2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2012,2013, by the GROMACS development team, led by
5 # David van der Spoel, Berk Hess, Erik Lindahl, and including many
6 # others, as listed in the AUTHORS file in the top-level source
7 # directory and at http://www.gromacs.org.
9 # GROMACS is free software; you can redistribute it and/or
10 # modify it under the terms of the GNU Lesser General Public License
11 # as published by the Free Software Foundation; either version 2.1
12 # of the License, or (at your option) any later version.
14 # GROMACS is distributed in the hope that it will be useful,
15 # but WITHOUT ANY WARRANTY; without even the implied warranty of
16 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
17 # Lesser General Public License for more details.
19 # You should have received a copy of the GNU Lesser General Public
20 # License along with GROMACS; if not, see
21 # http://www.gnu.org/licenses, or write to the Free Software Foundation,
22 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
24 # If you want to redistribute modifications to GROMACS, please
25 # consider that scientific software is very special. Version
26 # control is crucial - bugs must be traceable. We will be happy to
27 # consider code for inclusion in the official distribution, but
28 # derived work must not be called official GROMACS. Details are found
29 # in the README & COPYING files - if they are missing, get the
30 # official version at http://www.gromacs.org.
32 # To help us fund GROMACS development, we humbly ask that you cite
33 # the research papers on the package. Check out http://www.gromacs.org.
35 cmake_minimum_required(VERSION 2.8)
36 # Keep CMake suitably quiet on Cygwin
37 set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
39 # Allows CPack to act differently for normal tools and mdrun (e.g. because of MPI)
40 set(CPACK_COMPONENT_GROUP_TOOLS_DESCRIPTION "All GROMACS executable tools")
41 set(CPACK_COMPONENT_GROUP_MDRUN_DESCRIPTION "GROMACS executable for running simulations")
43 # CMake modules/macros are in a subdirectory to keep this file cleaner
44 # This needs to be set before project() in order to pick up toolchain files
45 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
49 mark_as_advanced(DART_ROOT)
51 # PROJECT_VERSION should have the following structure:
52 # VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
54 # The "-dev" suffix is important to keep because it makes possible to distinguish
55 # between a build from official release and a build from git release branch on a
56 # machine with no git.
58 # NOTE: when releasing the "-dev" suffix needs to be stripped off!
59 set(PROJECT_VERSION "4.6.2-dev")
60 # The version number of the regressiontest tarball against which this
61 # git branch can be tested. Normally, this will be the version of the
62 # last patch release. Comment the next line out for branches leading
63 # to a major/minor release.
64 set(REGRESSIONTEST_VERSION "4.6.1")
65 set(CUSTOM_VERSION_STRING ""
66 CACHE STRING "Custom version string (if empty, use hard-coded default)")
67 mark_as_advanced(CUSTOM_VERSION_STRING)
68 if (CUSTOM_VERSION_STRING)
69 set(PROJECT_VERSION ${CUSTOM_VERSION_STRING})
70 endif (CUSTOM_VERSION_STRING)
72 # It is a bit irritating, but this has to be set separately for now!
73 SET(CPACK_PACKAGE_VERSION_MAJOR "4")
74 SET(CPACK_PACKAGE_VERSION_MINOR "6")
75 SET(CPACK_PACKAGE_VERSION_PATCH "1")
77 # The numerical gromacs version. It is 40600 for 4.6.0.
78 # The #define GMX_VERSION in gmx_header_config_h is set to this value.
80 "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
81 if(CPACK_PACKAGE_VERSION_PATCH)
83 "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
86 # The API version tracks the numerical Gromacs version (for now).
87 # It is potentially different from the Gromacs version in the future, if
88 # the programs/libraries diverge from the presumably more stable API.
89 # The #define GMX_API_VERSION in version.h is set to this value to
90 # provide backward compatibility of software written against the Gromacs API.
91 set(API_VERSION ${NUM_VERSION})
93 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
94 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
97 include(gmxBuildTypeReference)
99 if(NOT CMAKE_BUILD_TYPE)
100 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference." FORCE)
101 endif(NOT CMAKE_BUILD_TYPE)
105 set(GMX_USE_RELATIVE_INSTALL_PATH OFF CACHE STRING "Use relative paths not absolute paths for cmake install. Has only an effect on cpack.")
106 mark_as_advanced(GMX_USE_RELATIVE_INSTALL_PATH)
108 set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
109 set(CPACK_PACKAGE_VENDOR "gromacs.org")
110 set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
111 if (NOT GMX_USE_RELATIVE_INSTALL_PATH)
112 set(CPACK_SET_DESTDIR "ON")
114 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
115 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
116 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
117 set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
118 set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$")
119 set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
120 SET(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/man;man")
121 set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
123 #must come after all cpack settings!
126 ########################################################################
127 # Check and warn if cache generated on a different host is being reused
128 ########################################################################
130 execute_process(COMMAND hostname
131 OUTPUT_VARIABLE TMP_HOSTNAME
132 OUTPUT_STRIP_TRAILING_WHITESPACE)
133 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
135 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
136 is being reused! This could lead to inconsitencies; therefore, it is
137 recommended to regenerate the cache!")
139 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
140 "Hostname of the machine where the cache was generated.")
