# the research papers on the package. Check out http://www.gromacs.org.
cmake_minimum_required(VERSION 2.8.8)
+# When we require cmake >= 2.8.12, it will provide
+# CMAKE_MINIMUM_REQUIRED_VERSION automatically, but in the meantime we
+# need to set a variable, and it must have a different name.
+set(GMX_CMAKE_MINIMUM_REQUIRED_VERSION "2.8.8")
# CMake modules/macros are in a subdirectory to keep this file cleaner
# This needs to be set before project() in order to pick up toolchain files
# NOTE: when releasing the "-dev" suffix needs to be stripped off!
# REGRESSIONTEST_VERSION and REGRESSIONTEST_BRANCH should always be
# defined.
-set(PROJECT_VERSION "5.0-rc1-dev")
+set(PROJECT_VERSION "5.0.3-dev")
# If this is a released tarball, "-dev" will not be present in
# PROJECT_VERSION, and REGRESSIONTEST_VERSION specifies the version
# number of the regressiontest tarball against which the code tarball
# can be tested. This will be the version of the last patch release.
-set(REGRESSIONTEST_VERSION "5.0-rc1")
+set(REGRESSIONTEST_VERSION "5.0.3-dev")
+# The MD5 checksum of the regressiontest tarball. Only used if "-dev"
+# is not present in the PROJECT_VERSION
+set(REGRESSIONTEST_MD5SUM "004f2377adf252e2caa9c241390d4b9c")
# If this is not a released tarball, "-dev" will be present in
# PROJECT_VERSION, and REGRESSIONTEST_BRANCH specifies the name of the
# gerrit.gromacs.org branch whose HEAD can test this code, *if* this
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)
-
include(gmxBuildTypeReference)
include(gmxBuildTypeTSAN)
include(gmxBuildTypeASAN)
"List of configuration types"
FORCE)
endif()
-set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBUGINFO RELWITHASSERT MINSIZEREL)
+set(build_types_with_explicit_flags RELEASE DEBUG RELWITHDEBINFO RELWITHASSERT MINSIZEREL)
enable_language(C)
enable_language(CXX)
+set_property(GLOBAL PROPERTY FIND_LIBRARY_USE_LIB64_PATHS ON)
+set(CPACK_PACKAGE_NAME "gromacs")
set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
+set(CPACK_SOURCE_PACKAGE_FILE_NAME "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}")
set(CPACK_PACKAGE_VENDOR "gromacs.org")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
set(CPACK_RESOURCE_FILE_WELCOME "${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 "${CMAKE_SOURCE_DIR}/COPYING")
set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
-set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$")
+set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
-set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/share/man/man1;share/man/man1;${CMAKE_BINARY_DIR}/share/man/man7;share/man/man7;${CMAKE_BINARY_DIR}/share/html/final;share/html/final")
+# CPack source archives include only the directories we list here.
+# This variable is a list of pairs of names of source and destination
+# directories. Most of these are used for content GROMACS generates as
+# part of the configuration or build.
+set(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/src/programs/completion;src/programs/completion;${CMAKE_BINARY_DIR}/docs/man/man1;docs/man/man1;${CMAKE_BINARY_DIR}/docs/man/man7;docs/man/man7;${CMAKE_BINARY_DIR}/docs/old-html/final;docs/old-html/final;${CMAKE_BINARY_DIR}/docs/install-guide/final;/")
set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
+set(CPACK_GMX_BUILD_HELP "${GMX_BUILD_HELP}") #Works even though GMX_BUILD_HELP is defined later because it is off by default.
#must come after all cpack settings!
include(CPack)
"Hostname of the machine where the cache was generated.")
endif()
+########################################################################
+# Detect architecture before setting options so we can alter defaults
+########################################################################
+# Detect the architecture the compiler is targetting, detect
+# SIMD instructions possibilities on that hardware, suggest SIMD instruction set
+# to use if none is specified, and populate the cache option for CPU
+# SIMD.
+include(gmxDetectTargetArchitecture)
+gmx_detect_target_architecture()
+
########################################################################
# User input options #
########################################################################
set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
-option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
+if(GMX_TARGET_FUJITSU_SPARC64)
+ # Fujitsu only has SIMD in double precision, so this will be faster
+ set(GMX_DOUBLE_DEFAULT ON)
+else()
+ set(GMX_DOUBLE_DEFAULT OFF)
+endif()
+option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" ${GMX_DOUBLE_DEFAULT})
+option(GMX_RELAXED_DOUBLE_PRECISION "Accept single precision 1/sqrt(x) when using Fujitsu HPC-ACE SIMD" OFF)
+mark_as_advanced(GMX_RELAXED_DOUBLE_PRECISION)
+
option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
gmx_dependent_option(
mark_as_advanced(GMX_COOL_QUOTES)
gmx_add_cache_dependency(GMX_COOL_QUOTES BOOL "NOT GMX_FAHCORE" OFF)
-# decide on GPU settings based on user-settings and GPU/CUDA detection
+# Decide on GPU settings based on user-settings and GPU/CUDA detection.
+# We support CUDA >=v4.0 on *nix, but <= v4.1 doesn't work with MSVC
+if(MSVC)
+ set(REQUIRED_CUDA_VERSION 4.1)
+else()
+ set(REQUIRED_CUDA_VERSION 4.0)
+endif()
+set(REQUIRED_CUDA_COMPUTE_CAPABILITY 2.0)
include(gmxManageGPU)
-# Detect the architecture the compiler is targetting, detect
-# SIMD instructions possibilities on that hardware, suggest SIMD instruction set
-# to use if none is specified, and populate the cache option for CPU
-# SIMD.
-include(gmxDetectTargetArchitecture)
-gmx_detect_target_architecture()
-
if(GMX_CPU_ACCELERATION)
# Stay compatible with old Jenkins command line options for specific SIMD acceleration
set(GMX_SIMD "${GMX_CPU_ACCELERATION}" CACHE STRING "SIMD instruction set level and compiler optimization" FORCE)
OFF)
mark_as_advanced(GMX_BUILD_FOR_COVERAGE)
+option(GMX_DEVELOPER_BUILD
+ "Enable Developer convenience features: always build unit-tests"
+ OFF)
+mark_as_advanced(GMX_DEVELOPER_BUILD)
######################################################################
# Detect OpenMP support
#####################################################################
# The cmake/Check{C,CXX}CompilerFlag.cmake files in the GROMACS distribution
-# are used with permission from CMake v2.8.9 so that GROMACS can detect
-# invalid options with the Intel Compilers.
+# are used with permission from CMake v3.0.0 so that GROMACS can detect
+# invalid options with the Intel Compilers, and we have added a line
+# to detect warnings with the Fujitsu compilers on K computer and ICC.
+# CMake-3.0 also has a bug where the FAIL_REGEX pattern for AIX contains
+# a semicolon. Since this is also used as a separator in lists inside CMake,
+# that string ends up being split into two separate patterns, and the last
+# part is just a single word that also matches other messages. We solved this
+# by replacing the semicolon with a period that matches any character.
+#
# These files should be removed from the source tree when a CMake version that
# includes the features in question becomes required for building GROMACS.
include(CheckCCompilerFlag)
include(CheckCXXCompilerFlag)
-
include(gmxCFlags)
gmx_c_flags()
if(GMX_DOUBLE)
add_definitions(-DGMX_DOUBLE)
set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_DOUBLE")
+ if(GMX_RELAXED_DOUBLE_PRECISION)
+ add_definitions(-DGMX_RELAXED_DOUBLE_PRECISION)
+ endif()
endif()
if(GMX_SOFTWARE_INVSQRT)
set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_SOFTWARE_INVSQRT")
endif()
if(WIN32 AND NOT CYGWIN)
- set(GMX_WSOCKLIB_PATH CACHE PATH "Path to winsock (wsock32.lib) library.")
- mark_as_advanced(GMX_WSOCKLIB_PATH)
- find_library(WSOCK32_LIBRARY NAMES wsock32 PATHS ${GMX_WSOCKLIB_PATH})
- if(WSOCK32_LIBRARY)
- list(APPEND GMX_EXTRA_LIBRARIES ${WSOCK32_LIBRARY})
- add_definitions(-DGMX_HAVE_WINSOCK)
- else()
- message(STATUS "No winsock found. Cannot use interactive molecular dynamics (IMD).")
- endif(WSOCK32_LIBRARY)
+ list(APPEND GMX_EXTRA_LIBRARIES "wsock32")
+ add_definitions(-DGMX_HAVE_WINSOCK)
endif()
check_function_exists(_commit HAVE__COMMIT)
check_function_exists(sigaction HAVE_SIGACTION)
check_function_exists(sysconf HAVE_SYSCONF)
-check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
-check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
check_function_exists(rsqrt HAVE_RSQRT)
check_function_exists(rsqrtf HAVE_RSQRTF)
check_function_exists(sqrtf HAVE_SQRTF)
check_library_exists(m sqrt "" HAVE_LIBM)
check_library_exists(rt clock_gettime "" HAVE_CLOCK_GETTIME)
+include(TestSchedAffinity)
+test_sched_affinity(HAVE_SCHED_AFFINITY)
+
include(TestBigEndian)
test_big_endian(GMX_INTEGER_BIG_ENDIAN)
include(gmxManageBlueGene)
endif()
+if(GMX_TARGET_FUJITSU_SPARC64)
+ include(gmxManageFujitsuSparc64)
+endif()
+
########################################################################
#Process MPI settings
########################################################################
# tests. This exports LIBXML2_FOUND, which we should not use because
# it does not tell us that linking will succeed. Instead, we test that
# next.
+if(DEFINED LIBXML2_LIBRARIES)
+ set(LibXml2_FIND_QUIETLY TRUE)
+endif()
find_package(LibXml2)
include(gmxTestLibXml2)
gmx_test_libxml2(HAVE_LIBXML2)
"version of Boost included with Gromacs.")
endif()
+if(NOT DEFINED GMX_BUILD_UNITTESTS AND NOT HAVE_LIBXML2)
+ message(WARNING "libxml2 not found. Will build GROMACS without unit-tests. This is not recommended, because the unit-tests help to verify that GROMACS functions correctly. Most likely you are missing the libxml2-dev(el) package. After you installed it, set GMX_BUILD_UNITTESTS=ON.")
+endif()
option(GMX_BUILD_UNITTESTS "Build unit tests with BUILD_TESTING (uses Google C++ Testing and Mocking Frameworks, requires libxml2)" ${HAVE_LIBXML2})
mark_as_advanced(GMX_BUILD_UNITTESTS)
gmx_add_cache_dependency(GMX_BUILD_UNITTESTS BOOL BUILD_TESTING OFF)
"Either set GMX_BUILD_UNITTESTS=OFF or tell CMake how to find a working version of libxml2.")
endif()
+if(GMX_USE_TNG AND NOT GMX_EXTERNAL_TNG)
+ # TNG wants zlib if it is available
+ find_package(ZLIB QUIET)
+ include(gmxTestZLib)
+ gmx_test_zlib(HAVE_ZLIB)
+endif()
+
########################################################################
# Generate development version info for cache
########################################################################
########################################################################
add_definitions( -DHAVE_CONFIG_H )
-include_directories(${CMAKE_SOURCE_DIR}/src)
-include_directories(${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
+include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src)
+include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/thread_mpi/include)
# Required for config.h, maybe should only be set in src/CMakeLists.txt
-include_directories(${CMAKE_BINARY_DIR}/src)
+include_directories(BEFORE ${CMAKE_BINARY_DIR}/src)
# Required for gmx_header_config_gen.h to be found before installation
-include_directories(${CMAKE_BINARY_DIR}/src/gromacs/utility)
+include_directories(BEFORE ${CMAKE_BINARY_DIR}/src/gromacs/utility)
# Required for now to make old code compile
-include_directories(${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
+include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/gromacs/legacyheaders)
include(gmxTestInlineASM)
gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
# so, should we use plug-ins?
if((WIN32 AND NOT CYGWIN) OR (HAVE_DLOPEN AND BUILD_SHARED_LIBS))
if(NOT VMD_QUIETLY)
- MESSAGE(STATUS
- "Found the ability to use plug-ins when building shared libaries, "
- "so will compile to use plug-ins (e.g. to read VMD-supported file "
- "formats).")
+ MESSAGE(STATUS "Using dynamic plugins (e.g VMD-supported file formats)")
endif()
if(NOT GMX_VMD_PLUGIN_PATH)
find_package(VMD)
########################################################################
# Specify install locations
########################################################################
-# Use GNUInstallDirst to set paths on multiarch systems
+# Use GNUInstallDirs to set paths on multiarch systems.
include(GNUInstallDirs)
+# Customization for the installation tree paths.
set(GMX_LIB_INSTALL_DIR ${CMAKE_INSTALL_LIBDIR} CACHE STRING
"Library installation directory (default: ${CMAKE_INSTALL_LIBDIR})")
set(GMX_DATA_INSTALL_DIR gromacs CACHE STRING
"Data installation directory under share/ (default: gromacs)")
mark_as_advanced(GMX_LIB_INSTALL_DIR GMX_DATA_INSTALL_DIR)
-set(LIB_INSTALL_DIR ${GMX_INSTALL_PREFIX}${GMX_LIB_INSTALL_DIR})
-set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
-set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/${GMX_DATA_INSTALL_DIR})
-set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
-set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
+# These variables are used internally to provide a central location for
+# customizing the install locations.
+set(LIB_INSTALL_DIR ${GMX_LIB_INSTALL_DIR})
+set(BIN_INSTALL_DIR bin)
+set(DATA_INSTALL_DIR share/${GMX_DATA_INSTALL_DIR})
+set(MAN_INSTALL_DIR share/man)
+set(INCL_INSTALL_DIR include)
+# These variables get written into config.h for use in finding the data
+# directories.
set(GMXLIB_SEARCH_DIR share/${GMX_DATA_INSTALL_DIR}/top)
set(GMXLIB_FALLBACK ${CMAKE_INSTALL_PREFIX}/${DATA_INSTALL_DIR}/top)
include(gmxManageSuffixes)
################################################################
-# Shared library settings
+# Shared library load path settings
################################################################
-if((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (CMAKE_VERSION VERSION_GREATER 2.8.11)))
+# CMake supports RPATH on OS X only from 2.8.12 upwards.
+# CMAKE_SYSTEM_VERSION > 8.0 matches OS X 10.5 and above, where RPATH support
+# was added.
+if((NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin") OR
+ ((CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) AND (NOT CMAKE_VERSION VERSION_LESS 2.8.12)))
+ # The build folder always has bin/ and lib/; if we are also going to
+ # install to lib/, then the installation RPATH works also in the build
+ # tree. This makes installation slightly faster (no need to rewrite the
+ # RPATHs), and makes the binaries in the build tree relocatable.
if(GMX_LIB_INSTALL_DIR STREQUAL "lib")
set(CMAKE_BUILD_WITH_INSTALL_RPATH TRUE)
endif()
+ # Set the RPATH as relative to the executable location to make the
+ # binaries relocatable.
if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
set(CMAKE_INSTALL_RPATH "\$ORIGIN/../${GMX_LIB_INSTALL_DIR}")
else()
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
set(CMAKE_MACOSX_RPATH 1)
else()
- # We are on Darwin/OSX, and cmake cannot handle proper RPATHs
- if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0) #rpath supported for >10.4
+ # We are on Darwin/OSX, and CMake cannot handle RPATHs automatically.
+ if(CMAKE_SYSTEM_VERSION VERSION_GREATER 8.0)
+ # Set the RPATH options manually.
set(CMAKE_INSTALL_NAME_DIR "@rpath")
set(GMX_EXE_LINKER_FLAGS ${GMX_EXE_LINKER_FLAGS} "-Wl,-rpath,@executable_path/../${GMX_LIB_INSTALL_DIR}")
else()
+ # Use the old INSTALL_NAME_DIR mechanism if RPATH is not supported.
set(CMAKE_INSTALL_NAME_DIR "${CMAKE_INSTALL_PREFIX}/${LIB_INSTALL_DIR}")
endif()
endif()
include_directories(${Boost_INCLUDE_DIRS})
set(PKG_CFLAGS "${PKG_CFLAGS} -I${Boost_INCLUDE_DIRS}")
else()
- include_directories(${CMAKE_SOURCE_DIR}/src/external/boost)
+ include_directories(BEFORE ${CMAKE_SOURCE_DIR}/src/external/boost)
# typeid not supported for minimal internal version
# (would add significant amount of code)
add_definitions(-DBOOST_NO_TYPEID)
endif()
endif()
-if(GMX_USE_TNG)
- find_package(ZLIB QUIET)
- include(gmxTestZLib)
- gmx_test_zlib(HAVE_ZLIB)
- set(TNG_BUILD_WITH_ZLIB ${HAVE_ZLIB} CACHE BOOL "Build TNG with zlib compression")
- set(TNG_BUILD_FORTRAN OFF CACHE BOOL "Build Fortran compatible TNG library and examples for testing")
- set(TNG_BUILD_EXAMPLES OFF CACHE BOOL "Build examples showing usage of the TNG API")
- set(TNG_BUILD_COMPRESSION_TESTS OFF CACHE BOOL "Build tests of the TNG compression library")
- set(TNG_BUILD_DOCUMENTATION OFF CACHE BOOL "Use Doxygen to create the HTML based TNG API documentation")
- set(TNG_BUILD_TEST OFF CACHE BOOL "Build TNG testing binary.")
- add_subdirectory(${CMAKE_SOURCE_DIR}/src/external/tng_io)
- set(GMX_TNG_LIBRARIES tng_io)
-endif()
-mark_as_advanced(TNG_BUILD_FORTRAN)
-mark_as_advanced(TNG_BUILD_EXAMPLES)
-mark_as_advanced(TNG_BUILD_COMPRESSION_TESTS)
-mark_as_advanced(TNG_BUILD_DOCUMENTATION)
-mark_as_advanced(TNG_BUILD_TEST)
-mark_as_advanced(TNG_EXAMPLE_FILES_DIR)
-
if (GMX_BUILD_FOR_COVERAGE)
# Code heavy with asserts makes conditional coverage close to useless metric,
# as by design most of the false branches are impossible to trigger in
endif()
if (NOT GMX_BUILD_MDRUN_ONLY)
- add_subdirectory(doxygen)
+ add_subdirectory(docs)
add_subdirectory(share)
add_subdirectory(scripts)
endif()
###########################
set_directory_properties(PROPERTIES
ADDITIONAL_MAKE_CLEAN_FILES "install_manifest.txt")
-
-########################################################################
-# Manual #
-########################################################################
-
-option(GMX_BUILD_MANUAL "Whether to try to configure to build the PDF manual" OFF)
-mark_as_advanced(GMX_BUILD_MANUAL)
-if(GMX_BUILD_MANUAL)
- # Make sure we only do detection of manual-building dependencies
- # when the user opted in for that.
- add_subdirectory(manual)
-endif()
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff