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 "4.6.3-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 "4.6.2")
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 # This variable should be used for additional compiler flags which are not
284 # generated in gmxCFlags nor are acceleration or MPI related.
285 set(EXTRA_C_FLAGS "")
287 # gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
288 # Detect here whether applying a workaround is needed and will apply it later
289 # on the affected files.
290 include(gmxGCC44O3BugWorkaround)
291 gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
293 # clang 3.0 is buggy for some unknown reason detected during adding
294 # the SSE2 group kernels for GROMACS 4.6. If we ever work out what
295 # that is, we should replace these tests with a compiler feature test,
296 # update GROMACS Redmine task #1039 and perhaps report a clang bug.
298 # In the meantime, until we require CMake 2.8.10 we cannot rely on it to detect
299 # the compiler version for us. So we need a manual check for clang 3.0.
300 include(gmxDetectClang30)
301 gmx_detect_clang_3_0(COMPILER_IS_CLANG_3_0)
302 if(COMPILER_IS_CLANG_3_0)
303 message(FATAL_ERROR "Your compiler is clang version 3.0, which is known to be buggy for GROMACS. Use a different compiler.")
306 # clang <=3.2 contains a bug that causes incorrect code to be generated for the
307 # vfmaddps instruction and therefore the bug is triggered with AVX_128_FMA.
308 # (see: http://llvm.org/bugs/show_bug.cgi?id=15040).
309 # We can work around this by not using the integrated assembler (except on OS X
310 # which has an outdated assembler that does not support AVX instructions).
311 if (${CMAKE_C_COMPILER_ID} MATCHES "Clang" AND C_COMPILER_VERSION VERSION_LESS "3.3")
312 set(GMX_USE_CLANG_FMA_BUG_WORKAROUND TRUE)
315 if (CMAKE_C_COMPILER_ID STREQUAL "PGI")
316 message(WARNING "All tested PGI compiler versions (up to 12.9.0) generate binaries which produce incorrect results, or even fail to compile Gromacs. Highly recommended to use a different compiler. If you choose to use PGI, make sure to run the regressiontests.")
319 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_LESS "12.0.0")
320 message(WARNING "Intel compilers before 12.0.0 are not routinely tested, so there may be problems. Version 11.1 with SSE4.1 is known to produce incorrect results. It is highly recommended to use a more up-to-date compiler. If you choose to use this version, make sure you run the regressiontests.")
323 ########################################################################
324 # Set up binary and library suffixing
325 ########################################################################
326 set(GMX_BINARY_SUFFIX "" CACHE STRING "Suffix for GROMACS binaries (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
327 set(GMX_LIBS_SUFFIX ""
328 CACHE STRING "Suffix for GROMACS libs (default: _d for double, _mpi for MPI, _mpi_d for MPI and double).")
329 if (GMX_DEFAULT_SUFFIX)
330 set(GMX_BINARY_SUFFIX "")
331 set(GMX_LIBS_SUFFIX "")
333 set(GMX_BINARY_SUFFIX "_mpi")
334 set(GMX_LIBS_SUFFIX "_mpi")
337 set (GMX_BINARY_SUFFIX "${GMX_BINARY_SUFFIX}_d")
338 set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
340 mark_as_advanced(FORCE GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
341 if (NOT SUFFIX_QUIETLY)
342 message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
343 message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
344 endif (NOT SUFFIX_QUIETLY)
345 else(GMX_DEFAULT_SUFFIX)
346 mark_as_advanced(CLEAR GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
347 if (NOT SUFFIX_QUIETLY)
348 message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
349 message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
350 endif (NOT SUFFIX_QUIETLY)
351 endif(GMX_DEFAULT_SUFFIX)
352 set(SUFFIX_QUIETLY TRUE CACHE INTERNAL "")
356 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
358 if(GMX_SOFTWARE_INVSQRT)
359 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
360 endif(GMX_SOFTWARE_INVSQRT)
364 ########################################################################
365 # Basic system tests (standard libraries, headers, functions, types) #
366 ########################################################################
367 include(CheckIncludeFiles)
368 check_include_files(string.h HAVE_STRING_H)
369 check_include_files(math.h HAVE_MATH_H)
370 check_include_files(limits.h HAVE_LIMITS_H)
371 check_include_files(memory.h HAVE_MEMORY_H)
372 check_include_files(unistd.h HAVE_UNISTD_H)
373 check_include_files(direct.h HAVE_DIRECT_H)