143 ########################################################################
144 # User input options - enable C++ - before any CXX flags are changed #
145 ########################################################################
147 # decide on GPU settings based on user-settings and GPU/CUDA detection
148 include(gmxManageGPU)
150 option(GMX_FORCE_CXX "Enable C++ compilation even if not necessary" OFF)
151 mark_as_advanced(GMX_FORCE_CXX)
153 option(GMX_COOL_QUOTES "Enable Gromacs cool quotes" ON)
154 mark_as_advanced(GMX_COOL_QUOTES)
156 if(GMX_GPU OR GMX_FORCE_CXX OR GMX_OPENMM)
159 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
161 ########################################################################
162 # User input options #
163 ########################################################################
164 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
165 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
166 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
167 option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
168 mark_as_advanced(GMX_SOFTWARE_INVSQRT)
169 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
170 mark_as_advanced(GMX_FAHCORE)
172 include(gmxDetectAcceleration)
173 if(NOT DEFINED GMX_CPU_ACCELERATION)
174 if(CMAKE_CROSSCOMPILING)
175 if("${CMAKE_SYSTEM_NAME}" MATCHES "BlueGeneQ")
176 set(GMX_SUGGESTED_CPU_ACCELERATION "IBM_QPX")
178 set(GMX_SUGGESTED_CPU_ACCELERATION "None")
180 else(CMAKE_CROSSCOMPILING)
181 gmx_detect_acceleration(GMX_SUGGESTED_CPU_ACCELERATION)
182 endif(CMAKE_CROSSCOMPILING)
183 endif(NOT DEFINED GMX_CPU_ACCELERATION)
185 set(GMX_CPU_ACCELERATION "@GMX_SUGGESTED_CPU_ACCELERATION@"
186 CACHE STRING "Accelerated CPU kernels. Pick one of: None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX, Sparc64_HPC_ACE")
188 set(GMX_FFT_LIBRARY "fftw3"
189 CACHE STRING "FFT library choices: fftw3,mkl,fftpack[built-in]")
190 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)
191 mark_as_advanced(GMX_BUILD_OWN_FFTW)
192 option(GMX_DISABLE_FFTW_MEASURE
193 "Do not optimize FFTW setups (not needed with SSE)" OFF)
194 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
195 set(GMX_QMMM_PROGRAM "none"
196 CACHE STRING "QM package choices: none,gaussian,mopac,gamess,orca")
197 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
198 mark_as_advanced(GMX_BROKEN_CALLOC)
199 option(GMX_MPI_IN_PLACE "Enable MPI_IN_PLACE for MPIs that have it defined" ON)
200 mark_as_advanced(GMX_MPI_IN_PLACE)
201 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
202 mark_as_advanced(GMX_LOAD_PLUGINS)
204 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
206 option(USE_VERSION_H "Generate development version string/information" ON)
207 mark_as_advanced(USE_VERSION_H)
209 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)
212 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)
213 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
216 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
217 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
219 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
220 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
222 ######################################################################
224 # These need to be done early (before further tests).
225 #####################################################################
227 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
228 # are used with permission from CMake v2.8.9 so that GROMACS can detect
229 # invalid options with the Intel Compilers.
230 # These files should be removed from the source tree when a CMake version that
231 # includes the features in question becomes required for building GROMACS.
232 include(CheckCCompilerFlag)
233 if(CMAKE_CXX_COMPILER_LOADED)
234 include(CheckCXXCompilerFlag)
237 # Get compiler version information, needs to be done early as check that depend
238 # on compiler verison follow below.
239 include(gmxGetCompilerInfo)
240 get_compiler_version()
242 # First exclude compilers known to not work with OpenMP although claim to support it:
243 # gcc 4.2.1 and gcc-llvm 4.2.1 (also claims to be 4.2.1) on Mac OS X
244 # This fixes redmine 900 and needs to run before OpenMP flags are set below.
245 if (CMAKE_SYSTEM_NAME STREQUAL "Darwin" AND
246 (CMAKE_COMPILER_IS_GNUCC AND C_COMPILER_VERSION AND C_COMPILER_VERSION VERSION_LESS 4.3))
247 message(STATUS "OpenMP multithreading not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled")
248 set(GMX_OPENMP OFF CACHE BOOL
249 "OpenMP multithreading not not supported with gcc/llvm-gcc 4.2 on Mac OS X, disabled!" FORCE)
252 # OpenMP check must come before other CFLAGS!
256 # CMake on Windows doesn't support linker flags passed to target_link_libraries
257 # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
258 if(NOT (WIN32 AND NOT CYGWIN))
259 if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP)
260 set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
261 set(OpenMP_SHARED_LINKER_FLAGS "")
263 # Only set a linker flag if the user didn't set them manually
264 if(NOT DEFINED OpenMP_LINKER_FLAGS)
265 set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
267 if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
268 set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
274 "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.")
275 set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
283 # gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
284 # Detect here whether applying a workaround is needed and will apply it later
285 # on the affected files.
286 include(gmxGCC44O3BugWorkaround)
287 gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
289 # clang 3.0 is buggy for some unknown reason detected during adding
290 # the SSE2 group kernels for GROMACS 4.6. If we ever work out what
291 # that is, we should replace these tests with a compiler feature test,
292 # update GROMACS Redmine task #1039 and perhaps report a clang bug.
