# Keep CMake suitably quiet on Cygwin
set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
-# Allows CPack to act differently for normal tools and mdrun (e.g. because of MPI)
-set(CPACK_COMPONENT_GROUP_TOOLS_DESCRIPTION "All GROMACS executable tools")
-set(CPACK_COMPONENT_GROUP_MDRUN_DESCRIPTION "GROMACS executable for running simulations")
-
# override bugs on OS X where Cmake picks gcc (GNU) for C instead of system default cc (Clang).
if(APPLE)
set(CMAKE_C_COMPILER_INIT "cc")
endif(APPLE)
-project(Gromacs C)
+project(Gromacs)
include(Dart)
mark_as_advanced(DART_ROOT)
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
# PROJECT_VERSION should have the following structure:
# VERSION-dev[-SUFFIX] where the VERSION should have the for: vMajor.vMinor.vPatch
#
# machine with no git.
#
# NOTE: when releasing the "-dev" suffix needs to be stripped off!
-set(PROJECT_VERSION "4.6-dev")
+set(PROJECT_VERSION "5.0-dev")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
mark_as_advanced(CUSTOM_VERSION_STRING)
endif (CUSTOM_VERSION_STRING)
set(SOVERSION 6)
# It is a bit irritating, but this has to be set separately for now!
-SET(CPACK_PACKAGE_VERSION_MAJOR "4")
-SET(CPACK_PACKAGE_VERSION_MINOR "6")
+SET(CPACK_PACKAGE_VERSION_MAJOR "5")
+SET(CPACK_PACKAGE_VERSION_MINOR "0")
#SET(CPACK_PACKAGE_VERSION_PATCH "0")
# The numerical gromacs version. It is 40600 for 4.6.0.
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT AND UNIX)
-set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
+ set(CMAKE_INSTALL_PREFIX "/usr/local/gromacs" CACHE STRING "Installation prefix (installation will need write permissions here)" FORCE)
endif()
+set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
+mark_as_advanced(GMX_INSTALL_PREFIX)
+
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE)
endif(NOT CMAKE_BUILD_TYPE)
enable_language(C)
-
-set(GMX_USE_RELATIVE_INSTALL_PATH OFF CACHE STRING "Use relative paths not absolute paths for cmake install. Has only an effect on cpack.")
-mark_as_advanced(GMX_USE_RELATIVE_INSTALL_PATH)
+enable_language(CXX)
set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
set(CPACK_PACKAGE_VENDOR "gromacs.org")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
-if (NOT GMX_USE_RELATIVE_INSTALL_PATH)
- set(CPACK_SET_DESTDIR "ON")
-endif()
set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
# Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
#must come after all cpack settings!
include(CPack)
+set(SOURCE_IS_GIT_REPOSITORY OFF)
+if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
+ set(SOURCE_IS_GIT_REPOSITORY ON)
+endif()
+
########################################################################
# Check and warn if cache generated on a different host is being reused
########################################################################
"Hostname of the machine where the cache was generated.")
endif()
-########################################################################
-# User input options - enable C++ - before any CXX flags are changed #
-########################################################################
-option(GMX_GPU "Enable GPU acceleration" ON)
-option(GMX_OPENMM "Accelerated execution on GPUs through the OpenMM library (rerun cmake after changing to see relevant options)" OFF)
-option(GMX_FORCE_CXX "Enable C++ compilation even if not necessary" OFF)
-mark_as_advanced(GMX_FORCE_CXX)
-if(GMX_GPU OR GMX_OPENMM OR GMX_FORCE_CXX)
- enable_language(CXX)
-endif()
-
########################################################################
# Fix stupid flags on Windows
########################################################################
option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer static system libraries (MT instead of MD)!" ON)
mark_as_advanced(GMX_PREFER_STATIC_LIBS)
SET(SHARED_LIBS_DEFAULT OFF) #is currently not working on Windows
+ # This makes windows.h not declare min/max as macros that would break
+ # C++ code using std::min/std::max.
+ add_definitions(-DNOMINMAX)
IF (GMX_PREFER_STATIC_LIBS)
#Only setting Debug and Release flags. Others configurations current not used.