374 check_include_files(pwd.h HAVE_PWD_H)
375 check_include_files(stdint.h HAVE_STDINT_H)
376 check_include_files(stdlib.h HAVE_STDLIB_H)
377 check_include_files(pthread.h HAVE_PTHREAD_H)
378 check_include_files(dirent.h HAVE_DIRENT_H)
379 check_include_files(inttypes.h HAVE_INTTYPES_H)
380 check_include_files(regex.h HAVE_REGEX_H)
381 check_include_files(sys/types.h HAVE_SYS_TYPES_H)
382 check_include_files(sys/stat.h HAVE_SYS_STAT_H)
383 check_include_files(sys/time.h HAVE_SYS_TIME_H)
384 check_include_files(rpc/rpc.h HAVE_RPC_RPC_H)
385 check_include_files("rpc/rpc.h;rpc/xdr.h" HAVE_RPC_XDR_H)
386 check_include_files(io.h HAVE_IO_H)
387 check_include_files(sched.h HAVE_SCHED_H)
389 include(CheckFunctionExists)
390 check_function_exists(strcasecmp HAVE_STRCASECMP)
391 check_function_exists(strdup HAVE_STRDUP)
392 check_function_exists(vprintf HAVE_VPRINTF)
393 check_function_exists(memcmp HAVE_MEMCMP)
394 check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
395 check_function_exists(memalign HAVE_MEMALIGN)
396 check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
397 check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
398 check_function_exists(isnan HAVE_ISNAN)
399 check_function_exists(_isnan HAVE__ISNAN)
400 check_function_exists(fsync HAVE_FSYNC)
401 check_function_exists(_fileno HAVE__FILENO)
402 check_function_exists(fileno HAVE_FILENO)
403 check_function_exists(_commit HAVE__COMMIT)
404 check_function_exists(sigaction HAVE_SIGACTION)
405 check_function_exists(sysconf HAVE_SYSCONF)
406 check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
407 check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
408 check_function_exists(rsqrt HAVE_RSQRT)
409 check_function_exists(rsqrtf HAVE_RSQRTF)
410 check_function_exists(sqrtf HAVE_SQRTF)
412 include(CheckLibraryExists)
413 check_library_exists(m sqrt "" HAVE_LIBM)
414 check_library_exists(m cbrt "" HAVE_CBRT)
417 include(CheckTypeSize)
419 check_type_size("bool" SIZEOF_BOOL) # will also set HAVE_BOOL
420 check_type_size("int" SIZEOF_INT)
421 check_type_size("long int" SIZEOF_LONG_INT)
422 check_type_size("long long int" SIZEOF_LONG_LONG_INT)
423 check_type_size("off_t" SIZEOF_OFF_T)
424 check_type_size("void *" SIZEOF_VOIDP)
426 if (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
428 else (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
429 set(GMX_64_BIT FALSE)
430 endif (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
432 # Check for some basic types that we *need*, so set these to int if they are not present
433 check_type_size(uid_t uid_t)
440 check_type_size(gid_t gid_t)
447 check_type_size(size_t size_t)
454 check_type_size(off_t off_t)
461 include(TestBigEndian)
462 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
465 if(APPLE OR CYGWIN OR ${CMAKE_SYSTEM_NAME} MATCHES "Linux|.*BSD")
466 # Maybe Solaris should be here? Patch this if you know!
467 SET(SHARED_LIBS_DEFAULT ON)
468 elseif(WIN32 OR ${CMAKE_SYSTEM_NAME} MATCHES "BlueGene")
469 # Support for shared libs on native Windows is a bit new. Its
470 # default might change later if/when we sort things out. Also,
471 # Cray should go here. What variable value can detect it?
472 SET(SHARED_LIBS_DEFAULT OFF)
474 message(STATUS "Defaulting to building static libraries")
475 SET(SHARED_LIBS_DEFAULT OFF)
478 # Management of GROMACS options for specific toolchains should go
479 # here. Because the initial settings for some of the main options have
480 # already happened, but things like library detection and MPI compiler
481 # feature detection have not, the docstrings for any over-rides of
482 # GROMACS defaults or user settings will make sense. Also, any
483 # toolchain-related reasons for choosing whether to detect various
484 # things can be sorted out now, before the detection takes place.
485 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
486 include(gmxManageBlueGene)
489 if(UNIX AND GMX_PREFER_STATIC_LIBS AND SHARED_LIBS_DEFAULT)
490 if(BUILD_SHARED_LIBS)
491 # Warn the user about the combination. But don't overwrite the request.
492 message(WARNING "Searching for static libraries requested, and building shared Gromacs libraries requested. This might cause problems linking later.")
493 elseif(NOT DEFINED BUILD_SHARED_LIBS)
494 # Change default to OFF. Don't warn if it's already off.
495 message(WARNING "Searching for static libraries requested, so the GROMACS libraries will also be built statically (BUILD_SHARED_LIBS=OFF)")
496 set(SHARED_LIBS_DEFAULT OFF)
500 # By now, all tool chains should have spoken up if they care about
501 # the setting of SHARED_LIBS_DEFAULT.