294 # In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
295 # the compiler version for us. So we need a manual check for clang 3.0.
296 include(gmxDetectClang30)
297 gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
298 if(COMPILER_IS_CLANG_3_0)
299 message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
302 if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
303 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.")
306 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_LESS "12.0.0")
307 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.")
310 ########################################################################
311 # Set up binary and library suffixing
312 ########################################################################
313 set(GMX_BINARY_SUFFIX "" CACHE STRING "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
314 set(GMX_LIBS_SUFFIX ""
315 CACHE STRING "Suffix for GROMACS libs (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
316 if (GMX_DEFAULT_SUFFIX)
317 set(GMX_BINARY_SUFFIX "")
318 set(GMX_LIBS_SUFFIX "")
320 set(GMX_BINARY_SUFFIX "_mpi")
321 set(GMX_LIBS_SUFFIX "_mpi")
324 set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
325 set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
327 mark_as_advanced(FORCE GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
328 if (NOT SUFFIX_QUIETLY)
329 message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
330 message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
331 endif (NOT SUFFIX_QUIETLY)
332 else(GMX_DEFAULT_SUFFIX)
333 mark_as_advanced(CLEAR GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
334 if (NOT SUFFIX_QUIETLY)
335 message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
336 message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
337 endif (NOT SUFFIX_QUIETLY)
338 endif(GMX_DEFAULT_SUFFIX)
339 set(SUFFIX_QUIETLY TRUE CACHE INTERNAL "")
343 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
345 if(GMX_SOFTWARE_INVSQRT)
346 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
347 endif(GMX_SOFTWARE_INVSQRT)
351 ########################################################################
352 # Basic system tests (standard libraries, headers, functions, types) #
353 ########################################################################
354 include(CheckIncludeFiles)
355 check_include_files(string.h HAVE_STRING_H)
356 check_include_files(math.h HAVE_MATH_H)
357 check_include_files(limits.h HAVE_LIMITS_H)
358 check_include_files(memory.h HAVE_MEMORY_H)
359 check_include_files(unistd.h HAVE_UNISTD_H)
360 check_include_files(direct.h HAVE_DIRECT_H)
361 check_include_files(pwd.h HAVE_PWD_H)
362 check_include_files(stdint.h HAVE_STDINT_H)
363 check_include_files(stdlib.h HAVE_STDLIB_H)
364 check_include_files(pthread.h HAVE_PTHREAD_H)
365 check_include_files(dirent.h HAVE_DIRENT_H)
366 check_include_files(inttypes.h HAVE_INTTYPES_H)
367 check_include_files(regex.h HAVE_REGEX_H)
368 check_include_files(sys/types.h HAVE_SYS_TYPES_H)
369 check_include_files(sys/stat.h HAVE_SYS_STAT_H)
370 check_include_files(sys/time.h HAVE_SYS_TIME_H)
371 check_include_files(rpc/rpc.h HAVE_RPC_RPC_H)
372 check_include_files("rpc/rpc.h;rpc/xdr.h" HAVE_RPC_XDR_H)
373 check_include_files(io.h HAVE_IO_H)
374 check_include_files(sched.h HAVE_SCHED_H)
376 include(CheckFunctionExists)
377 check_function_exists(strcasecmp HAVE_STRCASECMP)
378 check_function_exists(strdup HAVE_STRDUP)
379 check_function_exists(vprintf HAVE_VPRINTF)
380 check_function_exists(memcmp HAVE_MEMCMP)
381 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
382 check_function_exists(memalign HAVE_MEMALIGN)
383 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
384 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
385 check_function_exists(isnan HAVE_ISNAN)
386 check_function_exists(_isnan HAVE__ISNAN)
387 check_function_exists(fsync HAVE_FSYNC)
388 check_function_exists(_fileno HAVE__FILENO)
389 check_function_exists(fileno HAVE_FILENO)
390 check_function_exists(_commit HAVE__COMMIT)
391 check_function_exists(sigaction HAVE_SIGACTION)
392 check_function_exists(sysconf HAVE_SYSCONF)
393 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
394 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
395 check_function_exists(rsqrt HAVE_RSQRT)
396 check_function_exists(rsqrtf HAVE_RSQRTF)
397 check_function_exists(sqrtf HAVE_SQRTF)
399 include(CheckLibraryExists)
400 check_library_exists(m sqrt "" HAVE_LIBM)
401 check_library_exists(m cbrt "" HAVE_CBRT)
404 include(CheckTypeSize)
406 check_type_size("bool" SIZEOF_BOOL) # will also set HAVE_BOOL
407 check_type_size("int" SIZEOF_INT)
408 check_type_size("long int" SIZEOF_LONG_INT)
409 check_type_size("long long int" SIZEOF_LONG_LONG_INT)
410 check_type_size("off_t" SIZEOF_OFF_T)
411 check_type_size("void *" SIZEOF_VOIDP)
413 if (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
415 else (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
416 set(GMX_64_BIT FALSE)
417 endif (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
419 # Check for some basic types that we *need*, so set these to int if they are not present
420 check_type_size(uid_t uid_t)
427 check_type_size(gid_t gid_t)
434 check_type_size(size_t size_t)
441 check_type_size(off_t off_t)
448 include(TestBigEndian)
449 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
452 if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
453 # Maybe Solaris should be here? Patch this if you know!
454 SET(SHARED_LIBS_DEFAULT ON)
455 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
456 # Support for shared libs on native Windows is a bit new. Its
457 # default might change later if/when we sort things out. Also,
458 # Cray should go here. What variable value can detect it?
459 SET(SHARED_LIBS_DEFAULT OFF)
461 message(STATUS "Defaulting to building static libraries")
462 SET(SHARED_LIBS_DEFAULT OFF)
465 # Management of GROMACS options for specific toolchains should go
466 # here. Because the initial settings for some of the main options have
467 # already happened, but things like library detection and MPI compiler
468 # feature detection have not, the docstrings for any over-rides of
469 # GROMACS defaults or user settings will make sense. Also, any
470 # toolchain-related reasons for choosing whether to detect various
471 # things can be sorted out now, before the detection takes place.
472 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
473 include(gmxManageBlueGene)
476 if(UNIX AND GMX_PREFER_STATIC_LIBS AND SHARED_LIBS_DEFAULT)
477 if(BUILD_SHARED_LIBS)
478 # Warn the user about the combination. But don't overwrite the request.
479 message(WARNING "Searching for static libraries requested, and building shared Gromacs libraries requested. This might cause problems linking later.")
480 elseif(NOT DEFINED BUILD_SHARED_LIBS)
481 # Change default to OFF. Don't warn if it's already off.
482 message(WARNING "Searching for static libraries requested, so the GROMACS libraries will also be built statically (BUILD_SHARED_LIBS=OFF)")
483 set(SHARED_LIBS_DEFAULT OFF)
487 # By now, all tool chains should have spoken up if they care about
488 # the setting of SHARED_LIBS_DEFAULT.
489 option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic e.g. with MPI, or on some HPC systems)" ${SHARED_LIBS_DEFAULT})
491 ########################################################################
492 #Process MPI settings
493 ########################################################################
494 include(gmxManageMPI)
496 ########################################################################
497 # Find external packages #
498 ########################################################################
499 if(UNIX AND GMX_PREFER_STATIC_LIBS)
500 # On Linux .a is the static library suffix, on Mac OS X .lib can also
501 # be used, so we'll add both to the preference list.
502 SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
505 IF( WIN32 AND NOT CYGWIN)
506 if (NOT BUILD_SHARED_LIBS)
507 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" ON)
508 if(NOT GMX_PREFER_STATIC_LIBS)
509 message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
512 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" OFF)
513 if(GMX_PREFER_STATIC_LIBS)
514 #this combination segfaults (illigal passing of file handles)
515 message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
517 add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
518 set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
520 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
522 IF (GMX_PREFER_STATIC_LIBS)
523 #Only setting Debug and Release flags. Others configurations are current not used.
524 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
525 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
526 if(CMAKE_CXX_COMPILER_LOADED)
527 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
528 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
531 IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
532 if(BUILD_SHARED_LIBS) #not sure why incremental building with shared libs doesn't work
533 STRING(REPLACE "/INCREMENTAL:YES" "" CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS})
538 option(GMX_GSL "Add support for gsl" OFF)
543 include_directories(${GSL_INCLUDE_DIR})
549 option(GMX_X11 "Use X window system" OFF)
552 # X11 includes/libraries are only set in the ngmx subdirectory!
554 message(WARNING "X11 include files and/or libraries were not found. Will not build the GROMACS X11-binaries, such as ngmx")
559 set(THREAD_MPI_LIB thread_mpi)
562 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
564 endif(GMX_THREAD_MPI)
565 tmpi_get_source_list(THREAD_MPI_SRC)
568 # now that we have detected the dependencies, do the second configure pass
573 find_library(ACCELERATE_FRAMEWORK Accelerate)
574 list(APPEND GMX_EXTRA_LIBRARIES ${ACCELERATE_FRAMEWORK})
581 if(WIN32 AND NOT CYGWIN)
582 set(GMX_NATIVE_WINDOWS 1)
585 # only bother with finding git and using version.h if the source is a git repo
586 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
588 # We need at least git v1.5.3 be able to parse git's date output. If not
589 # found or the version is too small, we can't generate version information.
592 # Find out the git version
593 if(GIT_FOUND AND NOT GIT_VERSION)
594 execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
595 OUTPUT_VARIABLE _exec_out
596 OUTPUT_STRIP_TRAILING_WHITESPACE)
597 string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
598 set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
599 mark_as_advanced(GIT_VERSION)
602 if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
603 message("No compatible git version found, won't be able to generate proper development version information.")
604 set(USE_VERSION_H OFF)
608 set(USE_VERSION_H OFF)
611 ########################################################################
612 # Generate development version info for cache
613 ########################################################################
614 # set(GEN_VERSION_INFO_INTERNAL "ON")
615 # include(gmxGenerateVersionString)
617 ########################################################################
618 # Our own GROMACS tests
619 ########################################################################
621 add_definitions( -DHAVE_CONFIG_H )
622 include_directories(${CMAKE_BINARY_DIR}/src)
623 include_directories(${CMAKE_BINARY_DIR}/include)
624 include_directories(${CMAKE_SOURCE_DIR}/include)
626 include(gmxTestInlineASM)
627 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
629 include(gmxSetBuildInformation)
630 gmx_set_build_information()
631 if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
632 # The timestep counter headers do not include config.h
633 add_definitions(-DHAVE_RDTSCP)
634 endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
636 include(gmxTestFloatFormat)
637 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
638 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
639 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
641 include(gmxTestLargeFiles)
642 gmx_test_large_files(GMX_LARGEFILES)
644 include(gmxTestSignal)
645 gmx_test_sigusr1(HAVE_SIGUSR1)
647 include(gmxTestInline)
648 gmx_test_inline(INLINE_KEYWORD)
650 include(gmxTestRestrict)
651 gmx_test_restrict(RESTRICT_KEYWORD)
653 include(gmxTestPipes)
654 gmx_test_pipes(HAVE_PIPES)
656 include(gmxTestIsfinite)
657 gmx_test_isfinite(HAVE_ISFINITE)
658 gmx_test__isfinite(HAVE__ISFINITE)
659 gmx_test__finite(HAVE__FINITE)
662 gmx_test_xdr(GMX_SYSTEM_XDR)
663 if(NOT GMX_SYSTEM_XDR)
664 set(GMX_INTERNAL_XDR 1)
665 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_INTERNAL_XDR")
666 endif(NOT GMX_SYSTEM_XDR)
668 # include avx test source, used if the AVX flags are set below
669 include(gmxTestAVXMaskload)
671 # Process nonbonded accelerated kernels settings
673 # Note that for the backward-compatible x86 SIMD architectures, the
674 # GMX_CPU_ACCELERATION determines the maximum level of the instruction
675 # set used (e.g. GMX_CPU_ACCLERATION=SSE4.1 implies
676 # SSE2). Accordingly, there are a set of CMake variables
677 # GMX_<arch>_<feature-set> that are exported to the C code to specify
678 # CPU features that should be used. This means that the logic for
679 # requiring such backward compatibility is all located here.
680 string(TOUPPER ${GMX_CPU_ACCELERATION} GMX_CPU_ACCELERATION)
681 if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
683 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
685 GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" ACCELERATION_C_FLAGS)
686 if(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
687 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
688 endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
690 if (CMAKE_CXX_COMPILER_LOADED)
691 GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
692 if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
693 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
694 endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
697 # We dont warn for lacking SSE2 flag support, since that is probably standard today.
699 # Only test the include after we have tried to add the correct flag for SSE2 support
700 check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${ACCELERATION_C_FLAGS})
702 if(NOT HAVE_EMMINTRIN_H)
703 message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
704 endif(NOT HAVE_EMMINTRIN_H)
706 set(GMX_CPU_ACCELERATION_X86_SSE2 1)
707 # The user should not be able to set this orthogonally to the acceleration
709 if (NOT ACCELERATION_QUIETLY)
710 message(STATUS "Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.")
713 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
715 GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" ACCELERATION_C_FLAGS)
716 if (NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
717 GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" ACCELERATION_C_FLAGS)
718 endif(NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
719 if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
720 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
721 # intrinsics when SSE2 support is enabled, so we try that instead first.
722 if (GMX_NATIVE_WINDOWS)
723 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
724 message(WARNING "Neither SSE4.1 or SSE2 seems to be supported by your Windows compiler. Something is likely broken.")
726 message(WARNING "No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance")
728 endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
730 if (CMAKE_CXX_COMPILER_LOADED)
731 GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
732 if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
733 GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
734 endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
735 if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
736 message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
737 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
738 # intrinsics when SSE2 support is enabled, so we try that instead.
739 if (GMX_NATIVE_WINDOWS)
740 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
742 endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
745 # This must come after we have added the -msse4.1 flag on some platforms.
746 check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
748 if(NOT HAVE_SMMINTRIN_H)
749 message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
750 endif(NOT HAVE_SMMINTRIN_H)
752 set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
753 # The user should not be able to set this orthogonally to the acceleration
754 set(GMX_X86_SSE4_1 1)
756 if (NOT ACCELERATION_QUIETLY)
757 message(STATUS "Enabling SSE4.1 Gromacs acceleration, and it will help compiler optimization.")
760 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_EQUAL "11.1")
761 message(FATAL_ERROR "You are using Intel compiler version 11.1, and that compiler is known to produce incorrect results with SSE4.1 acceleration. You need to use another compiler (e.g. icc 12 or newer) or different acceleration (probably slower simulations).")
763 elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
765 # Set the AVX compiler flag for both these choices!
767 GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" ACCELERATION_C_FLAGS)
768 if (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
769 GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" ACCELERATION_C_FLAGS)
770 endif (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
771 if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
772 message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
773 endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
775 if (CMAKE_CXX_COMPILER_LOADED)
776 GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
777 if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
778 GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
779 endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
780 if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
781 message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
782 endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
785 # Set the FMA4 flags (MSVC doesn't require any)
786 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
787 if (${CMAKE_COMPILER_ID} MATCHES "Clang")
788 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.")
790 GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
791 if (NOT GNU_FMA_CFLAG)
792 message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
793 endif(NOT GNU_FMA_CFLAG)
794 GMX_TEST_CFLAG(GNU_XOP_CFLAG "-mxop" ACCELERATION_C_FLAGS)
795 # No big deal if we do not have xop, so no point yelling warnings about it.
796 if (CMAKE_CXX_COMPILER_LOADED)
797 GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" ACCELERATION_CXX_FLAGS)
798 if (NOT GNU_FMA_CXXFLAG)
799 message(WARNING "No C++ FMA flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
800 endif (NOT GNU_FMA_CXXFLAG)
801 GMX_TEST_CXXFLAG(GNU_XOP_CXXFLAG "-mxop" ACCELERATION_CXX_FLAGS)
802 # No big deal if we do not have xop, so no point yelling warnings about it.
806 # Only test the header after we have tried to add the flag for AVX support
807 check_include_file(immintrin.h HAVE_IMMINTRIN_H ${ACCELERATION_C_FLAGS})
809 if(NOT HAVE_IMMINTRIN_H)
810 message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
811 endif(NOT HAVE_IMMINTRIN_H)
813 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
814 try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
815 "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
816 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
818 message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
822 # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
823 check_include_file(x86intrin.h HAVE_X86INTRIN_H ${ACCELERATION_C_FLAGS})
824 check_include_file(intrin.h HAVE_INTRIN_H ${ACCELERATION_C_FLAGS})
826 # The user should not be able to set this orthogonally to the acceleration
827 set(GMX_X86_SSE4_1 1)
830 # But just enable one of the choices internally...
831 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
832 set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
833 set(GMX_X86_AVX_128_FMA 1)
834 if (NOT ACCELERATION_QUIETLY)
835 message(STATUS "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add), and it will help compiler optimization.")
838 # If we are not doing AVX_128, it must be AVX_256...
839 set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
840 set(GMX_X86_AVX_256 1)
841 if (NOT ACCELERATION_QUIETLY)
842 message(STATUS "Enabling 256-bit AVX Gromacs acceleration, and it will help compiler optimization.")
846 # Unfortunately gcc-4.5.2 and gcc-4.6.0 has a bug where they use the wrong datatype for the formal
847 # parameter of the mask for maskload/maskstore arguments. Check if this is present, since we can work around it.
848 gmx_test_avx_gcc_maskload_bug(${ACCELERATION_C_FLAGS} GMX_X86_AVX_GCC_MASKLOAD_BUG)
850 elseif(${GMX_CPU_ACCELERATION} STREQUAL "IBM_QPX")
852 if (CMAKE_C_COMPILER_ID MATCHES "XL")
853 GMX_TEST_CFLAG(XLC_BLUEGENEQ_CFLAG "-qarch=qp -qtune=qp" ACCELERATION_C_FLAGS)
854 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
855 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c"
856 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
858 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
861 if (CMAKE_CXX_COMPILER_ID MATCHES "XL" AND CMAKE_CXX_COMPILER_LOADED)
862 GMX_TEST_CXXFLAG(XLC_BLUEGENEQ_CXXFLAG "-qarch=qp -qtune=qp" ACCELERATION_CXX_FLAGS)
863 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
865 COMPILE_DEFINITIONS "${ACCELERATION_CXX_FLAGS")
867 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
872 message(WARNING "IBM QPX acceleration was selected and could be compiled, but the accelerated kernels are not yet available.")
873 set(GMX_CPU_ACCELERATION_IBM_QPX 1)
875 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.")
877 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SPARC64_HPC_ACE")
878 set(GMX_CPU_ACCELERATION_SPARC64_HPC_ACE 1)
879 else(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
880 MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_CPU_ACCELERATION}. Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX, Sparc64_HPC_ACE")
881 endif(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
882 set(ACCELERATION_QUIETLY TRUE CACHE INTERNAL "")
884 # Process QM/MM Settings
885 string(TOUPPER ${GMX_QMMM_PROGRAM} GMX_QMMM_PROGRAM)
886 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
887 set(GMX_QMMM_GAUSSIAN 1)
888 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
889 set(GMX_QMMM_MOPAC 1)
890 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
891 set(GMX_QMMM_GAMESS 1)
892 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
894 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
896 else(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
897 MESSAGE(FATAL_ERROR "Invalid QM/MM program option: ${GMX_QMMM_PROGRAM}. Choose one of: Gaussian, Mopac, Gamess, Orca, None")
898 endif(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
900 # Process FFT library settings
901 string(TOUPPER ${GMX_FFT_LIBRARY} GMX_FFT_LIBRARY)
904 set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
905 set(MKL_LIBRARIES "" CACHE STRING "List of libraries for linking to MKL. Only used with GMX_FFT_LIBRARY=mkl. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
906 set(MKL_INCLUDE_DIR "" CACHE PATH "Path to mkl.h (non-inclusive). Only used with GMX_FFT_LIBRARY=mkl.")
907 mark_as_advanced(FORCE MKL_LIBRARIES)
908 mark_as_advanced(FORCE MKL_INCLUDE_DIR)
909 if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
916 if(GMX_BUILD_OWN_FFTW)
917 add_subdirectory(src/contrib/fftw)
919 find_package(FFTW COMPONENTS ${FFTW})
922 string(TOUPPER "${FFTW}" FFTW)
923 set(PKG_FFT "${${FFTW}_PKG}")
924 include_directories(${${FFTW}_INCLUDE_DIRS})
925 set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
926 if(NOT ${FFTW}_FOUND)
927 MESSAGE(FATAL_ERROR "Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision GROMACS or libfftw3 for double-precision GROMACS). Either choose the right precision, choose another FFT(W) library, enable the advanced option to let GROMACS build FFTW 3 for you, or use the really slow GROMACS built-in fftpack library.")
932 if ((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
933 message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
936 if((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND ${FFTW}_HAVE_AVX)
937 # If we're not doing CPU acceleration, we don't care about FFTW performance on x86 either
938 message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
941 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
942 MESSAGE(STATUS "Using external FFT library - FFTW3")
944 elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
945 # Intel 11 and up makes life somewhat easy if you just want to use
946 # all their stuff. It's not easy if you only want some of their
948 if (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11")
949 # The next line takes care of everything for MKL
951 set(FFT_LINKER_FLAGS "/Qmkl=sequential")
953 set(FFT_LINKER_FLAGS "-mkl=sequential")
955 set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
957 # The user will have to provide the set of magic libraries in
958 # MKL_LIBRARIES, which we cache (non-advanced), so that they
959 # don't have to keep specifying it, and can easily see that
960 # CMake is still using that information.
961 set(MKL_LIBRARIES "${MKL_LIBRARIES}" CACHE STRING "User-specified libraries for linking to MKL")
962 mark_as_advanced(CLEAR MKL_LIBRARIES)
963 include_directories(${MKL_INCLUDE_DIR})
964 mark_as_advanced(CLEAR MKL_INCLUDE_DIR)
965 set(FFT_LIBRARIES "${MKL_LIBRARIES}")
966 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. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
967 # Convert the semi-colon separated list to a list of
968 # command-line linker arguments so that code using our
969 # pkgconfig setup can use it.
970 string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
973 # Check MKL works. If we were in a non-global scope, we wouldn't
974 # have to play nicely.
975 set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
976 set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
977 set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
978 set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
980 check_function_exists(DftiCreateDescriptor TEST_MKL)
982 set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
983 set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
986 # Hack to help the user vary MKL settings until they work.
987 # TODO Make this logic more useful.
988 unset(TEST_MKL CACHE)
989 message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
992 # Set variables to signal that we have MKL available and should use it for FFTs.
996 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
997 MESSAGE(STATUS "Using external FFT library - Intel MKL")
1000 #elseif(${GMX_FFT_LIBRARY} STREQUAL "ACML")
1001 # MESSAGE(STATUS "Using external FFT library - AMD core math library")
1002 # set(GMX_FFT_ACML 1)
1003 elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
1004 set(GMX_FFT_FFTPACK 1)
1005 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
1006 MESSAGE(STATUS "Using internal FFT library - fftpack")
1008 else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1009 MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, mkl, fftpack")
1010 endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1011 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.")
1013 # enable threaded fftw3 if we've found it
1014 if(FFTW3_THREADS OR FFTW3F_THREADS)
1015 add_definitions(-DFFT5D_FFTW_THREADS)
1018 set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use external BLAS instead of built-in")
1019 set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use external LAPACK instead of built-in")
1020 # MKL has BLAS/LAPACK routines
1021 if(NOT HAVE_LIBMKL AND NOT ACCELERATE_FRAMEWORK)
1022 if(GMX_EXTERNAL_BLAS)
1024 list(APPEND GMX_EXTRA_LIBRARIES ${GMX_BLAS_USER})
1026 set(BLAS_FIND_QUIETLY ON)
1029 list(APPEND GMX_EXTRA_LIBRARIES ${BLAS_LIBRARIES})
1031 MESSAGE(STATUS "Using internal BLAS library")
1032 set(GMX_EXTERNAL_BLAS FALSE CACHE BOOL "Use external BLAS instead of built-in" FORCE)
1034 endif(GMX_BLAS_USER)
1035 endif(GMX_EXTERNAL_BLAS)
1036 if(GMX_EXTERNAL_LAPACK)
1037 if (GMX_LAPACK_USER)
1038 list(APPEND GMX_EXTRA_LIBRARIES ${GMX_LAPACK_USER})
1039 else(GMX_LAPACK_USER)
1040 set(LAPACK_FIND_QUIETLY ON)
1041 find_package(LAPACK)
1043 list(APPEND GMX_EXTRA_LIBRARIES ${LAPACK_LIBRARIES})
1045 MESSAGE(STATUS "Using internal LAPACK library")
1046 set(GMX_EXTERNAL_LAPACK FALSE CACHE BOOL "Use external LAPACK instead of built-in" FORCE)
1048 endif(GMX_LAPACK_USER)
1049 endif(GMX_EXTERNAL_LAPACK)
1051 mark_as_advanced(GMX_EXTERNAL_LAPACK)
1052 mark_as_advanced(GMX_EXTERNAL_BLAS)
1054 set(GMX_USE_PLUGINS OFF CACHE INTERNAL "Whether GROMACS will really try to compile support for VMD plugins")
1056 if(GMX_LOAD_PLUGINS)
1057 if(CYGWIN OR NOT WIN32)
1058 # Native Windows does not have, nor need dlopen
1059 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
1060 include(gmxTestdlopen)
1061 gmx_test_dlopen(HAVE_DLOPEN)
1064 # so, should we use plug-ins?
1065 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
1068 "Found the ability to use plug-ins when building shared libaries, "
1069 "so will compile to use plug-ins (e.g. to read VMD-supported file "
1072 if(NOT GMX_VMD_PLUGIN_PATH)
1075 set(GMX_USE_PLUGINS ON)
1076 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
1077 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
1081 endif(GMX_LOAD_PLUGINS)
1082 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
1084 if(EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
1085 if(NOT CMAKE_CROSSCOMPILING)
1086 option(GMX_BUILD_MANPAGES "Build man pages" ON)
1088 message(STATUS "Building the man pages is not available when "
1089 "cross-compiling the developer version from git")
1092 #make sure source package contains all man pages
1093 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/man/man1/ngmx.1")
1094 message(FATAL_ERROR "Man pages are missing from source package.")
1097 mark_as_advanced(GMX_BUILD_MANPAGES)
1099 # Math and thread libraries must often come after all others when linking...
1101 list(APPEND GMX_EXTRA_LIBRARIES m)
1105 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
1106 "Path to swindirect.h")
1107 include_directories(${COREWRAP_INCLUDE_DIR})
1108 set_property(CACHE GMX_COOL_QUOTES VALUE OFF)
1111 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
1112 # these are set after everything else
1113 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
1114 set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_C_FLAGS}")
1115 set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_CXX_FLAGS}")
1116 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
1117 set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
1119 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
1120 message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${GMXC_CFLAGS}")
1121 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
1122 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
1123 if(CMAKE_CXX_COMPILER_LOADED)
1124 message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMXC_CXXFLAGS}")
1125 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
1126 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
1128 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
1129 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
1133 #Unset all OpenMP flags in case OpenMP was disabled either by the user
1134 #or because it was only partially detected (e.g. only for C but not C++ compiler)
1135 unset(OpenMP_C_FLAGS CACHE)
1136 unset(OpenMP_CXX_FLAGS CACHE)
1137 unset(OpenMP_LINKER_FLAGS CACHE)
1138 unset(OpenMP_SHARED_LINKER_FLAGS)
1140 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
1142 ######################################
1143 # Output compiler and CFLAGS used
1144 ######################################
1145 get_compiler_info(C BUILD_C_COMPILER BUILD_CFLAGS)
1146 if (CMAKE_CXX_COMPILER_LOADED)
1147 get_compiler_info(CXX BUILD_CXX_COMPILER BUILD_CXXFLAGS)
1150 ########################################################################
1151 # Specify install locations and which subdirectories to process #
1152 ########################################################################
1153 if (GMX_USE_RELATIVE_INSTALL_PATH)
1154 set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
1155 mark_as_advanced(GMX_INSTALL_PREFIX)
1157 set(GMX_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/")
1160 if ( NOT DEFINED GMXLIB )
1163 set(LIB_INSTALL_DIR "${GMX_INSTALL_PREFIX}${GMXLIB}")
1164 set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
1165 set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/gromacs)
1166 set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
1167 set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
1169 set(GMXLIBDIR ${DATA_INSTALL_DIR}/top)
1171 ##################################################################
1172 # Shared library settings - Darwin uses INSTALL_NAME_DIR instead!
1173 ##################################################################
1174 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
1175 set(CMAKE_SKIP_BUILD_RPATH FALSE)
1176 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
1177 set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
1178 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
1181 #COPYING file: Only necessary for binary distributions.
1182 #Simpler to always install.
1183 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
1185 add_subdirectory(share)
1186 add_subdirectory(include)
1187 add_subdirectory(src)
1188 add_subdirectory(scripts)
1190 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
1191 # Don't bother the user after the first configure pass.
1192 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1193 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
1194 unset(CUDA_NOTFOUND_AUTO)
1195 unset(CUDA_NOTFOUND_MESSAGE)
1197 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
1199 #######################
1201 #######################
1203 "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
1204 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
1206 ###########################
1207 ADD_CUSTOM_TARGET(uninstall
1208 "${CMAKE_COMMAND}" -P
1209 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
1210 ###########################
1212 ########################################################################
1214 ########################################################################
1217 mark_as_advanced(BUILD_TESTING)
1218 #gmxtests target builds all binaries required for running gmxtest
1219 add_custom_target(gmxtests DEPENDS grompp mdrun pdb2gmx gmxcheck editconf)
1222 add_subdirectory(tests)
1223 if(REGRESSIONTEST_PATH)
1224 #check target builds all to run tests and the runs tests
1225 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
1226 add_dependencies(check gmxtests)
1228 add_custom_target(check COMMAND ${CMAKE_COMMAND} -E echo "WARNING: No tests are run. Running the tests requires either of the cmake variables REGRESSIONTEST_PATH or REGRESSIONTEST_DOWNLOAD to be set.")