2 # This file is part of the GROMACS molecular simulation package.
4 # Copyright (c) 2009,2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
5 # Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
6 # and including many others, as listed in the AUTHORS file in the
7 # top-level source 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
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22 # Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
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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 2.8.8)
36 # When we require cmake >= 2.8.12, it will provide
37 # CMAKE_MINIMUM_REQUIRED_VERSION automatically, but in the meantime we
38 # need to set a variable, and it must have a different name.
39 set(GMX_CMAKE_MINIMUM_REQUIRED_VERSION "2.8.8")
41 # CMake modules/macros are in a subdirectory to keep this file cleaner
42 # This needs to be set before project() in order to pick up toolchain files
43 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake ${CMAKE_CURRENT_SOURCE_DIR}/cmake/Platform)
47 set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
48 set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
49 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
51 # Set up common version variables, as well as general information about
52 # the build tree (whether the build is from a source package or from a git
53 # repository). Also declares a few functions that will be used for generating
54 # version info files later.
55 include(gmxVersionInfo)
57 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
58 set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
60 if("${CMAKE_INSTALL_PREFIX}" STREQUAL "${CMAKE_BINARY_DIR}")
61 message(FATAL_ERROR "GROMACS cannot be installed into the build tree, choose a different location for CMAKE_INSTALL_PREFIX")
64 include(gmxBuildTypeReference)
65 include(gmxBuildTypeProfile)
66 include(gmxBuildTypeTSAN)
67 include(gmxBuildTypeASAN)
68 include(gmxBuildTypeMSAN)
69 include(gmxBuildTypeReleaseWithAssert)
71 if(NOT CMAKE_BUILD_TYPE)
72 set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference RelWithAssert Profile." FORCE)
73 # There's no need to offer a user the choice of ThreadSanitizer
74 # Set the possible values of build type for cmake-gui
75 set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
76 "MinSizeRel" "RelWithDebInfo" "Reference" "RelWithAssert" "Profile")
78 if(CMAKE_CONFIGURATION_TYPES)
79 # Add appropriate GROMACS-specific build types for the Visual
80 # Studio generator (Debug, Release, MinSizeRel and RelWithDebInfo
81 # are already present by default).
82 list(APPEND CMAKE_CONFIGURATION_TYPES "RelWithAssert" "Reference")
83 list(REMOVE_DUPLICATES CMAKE_CONFIGURATION_TYPES)
84 set(CMAKE_CONFIGURATION_TYPES "${CMAKE_CONFIGURATION_TYPES}" CACHE STRING
85 "List of configuration types"
88 set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBINFO RELWITHASSERT MINSIZEREL PROFILE)
90 set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
92 # Set a default valgrind suppression file.
93 # This unfortunately needs to duplicate information from CTest to work as
95 set(MEMORYCHECK_SUPPRESSIONS_FILE
96 "${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp"
98 "File that contains suppressions for the memory checker")
101 include(gmxCPackUtilities)
104 # Variables that accumulate stuff influencing the installed headers
105 set(INSTALLED_HEADER_INCLUDE_DIRS "")
106 set(INSTALLED_HEADER_DEFINITIONS "")
108 ########################################################################
109 # Check and warn if cache generated on a different host is being reused
110 ########################################################################
112 execute_process(COMMAND hostname
113 OUTPUT_VARIABLE TMP_HOSTNAME
114 OUTPUT_STRIP_TRAILING_WHITESPACE)
115 if(GMX_BUILD_HOSTNAME AND NOT "${GMX_BUILD_HOSTNAME}" STREQUAL "${TMP_HOSTNAME}")
117 The CMake cache, probably generated on a different host (${GMX_BUILD_HOSTNAME}),
118 is being reused! This could lead to inconsistencies; therefore, it is
119 recommended to regenerate the cache!")
121 set(GMX_BUILD_HOSTNAME "${TMP_HOSTNAME}" CACHE INTERNAL
122 "Hostname of the machine where the cache was generated.")
125 ########################################################################
126 # Detect architecture before setting options so we can alter defaults
127 ########################################################################
128 # Detect the architecture the compiler is targetting, detect
129 # SIMD instructions possibilities on that hardware, suggest SIMD instruction set
130 # to use if none is specified, and populate the cache option for CPU
132 include(gmxDetectTargetArchitecture)
133 gmx_detect_target_architecture()
136 ########################################################################
137 # Detect CXX11 support and flags
138 ########################################################################
139 # The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
140 # are used with permission from CMake v3.0.0 so that GROMACS can detect
141 # invalid options with the Intel Compilers, and we have added a line
142 # to detect warnings with the Fujitsu compilers on K computer and ICC.
143 # CMake-3.0 also has a bug where the FAIL_REGEX pattern for AIX contains
144 # a semicolon. Since this is also used as a separator in lists inside CMake,
145 # that string ends up being split into two separate patterns, and the last
146 # part is just a single word that also matches other messages. We solved this
147 # by replacing the semicolon with a period that matches any character.
149 # These files should be removed from the source tree when a CMake version that
150 # includes the features in question becomes required for building GROMACS.
151 include(CheckCCompilerFlag)
152 include(CheckCXXCompilerFlag)
154 # This must come early, since some of our configuration flag tests
155 # depend on being able to compile C++11 source files
156 include(gmxTestCXX11)
157 gmx_test_cxx11(GMX_CXX11_SUPPORTED GMX_CXX11_FLAGS)
158 if(NOT GMX_CXX11_SUPPORTED)
159 message(FATAL_ERROR "This version of GROMACS requires C++11. Please use a newer compiler or use the GROMACS 5.1.x release. Note it might be sufficient to instruct the compiler to use a newer STL version. See the installation guide for details.")
162 # Make sure all tests are run in C++11 mode
163 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${GMX_CXX11_FLAGS}")
165 ########################################################################
166 # User input options #
167 ########################################################################
168 include(gmxOptionUtilities)
170 set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
172 # Fujitsu only has SIMD in double precision, so this will be faster
173 gmx_set_boolean(GMX_DOUBLE_DEFAULT GMX_TARGET_FUJITSU_SPARC64)
174 option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" ${GMX_DOUBLE_DEFAULT})
175 option(GMX_RELAXED_DOUBLE_PRECISION "Accept single precision 1/sqrt(x) when using Fujitsu HPC-ACE SIMD" OFF)
176 mark_as_advanced(GMX_RELAXED_DOUBLE_PRECISION)
178 option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
179 option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
180 gmx_dependent_option(
182 "Enable MPI_IN_PLACE for MPIs that have it defined"
185 mark_as_advanced(GMX_MPI_IN_PLACE)
186 option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
187 mark_as_advanced(GMX_FAHCORE)
189 option(GMX_COOL_QUOTES "Enable GROMACS cool quotes" ON)
190 mark_as_advanced(GMX_COOL_QUOTES)
191 gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
193 option(GMX_USE_OPENCL "Enable OpenCL acceleration" OFF)
195 # Decide on GPU settings based on user-settings and GPU/CUDA detection.
196 # GCC 4.6 requires CUDA 5.0 and VS2015 requires CUDA 8.0
198 set(REQUIRED_CUDA_VERSION 8.0)
200 set(REQUIRED_CUDA_VERSION 5.0)
202 set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
204 # OpenCL required version: 1.1 or newer
205 set(REQUIRED_OPENCL_MIN_VERSION 1.1)
207 if(NOT GMX_USE_OPENCL)
208 # CUDA detection is done only if GMX_USE_OPENCL is OFF.
209 include(gmxManageGPU)
210 set(GMX_USE_CUDA ${GMX_GPU})
212 set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_CUDA")
214 set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_NONE")
217 #Now the OpenCL path (for both AMD and NVIDIA)
219 include(gmxManageOpenCL)
220 set(GMX_GPU_ACCELERATION_FRAMEWORK "GMX_GPU_OPENCL")
222 message(FATAL_ERROR "OpenCL requested but GPU option is not enabled (try -DGMX_GPU=on) ")
226 include(gmxDetectSimd)
227 gmx_detect_simd(GMX_SUGGESTED_SIMD)
229 gmx_option_multichoice(
231 "SIMD instruction set for CPU kernels and compiler optimization"
232 "${GMX_SUGGESTED_SIMD}"
233 None SSE2 SSE4.1 AVX_128_FMA AVX_256 AVX2_256 AVX_512 AVX_512_KNL MIC ARM_NEON ARM_NEON_ASIMD IBM_QPX IBM_VMX IBM_VSX Sparc64_HPC_ACE Reference)
236 set(GMX_FFT_LIBRARY_DEFAULT "mkl")
238 set(GMX_FFT_LIBRARY_DEFAULT "fftw3")
241 gmx_option_multichoice(
244 "${GMX_FFT_LIBRARY_DEFAULT}"
245 fftw3 mkl "fftpack[built-in]")
246 gmx_dependent_option(
248 "Download and build FFTW 3 during the GROMACS build process, rather than fall back on the really slow fftpack."
250 "GMX_FFT_LIBRARY STREQUAL FFTW3")
251 gmx_dependent_option(
252 GMX_DISABLE_FFTW_MEASURE
253 "Do not optimize FFTW setups (not needed with SSE)"
255 "GMX_FFT_LIBRARY STREQUAL FFTW3")
256 mark_as_advanced(GMX_BUILD_OWN_FFTW)
257 mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
259 gmx_option_multichoice(
261 "QM package for QM/MM"
263 none gaussian mopac gamess orca)
265 gmx_dependent_cache_variable(GMX_SIMD_REF_FLOAT_WIDTH "Reference SIMD single precision width" STRING "4" "GMX_SIMD STREQUAL REFERENCE")
266 gmx_dependent_cache_variable(GMX_SIMD_REF_DOUBLE_WIDTH "Reference SIMD double precision width" STRING "2" "GMX_SIMD STREQUAL REFERENCE")
268 # This should be moved to a separate NBNXN cmake module when that code is cleaned up and modularized
270 option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
271 mark_as_advanced(GMX_BROKEN_CALLOC)
272 option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
273 mark_as_advanced(GMX_LOAD_PLUGINS)
275 option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
277 option(GMX_USE_TNG "Use the TNG library for trajectory I/O" ON)
279 option(GMX_BUILD_MDRUN_ONLY "Build and install only the mdrun binary" OFF)
281 option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
282 mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
284 option(GMX_SKIP_DEFAULT_CFLAGS "Don't automatically add suggested/required Compiler flags." OFF)
285 mark_as_advanced(GMX_SKIP_DEFAULT_CFLAGS)
287 option(GMX_BUILD_FOR_COVERAGE
288 "Tune build for better code coverage metrics (e.g., disable asserts)"
290 mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
292 option(GMX_DEVELOPER_BUILD
293 "Enable Developer convenience features: always build unit-tests"
295 mark_as_advanced(GMX_DEVELOPER_BUILD)
297 gmx_set_boolean(GMX_COMPILER_WARNINGS_DEFAULT "NOT SOURCE_IS_SOURCE_DISTRIBUTION")
298 option(GMX_COMPILER_WARNINGS
299 "Enable a default set of compiler warnings"
300 ${GMX_COMPILER_WARNINGS_DEFAULT})
301 mark_as_advanced(GMX_COMPILER_WARNINGS)
302 # Always turn on compiler warnings with a developer build.
303 gmx_add_cache_dependency(GMX_COMPILER_WARNINGS BOOL "NOT GMX_DEVELOPER_BUILD" ON)
305 option(GMX_BUILD_SHARED_EXE
306 "Build exectuables as shared binaries. If not set, this disables rpath and dynamic linker flags in an attempt to build a static binary, but this may require setting up the toolchain properly and making appropriate libraries available."
308 mark_as_advanced(GMX_BUILD_SHARED_EXE)
310 ######################################################################
311 # Detect OpenMP support
312 ######################################################################
313 # The OpenMP detection _must_ come before tests for other CFLAGS.
314 include(gmxManageOpenMP)
318 ######################################################################
320 # These need to be done early (before further tests).
321 #####################################################################
326 # This variable should be used for additional compiler flags which are not
327 # generated in gmxCFlags nor are SIMD or MPI related.
328 set(EXTRA_C_FLAGS "")
329 set(EXTRA_CXX_FLAGS "")
331 # Run through a number of tests for buggy compilers and other issues
332 include(gmxTestCompilerProblems)
333 gmx_test_compiler_problems()
334 # GMX_SIMD will not be set automatically until the second
335 # pass (which is not strictly guaranteed to occur), so putting this
336 # check here among logically-related tests is inefficient, but the
337 # potential loss is likely zero.
338 if(GMX_SIMD STREQUAL "AVX_256"
339 AND CMAKE_COMPILER_IS_GNUCC
340 AND (C_COMPILER_VERSION VERSION_EQUAL "4.6.1"
341 OR CXX_COMPILER_VERSION VERSION_EQUAL "4.6.1"))
342 message(FATAL_ERROR "gcc 4.6.1 has buggy support for AVX, and GROMACS mdrun will not work. If you want simulation performance, use a more recent compiler. Otherwise, use GMX_SIMD=SSE4.1")
343 # See http://gcc.gnu.org/bugzilla/show_bug.cgi?id=49002
346 # Implement double-precision option. This is complicated because we
347 # need installed headers to use the precision mode of the build that
348 # produced the library, but cannot use config.h in that case. We also
349 # want such variables to always have a definition, because #if is more
350 # robust than #ifdef. So, we put this value on the compiler command
353 # GMX_RELAXED_DOUBLE_PRECISION does not need to be handled here,
354 # because no installed header needs it
356 set(GMX_DOUBLE_VALUE 1)
358 set(GMX_DOUBLE_VALUE 0)
360 add_definitions(-DGMX_DOUBLE=${GMX_DOUBLE_VALUE})
361 list(APPEND INSTALLED_HEADER_DEFINITIONS "-DGMX_DOUBLE=${GMX_DOUBLE_VALUE}")
364 list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
365 add_definitions(-DGMX_HAVE_WINSOCK)
370 ########################################################################
371 # Basic system tests (standard libraries, headers, functions, types) #
372 ########################################################################
373 include(CheckIncludeFiles)
374 include(CheckIncludeFileCXX)
375 check_include_files(unistd.h HAVE_UNISTD_H)
376 check_include_files(pwd.h HAVE_PWD_H)
377 check_include_files(dirent.h HAVE_DIRENT_H)
378 check_include_files(time.h HAVE_TIME_H)
379 check_include_files(sys/time.h HAVE_SYS_TIME_H)
380 check_include_files(io.h HAVE_IO_H)
381 check_include_files(sched.h HAVE_SCHED_H)
383 check_include_files(regex.h HAVE_POSIX_REGEX)
384 # TODO: It could be nice to inform the user if no regex support is found,
385 # as selections won't be fully functional.
387 include(CheckCXXSymbolExists)
388 check_cxx_symbol_exists(gettimeofday sys/time.h HAVE_GETTIMEOFDAY)
389 check_cxx_symbol_exists(sysconf unistd.h HAVE_SYSCONF)
390 check_cxx_symbol_exists(nice unistd.h HAVE_NICE)
391 check_cxx_symbol_exists(fsync unistd.h HAVE_FSYNC)
392 check_cxx_symbol_exists(_fileno stdio.h HAVE__FILENO)
393 check_cxx_symbol_exists(fileno stdio.h HAVE_FILENO)
394 check_cxx_symbol_exists(_commit io.h HAVE__COMMIT)
395 check_cxx_symbol_exists(sigaction signal.h HAVE_SIGACTION)
397 # We cannot check for the __builtins as symbols, but check if code compiles
398 check_cxx_source_compiles("int main(){ return __builtin_clz(1);}" HAVE_BUILTIN_CLZ)
399 check_cxx_source_compiles("int main(){ return __builtin_clzll(1);}" HAVE_BUILTIN_CLZLL)
401 check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned long i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE)
402 check_cxx_source_compiles("#include <intrin.h>\n int main(){unsigned long r;unsigned __int64 i=1;_BitScanReverse(&r,i);return r;}" HAVE_BITSCANREVERSE64)
403 elseif(CMAKE_CXX_COMPILER_ID MATCHES "XL")
404 check_cxx_source_compiles("int main(){ return __cntlz4(1);}" HAVE_CNTLZ4)
405 check_cxx_source_compiles("int main(){ return __cntlz8(1);}" HAVE_CNTLZ8)
408 include(CheckLibraryExists)
409 find_library(HAVE_LIBM m)
410 check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
411 check_library_exists(m feenableexcept "" HAVE_FEENABLEEXCEPT)
413 include(TestSchedAffinity)
414 test_sched_affinity(HAVE_SCHED_AFFINITY)
416 # Aligned memory allocation. We need to check for both mm_malloc(),
417 # posix_memalign(), memalign(), and on windows also _aligned_malloc()
418 include(gmxTestMMMalloc)
419 gmx_test_mm_malloc(HAVE__MM_MALLOC)
420 check_cxx_symbol_exists(posix_memalign stdlib.h HAVE_POSIX_MEMALIGN)
421 check_cxx_symbol_exists(memalign stdlib.h HAVE_MEMALIGN)
423 # No need to waste time on this test on platforms where it will never be true
424 check_cxx_symbol_exists(_aligned_malloc stdlib.h HAVE__ALIGNED_MALLOC)
427 include(TestBigEndian)
428 test_big_endian(GMX_INTEGER_BIG_ENDIAN)
430 gmx_set_boolean(GMX_USE_NICE "HAVE_UNISTD_H AND HAVE_NICE")
432 # Management of GROMACS options for specific toolchains should go
433 # here. Because the initial settings for some of the main options have
434 # already happened, but things like library detection and MPI compiler
435 # feature detection have not, the docstrings for any over-rides of
436 # GROMACS defaults or user settings will make sense. Also, any
437 # toolchain-related reasons for choosing whether to detect various
438 # things can be sorted out now, before the detection takes place.
439 if(${CMAKE_SYSTEM_NAME} MATCHES BlueGene)
440 include(gmxManageBlueGene)
443 if(GMX_TARGET_FUJITSU_SPARC64)
444 include(gmxManageFujitsuSparc64)
447 ########################################################################
448 #Process MPI settings
449 ########################################################################
450 include(gmxManageMPI)
453 ########################################################################
454 #Process shared/static library settings
455 ########################################################################
456 include(gmxManageSharedLibraries)
459 ########################################################################
460 # Find external packages #
461 ########################################################################
463 # TNG wants zlib if it is available. And static libxml2 might have a dependency
464 find_package(ZLIB QUIET)
466 gmx_test_zlib(HAVE_ZLIB)
468 # Unconditionally find the package, as it is also required for unit
469 # tests. This exports LIBXML2_FOUND, which we should not use because
470 # it does not tell us that linking will succeed. Instead, we test that
472 #if(DEFINED LIBXML2_LIBRARIES)
473 # set(LibXml2_FIND_QUIETLY TRUE)
475 #find_package(LibXml2)
476 #include(gmxTestLibXml2)
477 #gmx_test_libxml2(HAVE_LIBXML2)
478 #option(GMX_XML "Use libxml2 to parse xml files (currently has no effect)" ${HAVE_LIBXML2})
480 #mark_as_advanced(GMX_XML)
481 # Don't actually do anything, since libxml2 is currently not used by libgromacs
482 #if(GMX_XML AND NOT HAVE_LIBXML2)
483 # message(FATAL_ERROR "libxml2 not found. Set GMX_XML=OFF to compile without XML support")
486 # include_directories(${LIBXML2_INCLUDE_DIR})
487 # set(PKG_XML libxml-2.0)
488 # set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
491 if(DEFINED HWLOC_LIBRARIES)
492 set(Hwloc_FIND_QUIETLY TRUE)
494 find_package(Hwloc 1.5)
496 set(GMX_HWLOC_DEFAULT ON)
498 set(GMX_HWLOC_DEFAULT OFF)
500 option(GMX_HWLOC "Add support for hwloc Portable Hardware locality library" ${GMX_HWLOC_DEFAULT})
503 include_directories(${HWLOC_INCLUDE_DIRS})
504 list(APPEND GMX_EXTRA_LIBRARIES ${HWLOC_LIBRARIES})
506 message(FATAL_ERROR "Hwloc package support requested, but not found.")
510 option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
511 mark_as_advanced(GMX_EXTRAE)
516 include_directories(SYSTEM ${EXTRAE_INCLUDE_DIR})
519 message(FATAL_ERROR "EXTRAE library was not found. Please add the correct path to CMAKE_PREFIX_PATH")
523 option(GMX_X11 "Use X window system" OFF)
526 # X11 includes/libraries are only set in the ngmx subdirectory!
529 "X11 include files and/or libraries were not found. "
530 "Set GMX_X11=OFF to compile without X11 support. "
531 "gmx view will not be available.")
533 include_directories(SYSTEM ${X11_INCLUDE_DIR})
537 # Enable core threading facilities
538 tmpi_enable_core("${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include")
539 # Enable tMPI C++ support
542 # enable MPI functions
544 set(MPI_IN_PLACE_EXISTS 1)
546 # If atomics are manually disabled a define is needed because atomics.h doesn't depend on config.h
547 if (TMPI_ATOMICS_DISABLED)
548 add_definitions(-DTMPI_ATOMICS_DISABLED)
551 # now that we have detected the dependencies, do the second GPU configure pass
559 set(GMX_NATIVE_WINDOWS 1)
560 # This makes windows.h not declare min/max as macros that would break
561 # C++ code using std::min/std::max.
562 add_definitions(-DNOMINMAX)
565 if(CMAKE_SYSTEM_NAME STREQUAL "Darwin") #Work-around for cmake bug #10837
566 if (CMAKE_COMPILER_IS_GNUCC OR CMAKE_C_COMPILER_ID MATCHES "Intel" OR CMAKE_C_COMPILER_ID MATCHES "Clang")
567 set(CMAKE_INCLUDE_SYSTEM_FLAG_C "-isystem ")
569 if (CMAKE_COMPILER_IS_GNUCXX OR CMAKE_CXX_COMPILER_ID MATCHES "Intel" OR CMAKE_CXX_COMPILER_ID MATCHES "Clang")
570 set(CMAKE_INCLUDE_SYSTEM_FLAG_CXX "-isystem ")
574 option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING" ON)
575 mark_as_advanced(GMX_BUILD_UNITTESTS)
576 gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
578 ########################################################################
579 # Our own GROMACS tests
580 ########################################################################
582 add_definitions( -DHAVE_CONFIG_H )
583 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
584 include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
585 # Required for config.h, maybe should only be set in src/CMakeLists.txt
586 include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
588 include(gmxTestInlineASM)
589 gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
591 include(gmxSetBuildInformation)
592 gmx_set_build_information()
594 # - the build system's CPU supports it
595 # - the acceleration is set to AVX as all AVX-capable CPUs support AVX (which
596 # at this point means that the user set it).
597 # Note: it's better to not use the later set value of GMX_SIMD because
598 # it reflects the system's capability of both compiling and running AVX code.
599 # TODO: After merge with 5.0 one could implement a cache variable dependency
600 # such that GMX_USE_RDTSCP can change if GMX_SIMD is changed to AVX
601 # after the first cmake pass.
602 if (BUILD_CPU_FEATURES MATCHES "rdtscp" OR GMX_SIMD MATCHES "AVX")
603 set(GMX_USE_RDTSCP_DEFAULT_VALUE ON)
605 set(GMX_USE_RDTSCP_DEFAULT_VALUE OFF)
607 option(GMX_USE_RDTSCP "Use RDTSCP for better CPU-based timers (available on recent x86 CPUs; might need to be off when compiling for heterogeneous environments)" ${GMX_USE_RDTSCP_DEFAULT_VALUE})
608 mark_as_advanced(GMX_USE_RDTSCP)
613 include(gmxTestLargeFiles)
614 gmx_test_large_files(GMX_LARGEFILES)
616 include(gmxTestSignal)
617 gmx_test_sigusr1(HAVE_SIGUSR1)
619 include(gmxTestPipes)
620 gmx_test_pipes(HAVE_PIPES)
622 check_include_file_cxx(regex HAVE_CXX11_REGEX)
625 gmx_test_xdr(GMX_SYSTEM_XDR)
626 if(NOT GMX_SYSTEM_XDR)
627 set(GMX_INTERNAL_XDR 1)
631 ##################################################
632 # Process SIMD instruction settings
633 ##################################################
634 # This checks what flags to add in order to
635 # support the SIMD instructions we need, it sets
636 # correct defines for the SIMD instructions supported,
637 # and adds advanced options to control accuracy
638 # for SIMD math operations.
639 include(gmxManageSimd)
642 # Process QM/MM Settings
643 if(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
644 set(GMX_QMMM_GAUSSIAN 1)
645 elseif(${GMX_QMMM_PROGRAM} STREQUAL "MOPAC")
646 set(GMX_QMMM_MOPAC 1)
647 elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
648 set(GMX_QMMM_GAMESS 1)
649 elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
651 elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
654 gmx_invalid_option_value(GMX_QMMM_PROGRAM)
658 ##################################################
659 # Process FFT library settings
660 ##################################################
661 include(gmxManageFFTLibraries)
664 include(gmxManageLinearAlgebraLibraries)
666 # Whether GROMACS will really try to compile support for VMD plugins
667 set(GMX_USE_PLUGINS OFF)
671 # Native Windows does not have, nor need dlopen
672 include(gmxTestdlopen)
673 gmx_test_dlopen(HAVE_DLOPEN)
676 # so, should we use plug-ins?
677 if(WIN32 OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
679 MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
681 if(NOT GMX_VMD_PLUGIN_PATH)
684 set(GMX_USE_PLUGINS ON)
685 list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
686 set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
691 set(VMD_QUIETLY TRUE CACHE INTERNAL "")
693 # Link real-time library for POSIX timers. The check for clock_gettime
694 # confirms the linkability of rt.
695 if(HAVE_TIME_H AND HAVE_UNISTD_H AND HAVE_CLOCK_GETTIME)
696 list(APPEND GMX_EXTRA_LIBRARIES rt)
699 # Math and thread libraries must often come after all others when linking...
701 list(APPEND GMX_EXTRA_LIBRARIES m)
704 option(GMX_NACL "Configure for Native Client builds" OFF)
706 list(APPEND GMX_EXTRA_LIBRARIES nosys)
707 set(GMX_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lnosys")
708 # TODO: Is this still necessary with the check for its presence?
712 mark_as_advanced(GMX_NACL)
715 set(COREWRAP_INCLUDE_DIR "${CMAKE_SOURCE_DIR}/../corewrap" CACHE STRING
716 "Path to swindirect.h")
717 include_directories(${COREWRAP_INCLUDE_DIR})
720 # Value of GMX_BUILD_HELP=AUTO tries to generate things, but will only
721 # produce warnings if that fails.
722 set(build_help_default AUTO)
723 if (SOURCE_IS_SOURCE_DISTRIBUTION OR CMAKE_CROSSCOMPILING)
724 set(build_help_default OFF)
726 gmx_option_trivalue(GMX_BUILD_HELP "Build completions automatically (requires that compiled binaries can be executed on the build host) and install man pages if built (requires building the 'man' target manually)" ${build_help_default})
727 mark_as_advanced(GMX_BUILD_HELP)
728 if (GMX_BUILD_HELP AND SOURCE_IS_SOURCE_DISTRIBUTION AND BUILD_IS_INSOURCE)
730 "Rebuilding shell completions or man pages is not supported for "
731 "in-source builds from a source distribution. "
732 "Set GMX_BUILD_HELP=OFF or do an out-of-source build to proceed.")
735 # # # # # # # # # # NO MORE TESTS AFTER THIS LINE! # # # # # # # # # # #
736 # these are set after everything else
737 if (NOT GMX_SKIP_DEFAULT_CFLAGS)
738 set(CMAKE_C_FLAGS "${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${CMAKE_C_FLAGS}")
739 set(CMAKE_CXX_FLAGS "${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${CMAKE_CXX_FLAGS}")
740 set(CMAKE_EXE_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}")
741 set(CMAKE_SHARED_LINKER_FLAGS "${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}")
743 message("Recommended flags which are not added because GMX_SKIP_DEFAULT_CFLAGS=yes:")
744 message("CMAKE_C_FLAGS: ${SIMD_C_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_C_FLAGS} ${GMXC_CFLAGS}")
745 message("CMAKE_C_FLAGS_RELEASE: ${GMXC_CFLAGS_RELEASE}")
746 message("CMAKE_C_FLAGS_DEBUG: ${GMXC_CFLAGS_DEBUG}")
747 message("CMAKE_CXX_FLAGS: ${SIMD_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${EXTRA_CXX_FLAGS} ${GMXC_CXXFLAGS}")
748 message("CMAKE_CXX_FLAGS_RELEASE: ${GMXC_CXXFLAGS_RELEASE}")
749 message("CMAKE_CXX_FLAGS_DEBUG: ${GMXC_CXXFLAGS_DEBUG}")
750 message("CMAKE_EXE_LINKER_FLAGS: ${FFT_LINKER_FLAGS} ${MPI_LINKER_FLAGS}")
751 message("CMAKE_SHARED_LINKER_FLAGS: ${MPI_LINKER_FLAGS}")
755 #Unset all OpenMP flags in case OpenMP was disabled either by the user
756 #or because it was only partially detected (e.g. only for C but not C++ compiler)
757 unset(OpenMP_C_FLAGS CACHE)
758 unset(OpenMP_CXX_FLAGS CACHE)
760 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} ${OpenMP_LINKER_FLAGS})
761 set(GMX_SHARED_LINKER_FLAGS ${GMX_SHARED_LINKER_FLAGS} ${OpenMP_SHARED_LINKER_FLAGS})
764 ########################################################################
765 # Specify install locations
766 ########################################################################
767 # Use GNUInstallDirs to set paths on multiarch systems.
768 include(GNUInstallDirs)
770 # Customization for the installation tree paths.
771 set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
772 "Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
773 set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
774 "Data installation directory under share/ (default: gromacs)")
775 mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
777 # These variables are used internally to provide a central location for
778 # customizing the install locations.
779 set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
780 set(BIN_INSTALL_DIR bin)
781 # This variable also gets written into config.h for use in finding the data
783 set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
784 set(MAN_INSTALL_DIR share/man)
785 # If the nesting level wrt. the installation root is changed,
786 # gromacs-config.cmake.cmakein needs to be adapted.
787 set(CMAKE_INSTALL_DIR share/cmake)
788 # TODO: Make GMXRC adapt if this is changed
789 set(PKGCONFIG_INSTALL_DIR ${LIB_INSTALL_DIR}/pkgconfig)
790 set(OCL_INSTALL_DIR ${DATA_INSTALL_DIR}/opencl)
791 set(INCL_INSTALL_DIR include)
793 list(APPEND INSTALLED_HEADER_INCLUDE_DIRS ${INCL_INSTALL_DIR})
795 # Binary and library suffix options
796 include(gmxManageSuffixes)
798 ################################################################
799 # Shared library load path settings
800 ################################################################
801 # CMake supports RPATH on OS X only from 2.8.12 upwards.
802 # CMAKE_SYSTEM_VERSION > 8.0 matches OS X 10.5 and above, where RPATH support
805 if(NOT GMX_BUILD_SHARED_EXE)
807 set(CMAKE_SKIP_RPATH TRUE)
808 set(CMAKE_EXE_LINK_DYNAMIC_C_FLAGS) # remove -Wl,-Bdynamic
809 set(CMAKE_EXE_LINK_DYNAMIC_CXX_FLAGS)
810 elseif((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR
811 ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (NOT CMAKE_VERSION VERSION_LESS 2.8.12)))
812 # The build folder always has bin/ and lib/; if we are also going to
813 # install to lib/, then the installation RPATH works also in the build
814 # tree. This makes installation slightly faster (no need to rewrite the
815 # RPATHs), and makes the binaries in the build tree relocatable.
816 if(GMX_LIB_INSTALL_DIR STREQUAL "lib")
817 set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
819 # Set the RPATH as relative to the executable location to make the
820 # binaries relocatable.
821 if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
822 set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
824 set(CMAKE_INSTALL_RPATH "@executable_path/../${GMX_LIB_INSTALL_DIR}")
826 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
827 set(CMAKE_MACOSX_RPATH 1)
829 # We are on Darwin/OSX, and CMake cannot handle RPATHs automatically.
830 if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0)
831 # Set the RPATH options manually.
832 set(CMAKE_INSTALL_NAME_DIR "@rpath")
833 set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../${GMX_LIB_INSTALL_DIR}")
835 # Use the old INSTALL_NAME_DIR mechanism if RPATH is not supported.
836 set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
840 #COPYING file: Only necessary for binary distributions.
841 #Simpler to always install.
842 install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
844 if (GMX_BUILD_FOR_COVERAGE)
845 # Code heavy with asserts makes conditional coverage close to useless metric,
846 # as by design most of the false branches are impossible to trigger in
847 # correctly functioning code. And the benefit of testing those that could
848 # be triggered by using an API against its specification isn't usually
850 add_definitions(-DNDEBUG -DGMX_DISABLE_ASSERTS)
854 # "tests" target builds all the separate test binaries.
855 add_custom_target(tests)
856 # "run-ctest" is an internal target that actually runs the tests.
857 # This is necessary to be able to add separate targets that execute as part
858 # of 'make check', but are ensured to be executed after the actual tests.
859 add_custom_target(run-ctest
860 COMMAND ${CMAKE_CTEST_COMMAND} --output-on-failure
861 COMMENT "Running all tests"
863 add_dependencies(run-ctest tests)
864 # "check" target builds and runs all tests.
865 add_custom_target(check DEPENDS run-ctest)
868 if (NOT GMX_BUILD_MDRUN_ONLY)
869 add_subdirectory(docs)
870 add_subdirectory(share)
871 add_subdirectory(scripts)
873 add_subdirectory(src)
876 add_subdirectory(tests)
879 gmx_cpack_write_config()
881 # Issue a warning if NVIDIA GPUs were detected, but CUDA was not found.
882 # Don't bother the user after the first configure pass.
883 if ((CUDA_NOTFOUND_AUTO AND GMX_DETECT_GPU_AVAILABLE) AND NOT GMX_GPU_DETECTION_DONE)
884 message(WARNING "${CUDA_NOTFOUND_MESSAGE}")
886 set(GMX_GPU_DETECTION_DONE TRUE CACHE INTERNAL "Whether GPU detection has already been done")
888 #######################
890 #######################
891 CONFIGURE_FILE( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
892 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake"
894 ###########################
895 ADD_CUSTOM_TARGET(uninstall
896 "${CMAKE_COMMAND}" -P
897 "${CMAKE_CURRENT_BINARY_DIR}/cmake/cmake_uninstall.cmake")
898 ###########################
899 set_directory_properties(PROPERTIES
900 ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")