SET(CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} CACHE STRING "" FORCE)
STRING(REPLACE /MD /MT CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
SET(CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} CACHE STRING "" FORCE)
- if(CMAKE_CXX_COMPILER_LOADED)
- STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
- SET(CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE} CACHE STRING "" FORCE)
- STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
- SET(CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG} CACHE STRING "" FORCE)
- endif()
+ STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
+ SET(CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE} CACHE STRING "" FORCE)
+ STRING(REPLACE /MD /MT CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
+ SET(CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG} CACHE STRING "" FORCE)
ENDIF()
#Workaround for cmake bug 13174. Replace deprecated options.
STRING(REPLACE /GZ /RTC1 CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
SET(CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} CACHE STRING "" FORCE)
ENDIF()
- IF( CMAKE_CXX_COMPILER_ID MATCHES "Intel" AND CMAKE_CXX_COMPILER_LOADED)
+ IF( CMAKE_CXX_COMPILER_ID MATCHES "Intel" )
STRING(REPLACE /GZ /RTC1 CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
STRING(REPLACE /GX /EHsc CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG})
SET(CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG} CACHE STRING "" FORCE)
mark_as_advanced(GMX_POWERPC_INVSQRT)
option(GMX_FAHCORE "Build a library with mdrun functionality" OFF)
mark_as_advanced(GMX_FAHCORE)
+option(GMX_OPENMM "Accelerated execution on GPUs through the OpenMM library (rerun cmake after changing to see relevant options)" OFF)
include(gmxDetectAcceleration)
if(NOT DEFINED GMX_ACCELERATION)
option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
mark_as_advanced(GMX_LOAD_PLUGINS)
+option(GMX_GPU "Enable GPU acceleration" ON)
option(GMX_OPENMP "Enable OpenMP-based multithreading" ON)
-option(USE_VERSION_H "Generate development version string/information" ON)
-mark_as_advanced(USE_VERSION_H)
+option(GMX_GIT_VERSION_INFO "Generate git version information" ${SOURCE_IS_GIT_REPOSITORY})
+mark_as_advanced(GMX_GIT_VERSION_INFO)
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)
+if(UNIX)
+ option(GMX_SYMLINK_OLD_BINARY_NAMES "Create symbolic links for pre-5.0 binary names" ON)
+endif()
if(UNIX)
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)
# Remove these files from the source tree when a CMake version that
# includes the features in question becomes required.
include(CheckCCompilerFlag)
-if(CMAKE_CXX_COMPILER_LOADED)
- include(CheckCXXCompilerFlag)
-endif()
+include(CheckCXXCompilerFlag)
# OpenMP check must come before other CFLAGS!
if(GMX_OPENMP)
# Basic system tests (standard libraries, headers, functions, types) #
########################################################################
include(CheckIncludeFiles)
-check_include_files(string.h HAVE_STRING_H)
-check_include_files(math.h HAVE_MATH_H)
-check_include_files(limits.h HAVE_LIMITS_H)
-check_include_files(memory.h HAVE_MEMORY_H)
+include(CheckIncludeFileCXX)
check_include_files(unistd.h HAVE_UNISTD_H)
-check_include_files(direct.h HAVE_DIRECT_H)
check_include_files(pwd.h HAVE_PWD_H)
-check_include_files(stdint.h HAVE_STDINT_H)
-check_include_files(stdlib.h HAVE_STDLIB_H)
check_include_files(pthread.h HAVE_PTHREAD_H)
check_include_files(dirent.h HAVE_DIRENT_H)
-check_include_files(inttypes.h HAVE_INTTYPES_H)
-check_include_files(regex.h HAVE_REGEX_H)
-check_include_files(sys/types.h HAVE_SYS_TYPES_H)
-check_include_files(sys/stat.h HAVE_SYS_STAT_H)
check_include_files(sys/time.h HAVE_SYS_TIME_H)
-check_include_files(rpc/rpc.h HAVE_RPC_RPC_H)
-check_include_files("rpc/rpc.h;rpc/xdr.h" HAVE_RPC_XDR_H)
check_include_files(io.h HAVE_IO_H)
check_include_files(sched.h HAVE_SCHED_H)
+check_include_files(regex.h HAVE_POSIX_REGEX)
+check_include_file_cxx(regex HAVE_CXX11_REGEX)
+# TODO: It could be nice to inform the user if no regex support is found,
+# as selections won't be fully functional.
+
include(CheckFunctionExists)
-check_function_exists(strcasecmp HAVE_STRCASECMP)
check_function_exists(strdup HAVE_STRDUP)
-check_function_exists(vprintf HAVE_VPRINTF)
-check_function_exists(memcmp HAVE_MEMCMP)
check_function_exists(posix_memalign HAVE_POSIX_MEMALIGN)
check_function_exists(memalign HAVE_MEMALIGN)
check_function_exists(_aligned_malloc HAVE__ALIGNED_MALLOC)
check_function_exists(gettimeofday HAVE_GETTIMEOFDAY)
-check_function_exists(isnan HAVE_ISNAN)
-check_function_exists(_isnan HAVE__ISNAN)
check_function_exists(fsync HAVE_FSYNC)
check_function_exists(_fileno HAVE__FILENO)
check_function_exists(fileno HAVE_FILENO)
include(CheckTypeSize)
-check_type_size("bool" SIZEOF_BOOL) # will also set HAVE_BOOL
check_type_size("int" SIZEOF_INT)
check_type_size("long int" SIZEOF_LONG_INT)
check_type_size("long long int" SIZEOF_LONG_LONG_INT)
set(GMX_64_BIT FALSE)
endif (CMAKE_C_SIZEOF_DATA_PTR EQUAL 8)
-# Check for some basic types that we *need*, so set these to int if they are not present
-check_type_size(uid_t uid_t)
-if(NOT uid_t)
- set(uid_t int)
-else(NOT uid_t)
- set(uid_t 0)
-endif(NOT uid_t)
-
-check_type_size(gid_t gid_t)
-if(NOT gid_t)
- set(gid_t 1)
-else(NOT gid_t)
- set(gid_t 0)
-endif(NOT gid_t)
-
-check_type_size(size_t size_t)
-if(NOT size_t)
- set(size_t int)
-else(NOT size_t)
- set(size_t 0)
-endif(NOT size_t)
-
-check_type_size(off_t off_t)
-if(NOT off_t)
- set(off_t int)
-else(NOT off_t)
- set(off_t 0)
-endif(NOT off_t)
-
include(TestBigEndian)
test_big_endian(GMX_INTEGER_BIG_ENDIAN)
include_directories(${LIBXML2_INCLUDE_DIR})
set(PKG_XML libxml-2.0)
set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
- set(HAVE_LIBXML2 1)
endif(LIBXML2_FOUND)
endif(GMX_XML)
include(ThreadMPI)
set(THREAD_MPI_LIB thread_mpi)
if(GMX_THREAD_MPI)
- tmpi_get_source_list(THREAD_MPI_SRC)
+ tmpi_get_source_list(THREAD_MPI_SRC CXX)
set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
set(GMX_MPI 1)
else(GMX_THREAD_MPI)
- tmpi_get_source_list(THREAD_MPI_SRC NOMPI)
+ tmpi_get_source_list(THREAD_MPI_SRC CXX NOMPI)
endif(GMX_THREAD_MPI)
if(GMX_OPENMM)
endif()
# only bother with finding git and using version.h if the source is a git repo
-if(EXISTS "${CMAKE_SOURCE_DIR}/.git")
- if(USE_VERSION_H)
- # We need at least git v1.5.3 be able to parse git's date output. If not
- # found or the version is too small, we can't generate version information.
- find_package(Git)
-
- # Find out the git version
- if(GIT_FOUND AND NOT GIT_VERSION)
- execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
- OUTPUT_VARIABLE _exec_out
- OUTPUT_STRIP_TRAILING_WHITESPACE)
- string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
- set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
- mark_as_advanced(GIT_VERSION)
- endif()
-
- if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
- message("No compatible git version found, won't be able to generate proper development version information.")
- set(USE_VERSION_H OFF)
- endif()
+if(GMX_GIT_VERSION_INFO)
+ if (NOT SOURCE_IS_GIT_REPOSITORY)
+ message(FATAL_ERROR
+ "Cannot generate git version information from source tree not under git. "
+ "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
+ endif ()
+ # We need at least git v1.5.3 be able to parse git's date output. If not
+ # found or the version is too small, we can't generate version information.
+ find_package(Git)
+
+ # Find out the git version
+ if(GIT_FOUND AND NOT GIT_VERSION)
+ execute_process(COMMAND ${GIT_EXECUTABLE} "--version"
+ OUTPUT_VARIABLE _exec_out
+ OUTPUT_STRIP_TRAILING_WHITESPACE)
+ string(REGEX REPLACE "git version (.*)" "\\1" GIT_VERSION ${_exec_out})
+ set(GIT_VERSION ${GIT_VERSION} CACHE STRING "Git version")
+ mark_as_advanced(GIT_VERSION)
endif()
+
+ if(NOT GIT_FOUND OR GIT_VERSION VERSION_LESS "1.5.3")
+ message(FATAL_ERROR
+ "No compatible git version found (>= 1.5.3 required). "
+ "Won't be able to generate development version information. "
+ "Set GMX_GIT_VERSION_INFO=OFF to proceed.")
+ endif()
+endif()
+
+option(GMX_INTERNAL_BOOST "Use minimal internal version of boost" OFF)
+if ( NOT GMX_INTERNAL_BOOST )
+ find_package( Boost 1.44.0 )
+else ( NOT GMX_INTERNAL_BOOST )
+ set (Boost_FOUND FALSE)
+endif( NOT GMX_INTERNAL_BOOST )
+
+if(Boost_FOUND AND NOT Boost_VERSION VERSION_LESS "104400" )
+ include_directories(${Boost_INCLUDE_DIRS})
else()
- set(USE_VERSION_H OFF)
+ if(NOT BOOST_QUIETLY)
+ message("Boost >= 1.44 not found. Using minimal internal version. Not recommended if GROMACS is used as library!")
+ endif()
+ include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
+ add_definitions( -DBOOST_NO_TYPEID ) #TYPEID not supported for minimal internal version (would add significant more code)
+ # TODO: Propagate the above settings to the installed CMakeFiles.txt template
+ # (from share/template/)
+ # TODO: Reorder stuff such that INCL_INSTALL_DIR could be used here
+ set(PKG_CFLAGS "${PKG_CFLAGS} -DBOOST_NO_TYPEID -I${GMX_INSTALL_PREFIX}include/gromacs/external/boost")
+ install(DIRECTORY ${CMAKE_SOURCE_DIR}/src/external/boost/boost
+ DESTINATION ${GMX_INSTALL_PREFIX}include/gromacs/external/boost
+ COMPONENT development)
endif()
+set(BOOST_QUIETLY TRUE CACHE INTERNAL "")
+
+if (LIBXML2_FOUND)
+ option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ON)
+else (LIBXML2_FOUND)
+ set(GMX_BUILD_UNITTESTS OFF)
+endif (LIBXML2_FOUND)
+mark_as_advanced(GMX_BUILD_UNITTESTS)
+set(MEMORYCHECK_SUPPRESSIONS_FILE ${CMAKE_SOURCE_DIR}/cmake/legacy_and_external.supp)
########################################################################
# Generate development version info for cache
########################################################################
add_definitions( -DHAVE_CONFIG_H )
+include_directories(${CMAKE_SOURCE_DIR}/src)
+# Required for config.h, maybe should only be set in src/CMakeLists.txt
include_directories(${CMAKE_BINARY_DIR}/src)
-include_directories(${CMAKE_BINARY_DIR}/include)
-include_directories(${CMAKE_SOURCE_DIR}/include)
+# Required for gmx_header_config_gen.h to be found before installation
+include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
+# Required for now to make old code compile
+include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
include(gmxSetBuildInformation)
gmx_set_build_information()
- if(BUILD_CPU_FEATURES MATCHES "rdtscp")
+ if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
# The timestep counter headers do not include config.h
add_definitions(-DHAVE_RDTSCP)
- endif(BUILD_CPU_FEATURES MATCHES "rdtscp")
+ endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
include(gmxTestFloatFormat)
gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
gmx_test__isfinite(HAVE__ISFINITE)
gmx_test__finite(HAVE__FINITE)
+include(gmxTestCXX11)
+gmx_test_cxx11(GMX_CXX11 CXX11_FLAG)
+set(GROMACS_CXX_FLAGS "${CXX11_FLAG} ${GROMACS_CXX_FLAGS}")
+if(CXX11_FLAG)
+ #FIXME: add proper solution for progate all but cxx11 flag
+ set(CUDA_PROPAGATE_HOST_FLAGS no)
+ message(WARNING "Please manually add compiler flags to CUDA_NVCC_FLAGS. Automatic propogation temporary not working.")
+endif()
+
include(gmxTestXDR)
gmx_test_xdr(GMX_SYSTEM_XDR)
if(NOT GMX_SYSTEM_XDR)
GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" GROMACS_C_FLAGS)
endif(NOT GNU_SSE2_CFLAG)
- if (CMAKE_CXX_COMPILER_LOADED)
- GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" GROMACS_CXX_FLAGS)
- if(NOT GNU_SSE2_CXXFLAG)
- GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" GROMACS_CXX_FLAGS)
- endif(NOT GNU_SSE2_CXXFLAG)
- endif()
+ GMX_TEST_CXXFLAG(GNU_SSE2_CXXFLAG "-msse2" GROMACS_CXX_FLAGS)
+ if(NOT GNU_SSE2_CXXFLAG)
+ GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" GROMACS_CXX_FLAGS)
+ endif(NOT GNU_SSE2_CXXFLAG)
# We dont warn for lacking SSE2 flag support, since that is probably standard today.
GMX_TEST_CFLAG(MSVC_SSE2_CFLAG "/arch:SSE2" GROMACS_C_FLAGS)
endif(NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
- if (CMAKE_CXX_COMPILER_LOADED)
- GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" GROMACS_CXX_FLAG)
- if (NOT GNU_SSE4_CXXFLAG)
- GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" GROMACS_CXX_FLAGS)
- endif(NOT GNU_SSE4_CXXFLAG)
- if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
- message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or disable SSE4.1 for slightly lower performance.")
- # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
- # intrinsics when SSE2 support is enabled, so we try that instead.
- GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" GROMACS_CXX_FLAGS)
- endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
- endif()
+ GMX_TEST_CXXFLAG(GNU_SSE4_CXXFLAG "-msse4.1" GROMACS_CXX_FLAG)
+ if (NOT GNU_SSE4_CXXFLAG)
+ GMX_TEST_CXXFLAG(MSVC_SSE4_CXXFLAG "/arch:SSE4.1" GROMACS_CXX_FLAGS)
+ endif(NOT GNU_SSE4_CXXFLAG)
+ if (NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
+ message(WARNING "No C++ SSE4.1 flag found. Consider a newer compiler, or disable SSE4.1 for slightly lower performance.")
+ # Not surprising if we end up here! MSVC current does not support the SSE4.1 flag. However, it appears to accept SSE4.1
+ # intrinsics when SSE2 support is enabled, so we try that instead.
+ GMX_TEST_CXXFLAG(MSVC_SSE2_CXXFLAG "/arch:SSE2" GROMACS_CXX_FLAGS)
+ endif(NOT GNU_SSE4_CXXFLAG AND NOT MSVC_SSE4_CXXFLAG)
# This must come after we have added the -msse4.1 flag on some platforms.
check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${GROMACS_C_FLAGS})
message(WARNING "No C AVX flag found. Consider a newer compiler, or disable AVX for much lower performance.")
endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
- if (CMAKE_CXX_COMPILER_LOADED)
- GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" GROMACS_CXX_FLAGS)
- if (NOT GNU_AVX_CXXFLAG)
- GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" GROMACS_CXX_FLAGS)
- endif (NOT GNU_AVX_CXXFLAG)
- if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
- message(WARNING "No C++ AVX flag found. Consider a newer compiler, or disable AVX for much lower performance.")
- endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
- endif()
+ GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" GROMACS_CXX_FLAGS)
+ if (NOT GNU_AVX_CXXFLAG)
+ GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" GROMACS_CXX_FLAGS)
+ endif (NOT GNU_AVX_CXXFLAG)
+ if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
+ message(WARNING "No C++ AVX flag found. Consider a newer compiler, or disable AVX for much lower performance.")
+ endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
+ # Set the FMA4 flags (MSVC doesn't require any)
+ if(${GMX_ACCELERATION} STREQUAL "AVX_128_FMA" AND NOT MSVC)
+ GMX_TEST_CFLAG(GNU_FMA_CFLAG "-mfma4" GROMACS_C_FLAGS)
+ if (NOT GNU_FMA_CFLAG)
+ message(WARNING "No C FMA4 flag found. Consider a newer compiler, or disable AVX_128_FMA for much lower performance.")
+ endif(NOT GNU_FMA_CFLAG)
+ if (CMAKE_CXX_COMPILER_LOADED)
+ GMX_TEST_CXXFLAG(GNU_FMA_CXXFLAG "-mfma4" GROMACS_CXX_FLAGS)
+ if (NOT GNU_FMA_CXXFLAG)
+ message(WARNING "No C++ FMA flag found. Consider a newer compiler, or disable AVX_128_FMA for much lower performance.")
+ endif (NOT GNU_FMA_CXXFLAG)
+ endif()
+ endif()
+
# Only test the header after we have tried to add the flag for AVX support
check_include_file(immintrin.h HAVE_IMMINTRIN_H ${GROMACS_C_FLAGS})
message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
endif(NOT HAVE_IMMINTRIN_H)
- # AMD says we should include x86intrin.h for FMA support, but MSVC seems to do fine without it, so don't require it.
+ # GCC requires x86intrin.h for FMA support. MSVC 2010 requires intrin.h for FMA support.
check_include_file(x86intrin.h HAVE_X86INTRIN_H ${GROMACS_C_FLAGS})
+ check_include_file(intrin.h HAVE_INTRIN_H ${GROMACS_C_FLAGS})
# The user should not be able to set this orthogonally to the acceleration
set(GMX_X86_SSE4_1 1)
if(isupper)
set(F77_FUNCDEF "${prefix} NAME ${suffix}")
- set(F77_FUNCDEF_ "${prefix} NAME ${extrasuffix}")
+ # The underscored versions are not currently used.
+ #set(F77_FUNCDEF_ "${prefix} NAME ${extrasuffix}")
else(isupper)
set(F77_FUNCDEF "${prefix} name ${suffix}")
- set(F77_FUNCDEF_ "${prefix} name ${extrasuffix}")
+ #set(F77_FUNCDEF_ "${prefix} name ${extrasuffix}")
endif(isupper)
else(GMX_FORTRAN OR GMX_POWER6)
set(F77_FUNCDEF "name ## _")
- set(F77_FUNCDEF_ "name ## _")
+ #set(F77_FUNCDEF_ "name ## _")
endif(GMX_FORTRAN OR GMX_POWER6)
# Process QM/MM Settings
FORCE)
set(CMAKE_C_FLAGS "${GROMACS_C_FLAGS} ${CMAKE_C_FLAGS}" CACHE STRING
"Flags used by the compiler during all build types" FORCE)
- if (CMAKE_CXX_COMPILER_LOADED)
- set(CMAKE_CXX_FLAGS "${GROMACS_CXX_FLAGS} ${CMAKE_CXX_FLAGS}" CACHE STRING
- "Flags used by the compiler during all build types" FORCE)
- endif()
+ set(CMAKE_CXX_FLAGS "${GROMACS_CXX_FLAGS} ${CMAKE_CXX_FLAGS}" CACHE STRING
+ "Flags used by the compiler during all build types" FORCE)
set(CMAKE_EXE_LINKER_FLAGS
"${GROMACS_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}"
CACHE STRING "Linker flags for creating executables" FORCE)
########################################################################
# Specify install locations and which subdirectories to process #
########################################################################
-if (GMX_USE_RELATIVE_INSTALL_PATH)
- set(GMX_INSTALL_PREFIX "" CACHE STRING "Prefix gets appended to CMAKE_INSTALL_PREFIX. For cpack it sets the root folder of the archive.")
- mark_as_advanced(GMX_INSTALL_PREFIX)
-else()
- set(GMX_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/")
-endif()
-
if ( NOT DEFINED GMXLIB )
set(GMXLIB lib)
endif()
#Simpler to always install.
install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
+add_subdirectory(doxygen)
add_subdirectory(share)
-add_subdirectory(include)
add_subdirectory(src)
add_subdirectory(scripts)
include(CTest)
mark_as_advanced(BUILD_TESTING)
IF(BUILD_TESTING)
- enable_testing()
- add_subdirectory(tests)
+ enable_testing()
+ add_subdirectory(tests)
ENDIF()
-/* Manually created from config.h.in to work with cmake */
+/*! \libinternal \file
+ * \brief
+ * Include file for configuration macros from the build system.
+ *
+ * This header is not installed, so headers must not reference macros defined
+ * here.
+ *
+ * \inlibraryapi
+ */
+#include "gromacs/utility/gmx_header_config.h"
+
+/* TODO: For now, disable Doxygen warnings from here */
+/*! \cond */
/* Disable warnings about double-to-float conversion accuracy loss on MSVC */
#ifdef _MSC_VER
/* Version number of package (translate from cmake to autoconf macro name) */
#define VERSION "@PROJECT_VERSION@"
-/* Use the version string from generated version.h */
-#cmakedefine USE_VERSION_H
+/* Use extra version information generated with git */
+#cmakedefine GMX_GIT_VERSION_INFO
/* Default location of data files */
#define GMXLIBDIR "@GMXLIBDIR@"
/* User doing build */
#define BUILD_USER "@BUILD_USER@"
+/* Binary suffix for the created binaries */
+#define GMX_BINARY_SUFFIX "@GMX_BINARY_SUFFIX@"
+
+/* Source directory for the build */
+#cmakedefine CMAKE_SOURCE_DIR "@CMAKE_SOURCE_DIR@"
+
+/* Binary directory for the build */
+#cmakedefine CMAKE_BINARY_DIR "@CMAKE_BINARY_DIR@"
+
/* Turn off water-water neighborlist optimization only - not used right now */
#cmakedefine DISABLE_WATERWATER_NLIST
case), which must not contain underscores, for linking with Fortran. */
#define F77_FUNC(name,NAME) @F77_FUNCDEF@
-/* As F77_FUNC, but for C identifiers containing underscores. */
-#define F77_FUNC_(name,NAME) @F77_FUNCDEF_@
-
/* IEEE754 floating-point format. Memory layout is defined by macros
* GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER and GMX_IEEE754_BIG_ENDIAN_WORD_ORDER.
*/
/* Define for Linux pthread_setaffinity */
#cmakedefine HAVE_PTHREAD_SETAFFINITY
-/* Define for Windows NUMA-aware allocator functions*/
-#cmakedefine TMPI_WINDOWS_NUMA_API
-
/* Define for sysconf() */
#cmakedefine HAVE_SYSCONF
-/* Define for GetSystemInfo() */
-#cmakedefine HAVE_SYSTEM_INFO
-
/* Enable x86 gcc inline assembly */
#cmakedefine GMX_X86_GCC_INLINE_ASM
/* Use GPU native acceleration */
#cmakedefine GMX_GPU
-/* Define to 1 if the system has the type gmx_bool. */
-#cmakedefine HAVE_BOOL
-
/* Define to 1 if fseeko (and presumably ftello) exists and is declared. */
#cmakedefine HAVE_FSEEKO
/* Define to 1 if _fseeki64 (and presumably _fseeki64) exists and is declared. */
#cmakedefine HAVE__FSEEKI64
-/* Define to 1 if you have the m library (-lm). */
-#cmakedefine HAVE_LIBM
-
-/* Define to 1 if you have the mkl library (-lmkl). */
-#cmakedefine HAVE_LIBMKL
-
/* Define to 1 if you have the gsl library (-lgsl). */
#cmakedefine HAVE_LIBGSL
-/* Define to 1 if you have the xml2 library (-lxml2). */
-#cmakedefine HAVE_LIBXML2
-
-/* Define to 1 if you have the dl library (-ldl). */
-#cmakedefine HAVE_LIBDL
-
/* Have io.h (windows)*/
#cmakedefine HAVE_IO_H
-/* Define to 1 if you have the strcasecmp() function. */
-#cmakedefine HAVE_STRCASECMP
-
/* Define to 1 if you have the strdup() function. */
#cmakedefine HAVE_STRDUP
-/* Define to 1 if you have the vfprintf() function. */
-#cmakedefine HAVE_VFPRINTF
-
-/* Define to 1 if you have the memcmp() function. */
-#cmakedefine HAVE_MEMCMP
-
/* Define to 1 if you have the posix_memalign() function. */
#cmakedefine HAVE_POSIX_MEMALIGN
/* Define to 1 if you have the cbrt() function. */
#cmakedefine HAVE_CBRT
-/* Define to 1 if you have the isnan() function. */
-#cmakedefine HAVE_ISNAN
-
-/* Define to 1 if you have the _isnan() function. */
-#cmakedefine HAVE__ISNAN
-
/* Define to 1 if you have the isfinite() function. */
#cmakedefine HAVE_ISFINITE
/* Define to 1 if you have the sqrtf() function. */
#cmakedefine HAVE_SQRTF
-/* Define to 1 if you have the <string.h> header file. */
-#cmakedefine HAVE_STRING_H
-
-/* Define to 1 if yo have the <math.h> header file. */
-#cmakedefine HAVE_MATH_H
-
-/* Define to 1 if yo have the <limits.h> header file. */
-#cmakedefine HAVE_LIMITS_H
-
-/* Define to 1 if yo have the <memory.h> header file. */
-#cmakedefine HAVE_MEMORY_H
-
/* Define to 1 if yo have the <unistd.h> header file. */
#cmakedefine HAVE_UNISTD_H
-/* Define to 1 if yo have the <direct.h> header file. */
-#cmakedefine HAVE_DIRECT_H
-
/* Define to 1 if yo have the <pwd.h> header file. */
#cmakedefine HAVE_PWD_H
-/* Define to 1 if yo have the <stdint.h> header file. */
-#cmakedefine HAVE_STDINT_H
-
-/* Define to 1 if yo have the <stdlib.h> header file. */
-#cmakedefine HAVE_STDLIB_H
-
/* Define to 1 if yo have the <pthread.h> header file. */
#cmakedefine HAVE_PTHREAD_H
/* Define to 1 if yo have the <dirent.h> header file. */
#cmakedefine HAVE_DIRENT_H
-/* Define to 1 if yo have the <inttypes.h> header file. */
-#cmakedefine HAVE_INTTYPES_H
-
-/* Define to 1 if yo have the <regex.h> header file. */
-#cmakedefine HAVE_REGEX_H
-
-/* Define to 1 if you have the <sys/types.h> header file. */
-#cmakedefine HAVE_SYS_TYPES_H
-
-/* Define to 1 if you have the <sys/stat.h> header file. */
-#cmakedefine HAVE_SYS_STAT_H
-
/* Define to 1 if you have the <sys/time.h> header file. */
#cmakedefine HAVE_SYS_TIME_H
-/* Define to 1 if you have the <rpc/rpc.h> header file. */
-#cmakedefine HAVE_RPC_RPC_H
-
-/* Define to 1 if you have the <rpc/xdr.h> header file. */
-#cmakedefine HAVE_RPC_XDR_H
-
/* Define to 1 if you have the <x86intrin.h> header file */
#cmakedefine HAVE_X86INTRIN_H
+ /* Define to 1 if you have the <intrin.h> header file */
+ #cmakedefine HAVE_INTRIN_H
+
/* Define to 1 if you have the <sched.h> header */
#cmakedefine HAVE_SCHED_H
-/* Define to 1 if you have the vprintf() function. */
-#cmakedefine HAVE_VPRINTF
+/* Define to 1 if you have the POSIX <regex.h> header file. */
+#cmakedefine HAVE_POSIX_REGEX
+
+/* Define to 1 if you have the C++11 <regex> header file. */
+#cmakedefine HAVE_CXX11_REGEX
/* Define to 1 if you have the sysconf() function */
#cmakedefine HAVE_SYSCONF
/* Some systems requires this to be set to 64 for large file support */
#cmakedefine _FILE_OFFSET_BITS @_FILE_OFFSET_BITS@
-/* Gromacs shortcut define for fseeko & ftello being present with 64-bit support */
-#cmakedefine GMX_LARGEFILES
-
-/* Define to int if <sys/types.h> does not define. */
-#cmakedefine gid_t int
-
/* Define to __inline__ or __inline if that is what the C compiler
calls it, or to nothing if inline is not supported under any name.
Please do NOT remove the gmx_inline keyword from here. The classical
to identify the language standard level. If it is not supported, it
is still defined to an empty string here. */
#define gmx_restrict ${RESTRICT_KEYWORD}
-
-#ifndef CPLUSPLUS
-#ifdef __cplusplus
-#define CPLUSPLUS
-#endif
-#endif
-
-/* Define to long int if <sys/types.h> does not define. */
-#cmakedefine off_t int
-
-/* Define to unsigned int if <sys/types.h> does not define. */
-#cmakedefine size_t int
-
-/* Define to int if <sys/types.h> does not define. */
-#cmakedefine uid_t int
-
/* Build special-purpose mdrun library */
#cmakedefine GMX_FAHCORE
/* Define if we have pipes */
#cmakedefine HAVE_PIPES
-
/* Catch stupid CMake problems on OS X */
#ifdef __APPLE__
# if ((defined(__LP64__) && __LP64__ && defined(SIZEOF_VOIDP) && SIZEOF_VOIDP<8) || ( (!defined(__LP64__) || __LP64__==0) && (defined(SIZEOF_VOIDP) && SIZEOF_VOIDP>4)))
# error "or create a new such entry with your choice in the GUI _before_ hitting 'configure'."
# endif
#endif
+
+/*! \endcond */
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff