmx_header_config_gen.h to be found before installation
620 include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
621 # Required for now to make old code compile
622 include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
624 include(gmxTestInlineASM)
625 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
627 include(gmxSetBuildInformation)
628 gmx_set_build_information()
629 if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
630 # The timestep counter headers do not include config.h
631 add_definitions(-DHAVE_RDTSCP)
632 endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
634 include(gmxTestFloatFormat)
635 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
636 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
637 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
639 include(gmxTestLargeFiles)
640 gmx_test_large_files(GMX_LARGEFILES)
642 include(gmxTestSignal)
643 gmx_test_sigusr1(HAVE_SIGUSR1)
645 include(gmxTestInline)
646 gmx_test_inline(INLINE_KEYWORD)
648 include(gmxTestRestrict)
649 gmx_test_restrict(RESTRICT_KEYWORD)
651 include(gmxTestPipes)
652 gmx_test_pipes(HAVE_PIPES)
654 include(gmxTestIsfinite)
655 gmx_test_isfinite(HAVE_ISFINITE)
656 gmx_test__isfinite(HAVE__ISFINITE)
657 gmx_test__finite(HAVE__FINITE)
659 include(gmxTestCXX11)
660 gmx_test_cxx11(GMX_CXX11 GMX_CXX11_FLAGS)
661 if(CXX11_FLAG AND GMX_GPU)
662 #FIXME: add proper solution for progate all but cxx11 flag
663 set(CUDA_PROPAGATE_HOST_FLAGS no)
664 message(WARNING "Please manually add compiler flags to CUDA_NVCC_FLAGS. Automatic propogation temporary not working.")
668 gmx_test_xdr(GMX_SYSTEM_XDR)
669 if(NOT GMX_SYSTEM_XDR)
670 set(GMX_INTERNAL_XDR 1)
671 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_INTERNAL_XDR")
672 endif(NOT GMX_SYSTEM_XDR)
674 # include avx test source, used if the AVX flags are set below
675 include(gmxTestAVXMaskload)
677 # Process nonbonded accelerated kernels settings
679 # Note that for the backward-compatible x86 SIMD architectures, the
680 # GMX_CPU_ACCELERATION determines the maximum level of the instruction
681 # set used (e.g. GMX_CPU_ACCLERATION=SSE4.1 implies
682 # SSE2). Accordingly, there are a set of CMake variables
683 # GMX_<arch>_<feature-set> that are exported to the C code to specify
684 # CPU features that should be used. This means that the logic for
685 # requiring such backward compatibility is all located here.
686 string(TOUPPER ${GMX_CPU_ACCELERATION} GMX_CPU_ACCELERATION)
687 if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
689 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
691 GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" ACCELERATION_C_FLAGS)
692 if(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
693 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
694 endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
696 GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
697 if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
698 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
699 endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
701 # We dont warn for lacking SSE2 flag support, since that is probably standard today.
703 # Only test the include after we have tried to add the correct flag for SSE2 support
704 check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${ACCELERATION_C_FLAGS})
706 if(NOT HAVE_EMMINTRIN_H)
707 message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
708 endif(NOT HAVE_EMMINTRIN_H)
710 set(GMX_CPU_ACCELERATION_X86_SSE2 1)
711 # The user should not be able to set this orthogonally to the acceleration
713 if (NOT ACCELERATION_QUIETLY)
714 message(STATUS "Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.")
717 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
719 GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" ACCELERATION_C_FLAGS)
720 if (NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
721 GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" ACCELERATION_C_FLAGS)
722 endif(NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
723 if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
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 first.
726 if (GMX_NATIVE_WINDOWS)
727 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
728 message(WARNING "Neither SSE4.1 or SSE2 seems to be supported by your Windows compiler. Something is likely broken.")
730 message(WARNING "No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance")
732 endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
734 GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
735 if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
736 GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
737 endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
738 if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
739 message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
740 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
741 # intrinsics when SSE2 support is enabled, so we try that instead.
742 if (GMX_NATIVE_WINDOWS)
743 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
745 endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
747 # This must come after we have added the -msse4.1 flag on some platforms.
748 check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
750 if(NOT HAVE_SMMINTRIN_H)
751 message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
752 endif(NOT HAVE_SMMINTRIN_H)
754 set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
755 # The user should not be able to set this orthogonally to the acceleration
756 set(GMX_X86_SSE4_1 1)
758 if (NOT ACCELERATION_QUIETLY)
759 message(STATUS "Enabling SSE4.1 Gromacs acceleration, and it will help compiler optimization.")
762 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_EQUAL "11.1")
763 message(FATAL_ERROR "You are using Intel compiler version 11.1, and that compiler is known to produce incorrect results with SSE4.1 acceleration. You need to use another compiler (e.g. icc 12 or newer) or different acceleration (probably slower simulations).")
765 elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
767 # Set the AVX compiler flag for both these choices!
769 GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" ACCELERATION_C_FLAGS)
770 if (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
771 GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" ACCELERATION_C_FLAGS)
772 endif (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
773 if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
774 message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
775 endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
777 GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
778 if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
779 GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
780 endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
781 if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
782 message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
783 endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
785 # Set the FMA4 flags (MSVC doesn't require any)
786 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
787 GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
788 if (NOT GNU_FMA_CFLAG)
789 message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
790 endif(NOT GNU_FMA_CFLAG)
791 GMX_TEST_CFLAG(GNU_XOP_CFLAG "-mxop" ACCELERATION_C_FLAGS)
792 # No big deal if we do not have xop, so no point yelling warnings about it.
793 if (CMAKE_CXX_COMPILER_LOADED)
794 GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" ACCELERATION_CXX_FLAGS)
795 if (NOT GNU_FMA_CXXFLAG)
796 message(WARNING "No C++ FMA flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
797 endif (NOT GNU_FMA_CXXFLAG)
798 GMX_TEST_CXXFLAG(GNU_XOP_CXXFLAG "-mxop" ACCELERATION_CXX_FLAGS)
799 # No big deal if we do not have xop, so no point yelling warnings about it.
803 # Only test the header after we have tried to add the flag for AVX support
804 check_include_file(immintrin.h HAVE_IMMINTRIN_H ${ACCELERATION_C_FLAGS})
806 if(NOT HAVE_IMMINTRIN_H)
807 message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
808 endif(NOT HAVE_IMMINTRIN_H)
810 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
811 try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
812 "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
813 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
815 message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
819 # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
820 check_include_file(x86intrin.h HAVE_X86INTRIN_H ${ACCELERATION_C_FLAGS})
821 check_include_file(intrin.h HAVE_INTRIN_H ${ACCELERATION_C_FLAGS})
823 # The user should not be able to set this orthogonally to the acceleration
824 set(GMX_X86_SSE4_1 1)
827 # But just enable one of the choices internally...
828 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
829 set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
830 set(GMX_X86_AVX_128_FMA 1)
831 if (NOT ACCELERATION_QUIETLY)
832 message(STATUS "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add), and it will help compiler optimization.")
835 # We don't have the full compiler version string yet (BUILD_C_COMPILER),
836 # so we can't distinguish vanilla and Apple clang, but catering for AMD
837 # hackintoshes is not worth the effort.
838 if (APPLE AND (${CMAKE_C_COMPILER_ID} STREQUAL "Clang" OR
839 ${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
840 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.")
843 if (GMX_USE_CLANG_C_FMA_BUG_WORKAROUND)
844 # we assume that we have an external assembler that supports AVX
845 message(STATUS "Clang ${C_COMPILER_VERSION} detected, enabling FMA bug workaround")
846 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} -no-integrated-as")
848 if (GMX_USE_CLANG_CXX_FMA_BUG_WORKAROUND)
849 # we assume that we have an external assembler that supports AVX
850 message(STATUS "Clang ${CXX_COMPILER_VERSION} detected, enabling FMA bug workaround")
851 set(EXTRA_CXX_FLAGS "${EXTRA_CXX_FLAGS} -no-integrated-as")
855 # If we are not doing AVX_128, it must be AVX_256...
856 set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
857 set(GMX_X86_AVX_256 1)
858 if (NOT ACCELERATION_QUIETLY)
859 message(STATUS "Enabling 256-bit AVX Gromacs acceleration, and it will help compiler optimization.")
863 # Unfortunately gcc-4.5.2 and gcc-4.6.0 has a bug where they use the wrong datatype for the formal
864 # parameter of the mask for maskload/maskstore arguments. Check if this is present, since we can work around it.
865 gmx_test_avx_gcc_maskload_bug(${ACCELERATION_C_FLAGS} GMX_X86_AVX_GCC_MASKLOAD_BUG)
867 elseif(${GMX_CPU_ACCELERATION} STREQUAL "IBM_QPX")
869 if (CMAKE_C_COMPILER_ID MATCHES "XL")
870 GMX_TEST_CFLAG(XLC_BLUEGENEQ_CFLAG "-qarch=qp -qtune=qp" ACCELERATION_C_FLAGS)
871 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
872 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c"
873 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
875 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
878 if (CMAKE_CXX_COMPILER_ID MATCHES "XL" AND CMAKE_CXX_COMPILER_LOADED)
879 GMX_TEST_CXXFLAG(XLC_BLUEGENEQ_CXXFLAG "-qarch=qp -qtune=qp" ACCELERATION_CXX_FLAGS)
880 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
881 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c"
882 COMPILE_DEFINITIONS "${ACCELERATION_CXX_FLAGS}")
884 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
889 message(WARNING "IBM QPX acceleration was selected and could be compiled, but the accelerated kernels are not yet available.")
890 set(GMX_CPU_ACCELERATION_IBM_QPX 1)
892 message(FATAL_ERROR "Cannot compile IBM QPX intrinsics without the XL compiler. If you are compiling for BlueGene/Q, use 'cmake .. -DCMAKE_TOOLCHAIN_FILE=BlueGeneQ-static-XL-C' to set up the tool chain.")
894 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SPARC64_HPC_ACE")
895 set(GMX_CPU_ACCELERATION_SPARC64_HPC_ACE 1)
896 else(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
897 MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_CPU_ACCELERATION}. Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX, Sparc64_HPC_ACE")
898 endif(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
899 set(ACCELERATION_QUIETLY TRUE CACHE INTERNAL "")
901 # Process QM/MM Settings
902 string(TOUPPER ${GMX_QMMM_PROGRAM} GMX_QMMM_PROGRAM)
903 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
904 set(GMX_QMMM_GAUSSIAN 1)
905 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
906 set(GMX_QMMM_MOPAC 1)
907 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
908 set(GMX_QMMM_GAMESS 1)
909 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
911 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
913 else(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
914 MESSAGE(FATAL_ERROR "Invalid QM/MM program option: ${GMX_QMMM_PROGRAM}. Choose one of: Gaussian, Mopac, Gamess, Orca, None")
915 endif(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
917 # Process FFT library settings
918 string(TOUPPER ${GMX_FFT_LIBRARY} GMX_FFT_LIBRARY)
921 set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
922 set(MKL_LIBRARIES "" CACHE STRING "List of libraries for linking to MKL. Only used with GMX_FFT_LIBRARY=mkl. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
923 set(MKL_INCLUDE_DIR "" CACHE PATH "Path to mkl.h (non-inclusive). Only used with GMX_FFT_LIBRARY=mkl.")
924 mark_as_advanced(FORCE MKL_LIBRARIES)
925 mark_as_advanced(FORCE MKL_INCLUDE_DIR)
926 if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
933 if(GMX_BUILD_OWN_FFTW)
934 add_subdirectory(src/contrib/fftw)
936 find_package(FFTW COMPONENTS ${FFTW})
939 string(TOUPPER "${FFTW}" FFTW)
940 set(PKG_FFT "${${FFTW}_PKG}")
941 include_directories(${${FFTW}_INCLUDE_DIRS})
942 set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
943 if(NOT ${FFTW}_FOUND)
944 MESSAGE(FATAL_ERROR "Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision GROMACS or libfftw3 for double-precision GROMACS). Either choose the right precision, choose another FFT(W) library, enable the advanced option to let GROMACS build FFTW 3 for you, or use the really slow GROMACS built-in fftpack library.")
949 if ((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
950 message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
953 if((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND ${FFTW}_HAVE_AVX)
954 # If we're not doing CPU acceleration, we don't care about FFTW performance on x86 either
955 message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
958 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
959 MESSAGE(STATUS "Using external FFT library - FFTW3")
961 elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
962 # Intel 11 and up makes life somewhat easy if you just want to use
963 # all their stuff. It's not easy if you only want some of their
965 if (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11")
966 # The next line takes care of everything for MKL
968 set(FFT_LINKER_FLAGS "/Qmkl=sequential")
970 set(FFT_LINKER_FLAGS "-mkl=sequential")
972 # Some versions of icc require this in order that mkl.h can be
973 # found at compile time.
974 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} ${FFT_LINKER_FLAGS}")
976 set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
978 # The user will have to provide the set of magic libraries in
979 # MKL_LIBRARIES, which we cache (non-advanced), so that they
980 # don't have to keep specifying it, and can easily see that
981 # CMake is still using that information.
982 set(MKL_LIBRARIES "${MKL_LIBRARIES}" CACHE STRING "User-specified libraries for linking to MKL")
983 mark_as_advanced(CLEAR MKL_LIBRARIES)
984 include_directories(${MKL_INCLUDE_DIR})
985 mark_as_advanced(CLEAR MKL_INCLUDE_DIR)
986 set(FFT_LIBRARIES "${MKL_LIBRARIES}")
987 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. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
988 # Convert the semi-colon separated list to a list of
989 # command-line linker arguments so that code using our
990 # pkgconfig setup can use it.
991 string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
994 # Check MKL works. If we were in a non-global scope, we wouldn't
995 # have to play nicely.
996 set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
997 set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
998 set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
999 set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
1001 check_function_exists(DftiCreateDescriptor TEST_MKL)
1003 set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
1004 set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
1007 # Hack to help the user vary MKL settings until they work.
1008 # TODO Make this logic more useful.
1009 unset(TEST_MKL CACHE)
1010 message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
1013 # Set variables to signal that we have MKL available and should use it for FFTs.
1017 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
1018 MESSAGE(STATUS "Using external FFT library - Intel MKL")
1021 #elseif(${GMX_FFT_LIBRARY} STREQUAL "ACML")
1022 # MESSAGE(STATUS "Using external FFT library - AMD core math library")
1023 # set(GMX_FFT_ACML 1)
1024 elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
1025 set(GMX_FFT_FFTPACK 1)
1026 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
1027 MESSAGE(STATUS "Using internal FFT library - fftpack")
1029 else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1030 MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, mkl, fftpack")
1031 endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1032 set(GMX_FFT_LIBRARY_PREVIOUS_VALUE ${GMX_FFT_LIBRARY} CACHE INTERNAL "Previous value for GMX_FFT_LIBRARY, so that we can detect when it changes.")
1034 # enable threaded fftw3 if we've found it
1035 if(FFTW3_THREADS OR FFTW3F_THREADS)
1036 add_definitions(-DFFT5D_FFTW_THREADS)
1039 include(gmxManageLinearAlgebraLibraries)
1041 set(GMX_USE_PLUGINS OFF CACHE INTERNAL "Whether GROMACS will really try to compile support for VMD plugins")
1043 if(GMX_LOAD_PLUGINS)
1044 if(CYGWIN OR NOT WIN32)
1045 # Native Windows does not have, nor need dlopen
1046 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
1047 include(gmxTestdlopen)
1048 gmx_test_dlopen(HAVE_DLOPEN)
1051 # so, should we use plug-ins?
1052 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
1055 "Found the ability to use plug-ins when building shared libaries, "
1056 "so will compile to use plug-ins (e.g. to read VMD-supported file "
1059 if(NOT GMX_VMD_PLUGIN_PATH)
1062 set(GMX_USE_PLUGINS ON)
1063 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
1064 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
1068 endif(GMX_LOAD_PLUGINS)
1069 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
1071 if(EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
1072 if(NOT CMAKE_CROSSCOMPILING)
1073 option(GMX_BUILD_MANPAGES "Build man pages" ON)
1075 message(STATUS "Building the man pages is not available when "
1076 "cross-compiling the developer version from git")
1079 #make sure source package contains all man pages
1080 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/man/man1/ngmx.1")
1081 message(FATAL_ERROR "Man pages are missing from source package.")
1084 mark_as_advanced(GMX_BUILD_MANPAGES)
1086 # Math and thread libraries must often come after all others when linking...
1088 list(APPEND GMX_EXTRA_LIBRARIES m)
1092 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
1093 "Path to swindirect.h")
1094 include_directories(${COREWRAP_INCLUDE_DIR})
1095 set_property(CACHE GMX_COOL_QUOTES PROPERTY VALUE OFF)
1098 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
1099 # these are set after everything else
1100 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
1101 set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
1102 set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
1103 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
1104 set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
1106 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
1107 message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
1108 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
1109 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
1110 message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMX_CXX11_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
1111 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
1112 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
1113 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
1114 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
1118 #Unset all OpenMP flags in case OpenMP was disabled either by the user
1119 #or because it was only partially detected (e.g. only for C but not C++ compiler)
1120 unset(OpenMP_C_FLAGS CACHE)
1121 unset(OpenMP_CXX_FLAGS CACHE)
1123 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
1124 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
1126 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
1128 ######################################
1129 # Output compiler and CFLAGS used
1130 ######################################
1131 get_compiler_info(C BUILD_C_COMPILER BUILD_CFLAGS)
1132 if (CMAKE_CXX_COMPILER_LOADED)
1133 get_compiler_info(CXX BUILD_CXX_COMPILER BUILD_CXXFLAGS)
1136 get_cuda_compiler_info(CUDA_NVCC_COMPILER_INFO CUDA_NVCC_COMPILER_FLAGS)
1140 ########################################################################
1141 # Specify install locations
1142 ########################################################################
1143 if ( NOT DEFINED GMXLIB )
1146 set(LIB_INSTALL_DIR "${GMX_INSTALL_PREFIX}${GMXLIB}")
1147 set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
1148 set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/gromacs)
1149 set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
1150 set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
1152 set(GMXLIBDIR ${DATA_INSTALL_DIR}/top)
1154 ##################################################################
1155 # Shared library settings
1156 ##################################################################
1157 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
1158 set(CMAKE_SKIP_BUILD_RPATH FALSE)
1159 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
1160 set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
1161 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
1163 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) #rpath supported for >10.4
1164 set(CMAKE_INSTALL_NAME_DIR "@rpath")
1165 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../lib")
1167 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
1171 #COPYING file: Only necessary for binary distributions.
1172 #Simpler to always install.
1173 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
1175 if(GMX_EXTERNAL_BOOST)
1176 include_directories(${Boost_INCLUDE_DIRS})
1178 include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
1179 # typeid not supported for minimal internal version
1180 # (would add significant amount of code)
1181 add_definitions(-DBOOST_NO_TYPEID)
1182 # TODO: Propagate the above settings to the installed CMakeFiles.txt template
1183 # (from share/template/)
1184 set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${INCL_INSTALL_DIR}/gromacs/external/boost")
1185 install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
1186 DESTINATION ${INCL_INSTALL_DIR}/gromacs/external/boost
1187 COMPONENT development)
1190 if (GMX_BUILD_FOR_COVERAGE)
1191 # Code heavy with asserts makes conditional coverage close to useless metric,
1192 # as by design most of the false branches are impossible to trigger in
1193 # correctly functioning code. And the benefit of testing those that could
1194 # be triggered by using an API against its specification isn't usually
1196 add_definitions(-DNDEBUG -DBOOST_DISABLE_ASSERTS -DGMX_DISABLE_ASSERTS)
1199 add_subdirectory(doxygen)
1200 add_subdirectory(share)
1201 add_subdirectory(src)
1202 add_subdirectory(scripts)
1204 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
1205 # Don't bother the user after the first configure pass.
1206 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1207 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
1208 unset(CUDA_NOTFOUND_AUTO)
1209 unset(CUDA_NOTFOUND_MESSAGE)
1211 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
1213 #######################
1215 #######################
1217 "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
1218 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
1220 ###########################
1221 ADD_CUSTOM_TARGET(uninstall
1222 "${CMAKE_COMMAND}" -P
1223 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
1224 ###########################
1226 ########################################################################
1228 ########################################################################
1231 mark_as_advanced(BUILD_TESTING)
1232 #gmxtests target builds all binaries required for running gmxtest
1233 add_custom_target(gmxtests DEPENDS gmx links)
1236 add_subdirectory(tests)
1237 #"check" target builds and runs all tests
1238 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
1239 add_dependencies(check gmxtests tests)
1240 #TODO: Add warning if NOT REGRESSIONTEST_PATH OR NOT GMX_XML that regression/unit tests are not run.