502 option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic e.g. with MPI, or on some HPC systems)" ${SHARED_LIBS_DEFAULT})
504 ########################################################################
505 #Process MPI settings
506 ########################################################################
507 include(gmxManageMPI)
509 ########################################################################
510 # Find external packages #
511 ########################################################################
512 if(UNIX AND GMX_PREFER_STATIC_LIBS)
513 # On Linux .a is the static library suffix, on Mac OS X .lib can also
514 # be used, so we'll add both to the preference list.
515 SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
518 IF( WIN32 AND NOT CYGWIN)
519 if (NOT BUILD_SHARED_LIBS)
520 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" ON)
521 if(NOT GMX_PREFER_STATIC_LIBS)
522 message(WARNING "Shared system libraries requested, and static Gromacs libraries requested.")
525 option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" OFF)
526 if(GMX_PREFER_STATIC_LIBS)
527 #this combination segfaults (illigal passing of file handles)
528 message(FATAL_ERROR "Static system libraries requested, and shared Gromacs libraries requested.")
530 add_definitions(-DUSE_VISIBILITY -DTMPI_USE_VISIBILITY)
531 set(PKG_CFLAGS "$PKG_CFLAGS -DUSE_VISIBILITY -DTMPI_USE_VISIBILITY")
533 mark_as_advanced(GMX_PREFER_STATIC_LIBS)
535 IF (GMX_PREFER_STATIC_LIBS)
536 #Only setting Debug and Release flags. Others configurations are current not used.
537 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
538 STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
539 if(CMAKE_CXX_COMPILER_LOADED)
540 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
541 STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
544 IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
545 if(BUILD_SHARED_LIBS) #not sure why incremental building with shared libs doesn't work
546 STRING(REPLACE "/INCREMENTAL:YES" "" CMAKE_SHARED_LINKER_FLAGS ${CMAKE_SHARED_LINKER_FLAGS})
551 option(GMX_GSL "Add support for gsl" OFF)
556 include_directories(${GSL_INCLUDE_DIR})
562 option(GMX_X11 "Use X window system" OFF)
565 # X11 includes/libraries are only set in the ngmx subdirectory!
567 message(WARNING "X11 include files and/or libraries were not found. Will not build the GROMACS X11-binaries, such as ngmx")
572 set(THREAD_MPI_LIB thread_mpi)
575 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
577 endif(GMX_THREAD_MPI)
578 tmpi_get_source_list(THREAD_MPI_SRC)
581 # now that we have detected the dependencies, do the second configure pass
586 find_library(ACCELERATE_FRAMEWORK Accelerate)
587 list(APPEND GMX_EXTRA_LIBRARIES ${ACCELERATE_FRAMEWORK})
594 if(WIN32 AND NOT CYGWIN)
595 set(GMX_NATIVE_WINDOWS 1)
598 # only bother with finding git and using version.h if the source is a git repo
599 if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
601 # We need at least git v1.5.3 be able to parse git's date output. If not
602 # found or the version is too small, we can't generate version information.
605 # Find out the git version
606 if(GIT_FOUND AND NOT GIT_VERSION)
607 execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
608 OUTPUT_VARIABLE _exec_out
609 OUTPUT_STRIP_TRAILING_WHITESPACE)
610 string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
611 set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
612 mark_as_advanced(GIT_VERSION)
615 if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
616 message("No compatible git version found, won't be able to generate proper development version information.")
617 set(USE_VERSION_H OFF)
621 set(USE_VERSION_H OFF)
624 ########################################################################
625 # Generate development version info for cache
626 ########################################################################
627 # set(GEN_VERSION_INFO_INTERNAL "ON")
628 # include(gmxGenerateVersionString)
630 ########################################################################
631 # Our own GROMACS tests
632 ########################################################################
634 add_definitions( -DHAVE_CONFIG_H )
635 include_directories(${CMAKE_BINARY_DIR}/src)
636 include_directories(${CMAKE_BINARY_DIR}/include)
637 include_directories(${CMAKE_SOURCE_DIR}/include)
639 include(gmxTestInlineASM)
640 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
642 include(gmxSetBuildInformation)
643 gmx_set_build_information()
644 if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
645 # The timestep counter headers do not include config.h
646 add_definitions(-DHAVE_RDTSCP)
647 endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
649 include(gmxTestFloatFormat)
650 gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
651 GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER
652 GMX_IEEE754_BIG_ENDIAN_WORD_ORDER)
654 include(gmxTestLargeFiles)
655 gmx_test_large_files(GMX_LARGEFILES)
657 include(gmxTestSignal)
658 gmx_test_sigusr1(HAVE_SIGUSR1)
660 include(gmxTestInline)
661 gmx_test_inline(INLINE_KEYWORD)
663 include(gmxTestRestrict)
664 gmx_test_restrict(RESTRICT_KEYWORD)
666 include(gmxTestPipes)
667 gmx_test_pipes(HAVE_PIPES)
669 include(gmxTestIsfinite)
670 gmx_test_isfinite(HAVE_ISFINITE)
671 gmx_test__isfinite(HAVE__ISFINITE)
672 gmx_test__finite(HAVE__FINITE)
675 gmx_test_xdr(GMX_SYSTEM_XDR)
676 if(NOT GMX_SYSTEM_XDR)
677 set(GMX_INTERNAL_XDR 1)
678 set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_INTERNAL_XDR")
679 endif(NOT GMX_SYSTEM_XDR)
681 # include avx test source, used if the AVX flags are set below
682 include(gmxTestAVXMaskload)
684 # Process nonbonded accelerated kernels settings
686 # Note that for the backward-compatible x86 SIMD architectures, the
687 # GMX_CPU_ACCELERATION determines the maximum level of the instruction
688 # set used (e.g. GMX_CPU_ACCLERATION=SSE4.1 implies
689 # SSE2). Accordingly, there are a set of CMake variables
690 # GMX_<arch>_<feature-set> that are exported to the C code to specify
691 # CPU features that should be used. This means that the logic for
692 # requiring such backward compatibility is all located here.
693 string(TOUPPER ${GMX_CPU_ACCELERATION} GMX_CPU_ACCELERATION)
694 if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
696 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
698 GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" ACCELERATION_C_FLAGS)
699 if(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
700 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
701 endif(NOT GNU_SSE2_CFLAG AND GMX_NATIVE_WINDOWS)
703 if (CMAKE_CXX_COMPILER_LOADED)
704 GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" ACCELERATION_CXX_FLAGS)
705 if(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
706 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
707 endif(NOT GNU_SSE2_CXXFLAG AND GMX_NATIVE_WINDOWS)
710 # We dont warn for lacking SSE2 flag support, since that is probably standard today.
712 # Only test the include after we have tried to add the correct flag for SSE2 support
713 check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${ACCELERATION_C_FLAGS})
715 if(NOT HAVE_EMMINTRIN_H)
716 message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
717 endif(NOT HAVE_EMMINTRIN_H)
719 set(GMX_CPU_ACCELERATION_X86_SSE2 1)
720 # The user should not be able to set this orthogonally to the acceleration
722 if (NOT ACCELERATION_QUIETLY)
723 message(STATUS "Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.")
726 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
728 GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" ACCELERATION_C_FLAGS)
729 if (NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
730 GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" ACCELERATION_C_FLAGS)
731 endif(NOT GNU_SSE4_CFLAG AND GMX_NATIVE_WINDOWS)
732 if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
733 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
734 # intrinsics when SSE2 support is enabled, so we try that instead first.
735 if (GMX_NATIVE_WINDOWS)
736 GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" ACCELERATION_C_FLAGS)
737 message(WARNING "Neither SSE4.1 or SSE2 seems to be supported by your Windows compiler. Something is likely broken.")
739 message(WARNING "No C SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance")
741 endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
743 if (CMAKE_CXX_COMPILER_LOADED)
744 GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" ACCELERATION_CXX_FLAGS)
745 if (NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
746 GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" ACCELERATION_CXX_FLAGS)
747 endif(NOT GNU_SSE4_CXXFLAG AND GMX_NATIVE_WINDOWS)
748 if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
749 message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or use SSE2 for slightly lower performance.")
750 # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
751 # intrinsics when SSE2 support is enabled, so we try that instead.
752 if (GMX_NATIVE_WINDOWS)
753 GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" ACCELERATION_CXX_FLAGS)
755 endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
758 # This must come after we have added the -msse4.1 flag on some platforms.
759 check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${ACCELERATION_C_FLAGS})
761 if(NOT HAVE_SMMINTRIN_H)
762 message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
763 endif(NOT HAVE_SMMINTRIN_H)
765 set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
766 # The user should not be able to set this orthogonally to the acceleration
767 set(GMX_X86_SSE4_1 1)
769 if (NOT ACCELERATION_QUIETLY)
770 message(STATUS "Enabling SSE4.1 Gromacs acceleration, and it will help compiler optimization.")
773 if(CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_EQUAL "11.1")
774 message(FATAL_ERROR "You are using Intel compiler version 11.1, and that compiler is known to produce incorrect results with SSE4.1 acceleration. You need to use another compiler (e.g. icc 12 or newer) or different acceleration (probably slower simulations).")
776 elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
778 # Set the AVX compiler flag for both these choices!
780 GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" ACCELERATION_C_FLAGS)
781 if (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
782 GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" ACCELERATION_C_FLAGS)
783 endif (NOT GNU_AVX_CFLAG AND GMX_NATIVE_WINDOWS)
784 if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
785 message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
786 endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
788 if (CMAKE_CXX_COMPILER_LOADED)
789 GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" ACCELERATION_CXX_FLAGS)
790 if (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
791 GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" ACCELERATION_CXX_FLAGS)
792 endif (NOT GNU_AVX_CXXFLAG AND GMX_NATIVE_WINDOWS)
793 if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
794 message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
795 endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
798 # Set the FMA4 flags (MSVC doesn't require any)
799 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
800 GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" ACCELERATION_C_FLAGS)
801 if (NOT GNU_FMA_CFLAG)
802 message(WARNING "No C FMA4 flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
803 endif(NOT GNU_FMA_CFLAG)
804 GMX_TEST_CFLAG(GNU_XOP_CFLAG "-mxop" ACCELERATION_C_FLAGS)
805 # No big deal if we do not have xop, so no point yelling warnings about it.
806 if (CMAKE_CXX_COMPILER_LOADED)
807 GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" ACCELERATION_CXX_FLAGS)
808 if (NOT GNU_FMA_CXXFLAG)
809 message(WARNING "No C++ FMA flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
810 endif (NOT GNU_FMA_CXXFLAG)
811 GMX_TEST_CXXFLAG(GNU_XOP_CXXFLAG "-mxop" ACCELERATION_CXX_FLAGS)
812 # No big deal if we do not have xop, so no point yelling warnings about it.
816 # Only test the header after we have tried to add the flag for AVX support
817 check_include_file(immintrin.h HAVE_IMMINTRIN_H ${ACCELERATION_C_FLAGS})
819 if(NOT HAVE_IMMINTRIN_H)
820 message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
821 endif(NOT HAVE_IMMINTRIN_H)
823 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
824 try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
825 "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
826 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
828 message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
832 # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
833 check_include_file(x86intrin.h HAVE_X86INTRIN_H ${ACCELERATION_C_FLAGS})
834 check_include_file(intrin.h HAVE_INTRIN_H ${ACCELERATION_C_FLAGS})
836 # The user should not be able to set this orthogonally to the acceleration
837 set(GMX_X86_SSE4_1 1)
840 # But just enable one of the choices internally...
841 if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
842 set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
843 set(GMX_X86_AVX_128_FMA 1)
844 if (NOT ACCELERATION_QUIETLY)
845 message(STATUS "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add), and it will help compiler optimization.")
848 # We don't have the full compiler version string yet (BUILD_C_COMPILER),
849 # so we can't distinguish vanilla and Apple clang, but catering for AMD
850 # hackintoshes is not worth the effort.
851 if (APPLE AND ${CMAKE_C_COMPILER_ID} STREQUAL "Clang")
852 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.")
855 if (GMX_USE_CLANG_FMA_BUG_WORKAROUND)
856 # we assume that we have an external assembler that supports AVX
857 message(STATUS "Clang ${C_COMPILER_VERSION} detected, enabling FMA bug workaround")
858 set(EXTRA_C_FLAGS "${EXTRA_C_FLAGS} -no-integrated-as")
862 # If we are not doing AVX_128, it must be AVX_256...
863 set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
864 set(GMX_X86_AVX_256 1)
865 if (NOT ACCELERATION_QUIETLY)
866 message(STATUS "Enabling 256-bit AVX Gromacs acceleration, and it will help compiler optimization.")
870 # Unfortunately gcc-4.5.2 and gcc-4.6.0 has a bug where they use the wrong datatype for the formal
871 # parameter of the mask for maskload/maskstore arguments. Check if this is present, since we can work around it.
872 gmx_test_avx_gcc_maskload_bug(${ACCELERATION_C_FLAGS} GMX_X86_AVX_GCC_MASKLOAD_BUG)
874 elseif(${GMX_CPU_ACCELERATION} STREQUAL "IBM_QPX")
876 if (CMAKE_C_COMPILER_ID MATCHES "XL")
877 GMX_TEST_CFLAG(XLC_BLUEGENEQ_CFLAG "-qarch=qp -qtune=qp" ACCELERATION_C_FLAGS)
878 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
879 "${CMAKE_SOURCE_DIR}/cmake/TestQPX.c"
880 COMPILE_DEFINITIONS "${ACCELERATION_C_FLAGS}")
882 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
885 if (CMAKE_CXX_COMPILER_ID MATCHES "XL" AND CMAKE_CXX_COMPILER_LOADED)
886 GMX_TEST_CXXFLAG(XLC_BLUEGENEQ_CXXFLAG "-qarch=qp -qtune=qp" ACCELERATION_CXX_FLAGS)
887 try_compile(TEST_QPX ${CMAKE_BINARY_DIR}
889 COMPILE_DEFINITIONS "${ACCELERATION_CXX_FLAGS")
891 message(FATAL_ERROR "Cannot compile the requested IBM QPX intrinsics.")
896 message(WARNING "IBM QPX acceleration was selected and could be compiled, but the accelerated kernels are not yet available.")
897 set(GMX_CPU_ACCELERATION_IBM_QPX 1)
899 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.")
901 elseif(${GMX_CPU_ACCELERATION} STREQUAL "SPARC64_HPC_ACE")
902 set(GMX_CPU_ACCELERATION_SPARC64_HPC_ACE 1)
903 else(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
904 MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_CPU_ACCELERATION}. Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, IBM_QPX, Sparc64_HPC_ACE")
905 endif(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
906 set(ACCELERATION_QUIETLY TRUE CACHE INTERNAL "")
908 # Process QM/MM Settings
909 string(TOUPPER ${GMX_QMMM_PROGRAM} GMX_QMMM_PROGRAM)
910 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
911 set(GMX_QMMM_GAUSSIAN 1)
912 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
913 set(GMX_QMMM_MOPAC 1)
914 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
915 set(GMX_QMMM_GAMESS 1)
916 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
918 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
920 else(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
921 MESSAGE(FATAL_ERROR "Invalid QM/MM program option: ${GMX_QMMM_PROGRAM}. Choose one of: Gaussian, Mopac, Gamess, Orca, None")
922 endif(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
924 # Process FFT library settings
925 string(TOUPPER ${GMX_FFT_LIBRARY} GMX_FFT_LIBRARY)
928 set(MKL_LIBRARIES_FORMAT_DESCRIPTION "Use full paths to library files, in the right order, and separated by semicolons.")
929 set(MKL_LIBRARIES "" CACHE STRING "List of libraries for linking to MKL. Only used with GMX_FFT_LIBRARY=mkl. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
930 set(MKL_INCLUDE_DIR "" CACHE PATH "Path to mkl.h (non-inclusive). Only used with GMX_FFT_LIBRARY=mkl.")
931 mark_as_advanced(FORCE MKL_LIBRARIES)
932 mark_as_advanced(FORCE MKL_INCLUDE_DIR)
933 if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
940 if(GMX_BUILD_OWN_FFTW)
941 add_subdirectory(src/contrib/fftw)
943 find_package(FFTW COMPONENTS ${FFTW})
946 string(TOUPPER "${FFTW}" FFTW)
947 set(PKG_FFT "${${FFTW}_PKG}")
948 include_directories(${${FFTW}_INCLUDE_DIRS})
949 set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
950 if(NOT ${FFTW}_FOUND)
951 MESSAGE(FATAL_ERROR "Cannot find FFTW 3 (with correct precision - libfftw3f for single-precision GROMACS or libfftw3 for double-precision GROMACS). Either choose the right precision, choose another FFT(W) library, enable the advanced option to let GROMACS build FFTW 3 for you, or use the really slow GROMACS built-in fftpack library.")
956 if ((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND NOT ${FFTW}_HAVE_SIMD)
957 message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
960 if((${GMX_CPU_ACCELERATION} MATCHES "SSE" OR ${GMX_CPU_ACCELERATION} MATCHES "AVX") AND ${FFTW}_HAVE_AVX)
961 # If we're not doing CPU acceleration, we don't care about FFTW performance on x86 either
962 message(WARNING "The FFTW library was compiled with --enable-avx to enable AVX SIMD instructions. That might sound like a good idea for your processor, but for FFTW versions up to 3.3.3, these are slower than the SSE/SSE2 SIMD instructions for the way GROMACS uses FFTs. Limitations in the way FFTW allows GROMACS to measure performance make it awkward for either GROMACS or FFTW to make the decision for you based on runtime performance. You should compile a different FFTW library with --enable-sse or --enable-sse2. If you have a more recent FFTW, you may like to compare the performance of GROMACS with FFTW libraries compiled with and without --enable-avx. However, the GROMACS developers do not really expect the FFTW AVX optimization to help, because the performance is limited by memory access, not computation.")
965 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
966 MESSAGE(STATUS "Using external FFT library - FFTW3")
968 elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
969 # Intel 11 and up makes life somewhat easy if you just want to use
970 # all their stuff. It's not easy if you only want some of their
972 if (CMAKE_C_COMPILER_ID MATCHES "Intel" AND C_COMPILER_VERSION VERSION_GREATER "11")
973 # The next line takes care of everything for MKL
975 set(FFT_LINKER_FLAGS "/Qmkl=sequential")
977 set(FFT_LINKER_FLAGS "-mkl=sequential")
979 set(MKL_ERROR_MESSAGE "Make sure you have configured your compiler so that ${FFT_LINKER_FLAGS} will work.")
981 # The user will have to provide the set of magic libraries in
982 # MKL_LIBRARIES, which we cache (non-advanced), so that they
983 # don't have to keep specifying it, and can easily see that
984 # CMake is still using that information.
985 set(MKL_LIBRARIES "${MKL_LIBRARIES}" CACHE STRING "User-specified libraries for linking to MKL")
986 mark_as_advanced(CLEAR MKL_LIBRARIES)
987 include_directories(${MKL_INCLUDE_DIR})
988 mark_as_advanced(CLEAR MKL_INCLUDE_DIR)
989 set(FFT_LIBRARIES "${MKL_LIBRARIES}")
990 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. ${MKL_LIBRARIES_FORMAT_DESCRIPTION}")
991 # Convert the semi-colon separated list to a list of
992 # command-line linker arguments so that code using our
993 # pkgconfig setup can use it.
994 string(REGEX REPLACE ";" " " PKG_FFT_LIBS "${MKL_LIBRARIES}")
997 # Check MKL works. If we were in a non-global scope, we wouldn't
998 # have to play nicely.
999 set(old_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
1000 set(CMAKE_REQUIRED_FLAGS "${FFT_LINKER_FLAGS}")
1001 set(old_CMAKE_REQUIRED_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}")
1002 set(CMAKE_REQUIRED_LIBRARIES "${FFT_LIBRARIES}")
1004 check_function_exists(DftiCreateDescriptor TEST_MKL)
1006 set(CMAKE_REQUIRED_FLAGS "${old_CMAKE_REQUIRED_FLAGS}")
1007 set(CMAKE_REQUIRED_LIBRARIES "${old_CMAKE_REQUIRED_LIBRARIES}")
1010 # Hack to help the user vary MKL settings until they work.
1011 # TODO Make this logic more useful.
1012 unset(TEST_MKL CACHE)
1013 message(FATAL_ERROR "Linking with MKL was requested, but was not successful. ${MKL_ERROR_MESSAGE}")
1016 # Set variables to signal that we have MKL available and should use it for FFTs.
1020 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
1021 MESSAGE(STATUS "Using external FFT library - Intel MKL")
1024 #elseif(${GMX_FFT_LIBRARY} STREQUAL "ACML")
1025 # MESSAGE(STATUS "Using external FFT library - AMD core math library")
1026 # set(GMX_FFT_ACML 1)
1027 elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
1028 set(GMX_FFT_FFTPACK 1)
1029 if(NOT "${GMX_FFT_LIBRARY}" STREQUAL "${GMX_FFT_LIBRARY_PREVIOUS_VALUE}")
1030 MESSAGE(STATUS "Using internal FFT library - fftpack")
1032 else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1033 MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, mkl, fftpack")
1034 endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
1035 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.")
1037 # enable threaded fftw3 if we've found it
1038 if(FFTW3_THREADS OR FFTW3F_THREADS)
1039 add_definitions(-DFFT5D_FFTW_THREADS)
1042 set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use external BLAS instead of built-in")
1043 set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use external LAPACK instead of built-in")
1044 # MKL has BLAS/LAPACK routines
1045 if(NOT HAVE_LIBMKL AND NOT ACCELERATE_FRAMEWORK)
1046 if(GMX_EXTERNAL_BLAS)
1048 list(APPEND GMX_EXTRA_LIBRARIES ${GMX_BLAS_USER})
1050 set(BLAS_FIND_QUIETLY ON)
1053 list(APPEND GMX_EXTRA_LIBRARIES ${BLAS_LIBRARIES})
1055 MESSAGE(STATUS "Using internal BLAS library")
1056 set(GMX_EXTERNAL_BLAS FALSE CACHE BOOL "Use external BLAS instead of built-in" FORCE)
1058 endif(GMX_BLAS_USER)
1059 endif(GMX_EXTERNAL_BLAS)
1060 if(GMX_EXTERNAL_LAPACK)
1061 if (GMX_LAPACK_USER)
1062 list(APPEND GMX_EXTRA_LIBRARIES ${GMX_LAPACK_USER})
1063 else(GMX_LAPACK_USER)
1064 set(LAPACK_FIND_QUIETLY ON)
1065 find_package(LAPACK)
1067 list(APPEND GMX_EXTRA_LIBRARIES ${LAPACK_LIBRARIES})
1069 MESSAGE(STATUS "Using internal LAPACK library")
1070 set(GMX_EXTERNAL_LAPACK FALSE CACHE BOOL "Use external LAPACK instead of built-in" FORCE)
1072 endif(GMX_LAPACK_USER)
1073 endif(GMX_EXTERNAL_LAPACK)
1075 mark_as_advanced(GMX_EXTERNAL_LAPACK)
1076 mark_as_advanced(GMX_EXTERNAL_BLAS)
1078 set(GMX_USE_PLUGINS OFF CACHE INTERNAL "Whether GROMACS will really try to compile support for VMD plugins")
1080 if(GMX_LOAD_PLUGINS)
1081 if(CYGWIN OR NOT WIN32)
1082 # Native Windows does not have, nor need dlopen
1083 # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
1084 include(gmxTestdlopen)
1085 gmx_test_dlopen(HAVE_DLOPEN)
1088 # so, should we use plug-ins?
1089 if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
1092 "Found the ability to use plug-ins when building shared libaries, "
1093 "so will compile to use plug-ins (e.g. to read VMD-supported file "
1096 if(NOT GMX_VMD_PLUGIN_PATH)
1099 set(GMX_USE_PLUGINS ON)
1100 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
1101 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
1105 endif(GMX_LOAD_PLUGINS)
1106 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
1108 if(EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
1109 if(NOT CMAKE_CROSSCOMPILING)
1110 option(GMX_BUILD_MANPAGES "Build man pages" ON)
1112 message(STATUS "Building the man pages is not available when "
1113 "cross-compiling the developer version from git")
1116 #make sure source package contains all man pages
1117 if(NOT EXISTS "${CMAKE_SOURCE_DIR}/man/man1/ngmx.1")
1118 message(FATAL_ERROR "Man pages are missing from source package.")
1121 mark_as_advanced(GMX_BUILD_MANPAGES)
1123 # Math and thread libraries must often come after all others when linking...
1125 list(APPEND GMX_EXTRA_LIBRARIES m)
1129 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
1130 "Path to swindirect.h")
1131 include_directories(${COREWRAP_INCLUDE_DIR})
1132 set_property(CACHE GMX_COOL_QUOTES VALUE OFF)
1135 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
1136 # these are set after everything else
1137 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
1138 set(CMAKE_C_FLAGS "${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
1139 set(CMAKE_CXX_FLAGS "${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${CMAKE_CXX_FLAGS}")
1140 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
1141 set(CMAKE_SHARED_LINKER_FLAGS "${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
1143 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
1144 message("CMAKE_C_FLAGS: ${ACCELERATION_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
1145 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
1146 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
1147 if(CMAKE_CXX_COMPILER_LOADED)
1148 message("CMAKE_CXX_FLAGS: ${ACCELERATION_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${GMXC_CXXFLAGS}")
1149 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
1150 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
1152 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
1153 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
1157 #Unset all OpenMP flags in case OpenMP was disabled either by the user
1158 #or because it was only partially detected (e.g. only for C but not C++ compiler)
1159 unset(OpenMP_C_FLAGS CACHE)
1160 unset(OpenMP_CXX_FLAGS CACHE)
1161 unset(OpenMP_LINKER_FLAGS CACHE)
1162 unset(OpenMP_SHARED_LINKER_FLAGS)
1164 set(PKG_CFLAGS "${PKG_CFLAGS} ${OpenMP_C_FLAGS}")
1166 ######################################
1167 # Output compiler and CFLAGS used
1168 ######################################
1169 get_compiler_info(C BUILD_C_COMPILER BUILD_CFLAGS)
1170 if (CMAKE_CXX_COMPILER_LOADED)
1171 get_compiler_info(CXX BUILD_CXX_COMPILER BUILD_CXXFLAGS)
1174 ########################################################################
1175 # Specify install locations and which subdirectories to process #
1176 ########################################################################
1177 if (GMX_USE_RELATIVE_INSTALL_PATH)
1178 set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
1179 mark_as_advanced(GMX_INSTALL_PREFIX)
1181 set(GMX_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/")
1184 if ( NOT DEFINED GMXLIB )
1187 set(LIB_INSTALL_DIR "${GMX_INSTALL_PREFIX}${GMXLIB}")
1188 set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
1189 set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/gromacs)
1190 set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
1191 set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
1193 set(GMXLIBDIR ${DATA_INSTALL_DIR}/top)
1195 ##################################################################
1196 # Shared library settings - Darwin uses INSTALL_NAME_DIR instead!
1197 ##################################################################
1198 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
1199 set(CMAKE_SKIP_BUILD_RPATH FALSE)
1200 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
1201 set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
1202 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
1205 #COPYING file: Only necessary for binary distributions.
1206 #Simpler to always install.
1207 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
1209 add_subdirectory(share)
1210 add_subdirectory(include)
1211 add_subdirectory(src)
1212 add_subdirectory(scripts)
1214 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
1215 # Don't bother the user after the first configure pass.
1216 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
1217 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
1218 unset(CUDA_NOTFOUND_AUTO)
1219 unset(CUDA_NOTFOUND_MESSAGE)
1221 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
1223 #######################
1225 #######################
1227 "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
1228 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
1230 ###########################
1231 ADD_CUSTOM_TARGET(uninstall
1232 "${CMAKE_COMMAND}" -P
1233 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
1234 ###########################
1236 ########################################################################
1238 ########################################################################
1241 mark_as_advanced(BUILD_TESTING)
1242 #gmxtests target builds all binaries required for running gmxtest
1243 add_custom_target(gmxtests DEPENDS grompp mdrun pdb2gmx gmxcheck editconf)
1246 add_subdirectory(tests)
1247 if(REGRESSIONTEST_PATH)
1248 #check target builds all to run tests and the runs tests
1249 add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure)
1250 add_dependencies(check gmxtests)
1252 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.")