-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.8)
# Keep CMake suitably quiet on Cygwin
set(CMAKE_LEGACY_CYGWIN_WIN32 0) # Remove when CMake >= 2.8.4 is required
-project(Gromacs)
+# 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)
include(Dart)
mark_as_advanced(DART_ROOT)
# machine with no git.
#
# NOTE: when releasing the "-dev" suffix needs to be stripped off!
-set(PROJECT_VERSION "4.5.5-dev")
+set(PROJECT_VERSION "4.6-dev")
set(CUSTOM_VERSION_STRING ""
CACHE STRING "Custom version string (if empty, use hard-coded default)")
mark_as_advanced(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 "5")
-SET(CPACK_PACKAGE_VERSION_PATCH "5")
+SET(CPACK_PACKAGE_VERSION_MINOR "6")
+#SET(CPACK_PACKAGE_VERSION_PATCH "0")
+
+# The numerical gromacs version. It is 40600 for 4.6.0.
+# The #define GMX_VERSION in gmx_header_config_h is set to this value.
+math(EXPR NUM_VERSION
+ "${CPACK_PACKAGE_VERSION_MAJOR}*10000 + ${CPACK_PACKAGE_VERSION_MINOR}*100")
+if(CPACK_PACKAGE_VERSION_PATCH)
+ math(EXPR NUM_VERSION
+ "${NUM_VERSION} + ${CPACK_PACKAGE_VERSION_PATCH}")
+endif()
+# The API version tracks the numerical Gromacs version (for now).
+# It is potentially different from the Gromacs version in the future, if
+# the programs/libraries diverge from the presumably more stable API.
+# The #define GMX_API_VERSION in version.h is set to this value to
+# provide backward compatibility of software written against the Gromacs API.
+set(API_VERSION ${NUM_VERSION})
# Cmake modules/macros are in a subdirectory to keep this file cleaner
set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake)
-if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+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)
endif()
+include(gmxBuildTypeReference)
+
if(NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel." FORCE)
+ set(CMAKE_BUILD_TYPE "Release" CACHE STRING "Choose the type of build, options are: Debug Release RelWithDebInfo MinSizeRel Reference." 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)
+
set(CPACK_PACKAGE_VERSION ${PROJECT_VERSION})
set(CPACK_PACKAGE_VENDOR "gromacs.org")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
-set(CPACK_SET_DESTDIR "ON")
-set(CPACK_INCLUDE_TOPLEVEL_DIRECTORY 0)
+if (NOT GMX_USE_RELATIVE_INSTALL_PATH)
+ set(CPACK_SET_DESTDIR "ON")
+endif()
set(CPACK_RESOURCE_FILE_WELCOME "${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 "${CMAKE_SOURCE_DIR}/admin/InstallLicense.txt")
+set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING")
set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
+set(CPACK_SOURCE_IGNORE_FILES ".isreposource;.git;.gitignore")
+set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
+SET(CPACK_SOURCE_INSTALLED_DIRECTORIES "${CMAKE_SOURCE_DIR};/;${CMAKE_BINARY_DIR}/man;man")
+set(CPACK_PACKAGE_CONTACT "gmx-users@gromacs.org")
#must come after all cpack settings!
include(CPack)
"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()
+set(CMAKE_PREFIX_PATH "" CACHE STRING "Extra locations to search for external libraries and tools (give directory without lib, bin, or include)")
+
########################################################################
# Fix stupid flags on Windows
########################################################################
SET(SHARED_LIBS_DEFAULT ON)
-IF( MSVC )
+IF( WIN32 AND NOT CYGWIN)
+ 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
+
+ IF (GMX_PREFER_STATIC_LIBS)
+ #Only setting Debug and Release flags. Others configurations current not used.
STRING(REPLACE /MD /MT CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
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)
- SET(SHARED_LIBS_DEFAULT OFF)
-ENDIF()
+ 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()
+ ENDIF()
-IF( WIN32 AND NOT CYGWIN AND CMAKE_C_COMPILER_ID MATCHES "Intel" )
- STRING(REPLACE /GZ /RTC1 CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE})
- SET(CMAKE_C_FLAGS_RELEASE ${CMAKE_C_FLAGS_RELEASE} CACHE STRING "" FORCE)
+ #Workaround for cmake bug 13174. Replace deprecated options.
+ IF( CMAKE_C_COMPILER_ID MATCHES "Intel" )
STRING(REPLACE /GZ /RTC1 CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG})
- SET(CMAKE_C_FLAGS_DEBUG ${CMAKE_C_FLAGS_DEBUG} CACHE STRING "" FORCE)
- SET(SHARED_LIBS_DEFAULT OFF)
+ 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)
+ 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)
+
+ STRING(REPLACE /GX /EHsc CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE})
+ SET(CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE} CACHE STRING "" FORCE)
+ ENDIF()
ENDIF()
-set(GMX_EXTRA_LIBRARIES)
-
-
-
-######################################################################
-# compiler tests
-# these need ot be done early (before further tests).
-#####################################################################
-
-include(CheckCCompilerFlag)
-include(CheckCXXCompilerFlag)
-
-include(gmxCFlags)
-gmx_c_flags()
########################################################################
# User input options #
########################################################################
option(GMX_DOUBLE "Use double precision (much slower, use only if you really need it)" OFF)
option(GMX_MPI "Build a parallel (message-passing) version of GROMACS" OFF)
-option(GMX_THREADS "Build a parallel (thread-based) version of GROMACS (cannot be combined with MPI yet)" ON)
+option(GMX_THREAD_MPI "Build a thread-MPI-based multithreaded version of GROMACS (not compatible with MPI)" ON)
option(GMX_SOFTWARE_INVSQRT "Use GROMACS software 1/sqrt" ON)
mark_as_advanced(GMX_SOFTWARE_INVSQRT)
option(GMX_POWERPC_INVSQRT "Use PowerPC hardware 1/sqrt" OFF)
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)
-set(GMX_ACCELERATION "auto"
- CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran")
+
+include(gmxDetectAcceleration)
+if(NOT DEFINED GMX_CPU_ACCELERATION)
+ if(CMAKE_CROSSCOMPILING)
+ set(GMX_SUGGESTED_CPU_ACCELERATION "None")
+ else(CMAKE_CROSSCOMPILING)
+ gmx_detect_acceleration(GMX_SUGGESTED_CPU_ACCELERATION)
+ endif(CMAKE_CROSSCOMPILING)
+endif(NOT DEFINED GMX_CPU_ACCELERATION)
+
+set(GMX_CPU_ACCELERATION "@GMX_SUGGESTED_CPU_ACCELERATION@"
+ CACHE STRING "Accelerated CPU kernels. Pick one of: None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, BlueGene, Power6, Fortran")
set(GMX_FFT_LIBRARY "fftw3"
- CACHE STRING "FFT library choices: fftw3,fftw2,mkl,fftpack[built-in]")
+ CACHE STRING "FFT library choices: fftw3,mkl,fftpack[built-in]")
option(GMX_DISABLE_FFTW_MEASURE
"Do not optimize FFTW setups (not needed with SSE)" OFF)
mark_as_advanced(GMX_DISABLE_FFTW_MEASURE)
CACHE STRING "QM package choices: none,gaussian,mopac,gamess,orca")
option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
mark_as_advanced(GMX_BROKEN_CALLOC)
-option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic with MPI, Windows)" ${SHARED_LIBS_DEFAULT})
option(GMX_MPI_IN_PLACE "Enable MPI_IN_PLACE for MPIs that have it defined" ON)
mark_as_advanced(GMX_MPI_IN_PLACE)
-option(GMX_DLOPEN "Compile with dlopen, needed to read VMD supported file formats" ON)
-mark_as_advanced(GMX_DLOPEN)
-
+option(GMX_LOAD_PLUGINS "Compile with plugin support, needed to read VMD supported file formats" ON)
+mark_as_advanced(GMX_LOAD_PLUGINS)
-option(GMX_IA32_ASM "Add SSE assembly files for IA32" OFF)
-mark_as_advanced(GMX_IA32_ASM)
-option(GMX_X86_64_ASM "Add SSE assembly files for X86_64" OFF)
-mark_as_advanced(GMX_X86_64_ASM)
+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_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 AND NOT APPLE)
- option(GMX_PREFER_STATIC_LIBS "When finding libraries prefer \".a\" static archives (NOTE: this is enabled only for UNIX (excluding APPLE) platforms but it might not always work!" OFF)
+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)
mark_as_advanced(GMX_PREFER_STATIC_LIBS)
endif()
+option(GMX_CYCLE_SUBCOUNTERS "Enable cycle subcounters to get a more detailed cycle timings" OFF)
+mark_as_advanced(GMX_CYCLE_SUBCOUNTERS)
+
+######################################################################
+# Compiler tests
+# These need to be done early (before further tests).
+#####################################################################
+
+# 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.
+# 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)
+if(CMAKE_CXX_COMPILER_LOADED)
+ include(CheckCXXCompilerFlag)
+endif()
+
+# OpenMP check must come before other CFLAGS!
+if(GMX_OPENMP)
+ find_package(OpenMP)
+ if(OPENMP_FOUND)
+ # CMake on Windows doesn't support linker flags passed to target_link_libraries
+ # (i.e. it treats /openmp as \openmp library file). Also, no OpenMP linker flags are needed.
+ if(NOT (WIN32 AND NOT CYGWIN))
+ if(CMAKE_COMPILER_IS_GNUCC AND GMX_PREFER_STATIC_OPENMP)
+ set(OpenMP_LINKER_FLAGS "-Wl,-static -lgomp -lrt -Wl,-Bdynamic -lpthread")
+ set(OpenMP_SHARED_LINKER_FLAGS "")
+ else()
+ # Only set a linker flag if the user didn't set them manually
+ if(NOT DEFINED OpenMP_LINKER_FLAGS)
+ set(OpenMP_LINKER_FLAGS "${OpenMP_C_FLAGS}")
+ endif()
+ if(NOT DEFINED OpenMP_SHARED_LINKER_FLAGS)
+ set(OpenMP_SHARED_LINKER_FLAGS "${OpenMP_C_FLAGS}")
+ endif()
+ endif()
+ endif()
+ else(OPENMP_FOUND)
+ message(WARNING
+ "The compiler you are using does not support OpenMP parallelism. This might hurt your performance a lot, in particular with GPUs. Try using a more recent version, or a different compiler. For now, we are proceeding by turning off OpenMP.")
+ set(GMX_OPENMP OFF CACHE STRING "Whether GROMACS will use OpenMP parallelism." FORCE)
+ endif(OPENMP_FOUND)
+endif()
+
+
+include(gmxCFlags)
+gmx_c_flags()
+
+include(gmxGetCompilerInfo)
+get_compiler_version()
+
+# gcc 4.4.x is buggy and crashes when compiling some files with O3 and OpenMP on.
+# Detect here whether applying a workaround is needed and will apply it later
+# on the affected files.
+include(gmxGCC44O3BugWorkaround)
+gmx_check_gcc44_bug_workaround_needed(GMX_USE_GCC44_BUG_WORKAROUND)
+
########################################################################
# Set up binary and library suffixing
########################################################################
set (GMX_LIBS_SUFFIX "${GMX_LIBS_SUFFIX}_d")
endif(GMX_DOUBLE)
if (GMX_OPENMM)
- set (GMX_BINARY_SUFFIX "-gpu")
- set (GMX_LIBS_SUFFIX "_gpu")
+ set (GMX_BINARY_SUFFIX "-openmm")
+ set (GMX_LIBS_SUFFIX "_openmm")
endif(GMX_OPENMM)
mark_as_advanced(FORCE GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
- message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
- message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
+ if (NOT SUFFIX_QUIETLY)
+ message(STATUS "Using default binary suffix: \"${GMX_BINARY_SUFFIX}\"")
+ message(STATUS "Using default library suffix: \"${GMX_LIBS_SUFFIX}\"")
+ endif (NOT SUFFIX_QUIETLY)
else(GMX_DEFAULT_SUFFIX)
mark_as_advanced(CLEAR GMX_BINARY_SUFFIX GMX_LIBS_SUFFIX)
- message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
- message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
+ if (NOT SUFFIX_QUIETLY)
+ message(STATUS "Using manually set binary suffix: \"${GMX_BINARY_SUFFIX}\"")
+ message(STATUS "Using manually set library suffix: \"${GMX_LIBS_SUFFIX}\"")
+ endif (NOT SUFFIX_QUIETLY)
endif(GMX_DEFAULT_SUFFIX)
+set(SUFFIX_QUIETLY TRUE CACHE INTERNAL "")
set(PKG_CFLAGS "")
if(GMX_DOUBLE)
########################################################################
#Process MPI settings
########################################################################
-include(CheckCSourceCompiles) # for gmxTestMPI_IN_PLACE
-if(GMX_MPI)
- if(GMX_THREADS)
- #message(FATAL_ERROR "Thread-based parallelization conflicts with MPI.")
- set(GMX_THREADS OFF CACHE BOOL
- "Thread-based parallelization conflicts with MPI." FORCE)
- endif(GMX_THREADS)
- find_package(MPI)
- if(MPI_FOUND)
- set(GROMACS_C_FLAGS ${GROMACS_FLAGS} ${MPI_COMPILE_FLAGS})
- set(GROMACS_LINKER_FLAGS ${GROMACS_LINKER_FLAGS} ${MPI_LINK_FLAGS})
-
- include_directories(${MPI_INCLUDE_PATH})
- list(APPEND GMX_EXTRA_LIBRARIES ${MPI_LIBRARIES})
- if(GMX_FAHCORE)
- add_definitions( -DMPI ) #for FAHCORE
- endif(GMX_FAHCORE)
- include(gmxTestMPI_IN_PLACE)
- if (GMX_MPI_IN_PLACE)
- gmx_test_mpi_in_place(MPI_IN_PLACE_EXISTS)
- endif (GMX_MPI_IN_PLACE)
-
- # test for unsuitable versions of OpenMPI
- exec_program(${MPIEXEC}
- ARGS --version
- OUTPUT_VARIABLE MPI_TYPE
- RETURN_VALUE MPI_EXEC_RETURN)
- if(MPI_EXEC_RETURN EQUAL 0)
- if(MPI_TYPE MATCHES "Open MPI|OpenRTE")
- string(REGEX MATCH "[0-9]+\\.[0-9]*\\.?[0-9]*" MPI_VERSION ${MPI_TYPE})
- if(MPI_VERSION VERSION_LESS "1.4.1")
- MESSAGE(WARNING "
- There are known problems with OpenMPI version < 1.4.1.
- Please consider updating your OpenMPI.")
- endif(MPI_VERSION VERSION_LESS "1.4.1")
- unset(MPI_VERSION)
- else(MPI_TYPE MATCHES "Open MPI|OpenRTE")
- # This is not OpenMPI, so give the old generic warning message
- MESSAGE(WARNING "
- There are known problems with some MPI implementations:
- MVAPICH2 version <= 1.4.1
- Please consider updating your MPI if applicable.")
- endif(MPI_TYPE MATCHES "Open MPI|OpenRTE")
- unset(MPI_TYPE)
- endif(MPI_EXEC_RETURN EQUAL 0)
- else(MPI_FOUND)
- message(FATAL_ERROR "MPI support requested, but no MPI compiler found.")
- endif(MPI_FOUND)
- include(gmxTestCatamount)
- gmx_test_catamount(GMX_CRAY_XT3)
- if(GMX_CRAY_XT3)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_CRAY_XT3")
- set(GMX_NO_SYSTEM 1)
- set(GMX_NO_NICE 1)
- endif(GMX_CRAY_XT3)
- set(GMX_LIB_MPI 1)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_LIB_MPI")
-endif(GMX_MPI)
-
+include(gmxManageMPI)
#######################################################################
# Check for options incompatible with OpenMM build #
#######################################################################
if(GMX_OPENMM)
- cmake_minimum_required(VERSION 2.6.4)
# we'll use the built-in fft to avoid unnecessary dependencies
string(TOUPPER ${GMX_FFT_LIBRARY} GMX_FFT_LIBRARY)
if(NOT ${GMX_FFT_LIBRARY} STREQUAL "FFTPACK")
if(GMX_MPI)
message(FATAL_ERROR "The OpenMM build is not compatible with MPI!")
endif(GMX_MPI)
- if(GMX_THREADS)
- message(STATUS "Threads are not compatible with OpenMM build, disabled!")
- set(GMX_THREADS OFF CACHE BOOL
- "Threads are not compatible with OpenMM build, disabled!" FORCE)
- endif(GMX_THREADS)
+ if(GMX_THREAD_MPI)
+ message(STATUS "Thread-MPI not compatible with OpenMM, disabled!")
+ set(GMX_THREAD_MPI OFF CACHE BOOL
+ "Thread-MPI not compatible with OpenMM build, disabled!" FORCE)
+ endif(GMX_THREAD_MPI)
+ if(GMX_OPENMP)
+ message(STATUS "OpenMP multithreading not compatible with OpenMM, disabled")
+ set(GMX_OPENMP OFF CACHE BOOL
+ "OpenMP multithreading not compatible with OpenMM, disabled!" FORCE)
+ endif()
if(GMX_SOFTWARE_INVSQRT)
set(GMX_SOFTWARE_INVSQRT OFF CACHE STRING
"The OpenMM build does not need GROMACS software 1/sqrt!" FORCE)
endif(GMX_SOFTWARE_INVSQRT)
- string(TOUPPER ${GMX_ACCELERATION} GMX_ACCELERATION)
- if(NOT GMX_ACCELERATION STREQUAL "NONE")
- message(STATUS "Switching off CPU-based acceleration, the OpenMM build does not support/need any!")
- set(GMX_ACCELERATION "none" CACHE STRING
- "Switching off CPU-based acceleration, the OpenMM build does not support/need any!" FORCE)
+ string(TOUPPER ${GMX_CPU_ACCELERATION} GMX_CPU_ACCELERATION)
+ if(NOT GMX_CPU_ACCELERATION STREQUAL "NONE")
+ message(STATUS "Switching off CPU-based acceleration, the OpenMM build does not support/need any!")
+ set(GMX_CPU_ACCELERATION "None" CACHE STRING
+ "Switching off CPU-based acceleration, the OpenMM build does not support/need any!" FORCE)
endif()
if(GMX_FAHCORE)
message(FATAL_ERROR "The OpenMM build does not support FAH build!")
message(FATAL_ERROR "The OpenMM-build does not support double precision calculations!")
endif()
# mark as advanced the unused variables
- mark_as_advanced(FORCE GMX_ACCELERATION GMX_MPI GMX_FFT_LIBRARY
- GMX_QMMM_PROGRAM GMX_THREADS GMX_DOUBLE)
+ mark_as_advanced(FORCE GMX_CPU_ACCELERATION GMX_MPI GMX_FFT_LIBRARY
+ GMX_QMMM_PROGRAM GMX_THREAD_MPI GMX_DOUBLE)
else(GMX_OPENMM)
- mark_as_advanced(CLEAR GMX_ACCELERATION GMX_MPI GMX_FFT_LIBRARY
- GMX_QMMM_PROGRAM GMX_THREADS GMX_DOUBLE)
+ mark_as_advanced(CLEAR GMX_CPU_ACCELERATION GMX_MPI GMX_FFT_LIBRARY
+ GMX_QMMM_PROGRAM GMX_THREAD_MPI GMX_DOUBLE)
endif(GMX_OPENMM)
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)
-# SSE support
-check_include_files(xmmintrin.h HAVE_XMMINTRIN_H)
-check_include_files(emmintrin.h HAVE_EMMINTRIN_H)
-check_include_files(pmmintrin.h HAVE_PMMINTRIN_H)
-check_include_files(smmintrin.h HAVE_SMMINTRIN_H)
check_include_files(io.h HAVE_IO_H)
-
+check_include_files(sched.h HAVE_SCHED_H)
include(CheckFunctionExists)
check_function_exists(strcasecmp HAVE_STRCASECMP)
check_function_exists(_fileno HAVE__FILENO)
check_function_exists(fileno HAVE_FILENO)
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)
include(CheckLibraryExists)
check_library_exists(m sqrt "" HAVE_LIBM)
########################################################################
# Find external packages #
########################################################################
-if(UNIX AND NOT APPLE)
+if(UNIX)
if(GMX_PREFER_STATIC_LIBS)
- SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
- if(BUILD_SHARED_LIBS)
- message(WARNING "Static libraries requested, the GROMACS libraries will also be build static (BUILD_SHARED_LIBS=OFF)")
- set(BUILD_SHARED_LIBS OFF CACHE BOOL "Enable shared libraries (can be problematic with MPI, Windows)" FORCE)
+ # On Linux .a is the static library suffix, on Mac OS X .lib can also
+ # be used, so we'll add both to the preference list.
+ SET(CMAKE_FIND_LIBRARY_SUFFIXES ".lib;.a" ${CMAKE_FIND_LIBRARY_SUFFIXES})
+ if(SHARED_LIBS_DEFAULT)
+ if(BUILD_SHARED_LIBS) #Warn the user about the combination. But don't overwrite the request.
+ message(WARNING "Static libraries requested, and shared Gromacs libraries requested.")
+ elseif(NOT DEFINED BUILD_SHARED_LIBS) #Change default to OFF. Don't warn if it's already off.
+ message(WARNING "Static libraries requested, the GROMACS libraries will also be build static (BUILD_SHARED_LIBS=OFF)")
+ set(SHARED_LIBS_DEFAULT OFF)
+ endif()
endif()
endif()
endif()
-
-option(GMX_XML "Use libxml2 to parse xml files" ON)
-if (GMX_XML)
- find_package(LibXml2)
- set(PKG_XML "")
- if(LIBXML2_FOUND)
- include_directories(${LIBXML2_INCLUDE_DIR})
- set(PKG_XML libxml-2.0)
- set(XML_LIBRARIES ${LIBXML2_LIBRARIES})
- set(HAVE_LIBXML2 1)
- endif(LIBXML2_FOUND)
-endif(GMX_XML)
+option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic with MPI, Windows)" ${SHARED_LIBS_DEFAULT})
option(GMX_GSL "Add support for gsl" OFF)
if (GMX_GSL)
endif(X11_FOUND)
endif(GMX_X11)
-if(GMX_THREADS)
- set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREADS")
- include(ThreadMPI)
- set(THREAD_MPI_LIB thread_mpi)
+include(ThreadMPI)
+set(THREAD_MPI_LIB thread_mpi)
+if(GMX_THREAD_MPI)
+ tmpi_get_source_list(THREAD_MPI_SRC)
+ set(PKG_CFLAGS "${PKG_CFLAGS} -DGMX_THREAD_MPI")
set(GMX_MPI 1)
- string(TOUPPER ${GMX_FFT_LIBRARY} ${GMX_FFT_LIBRARY})
- if(${GMX_FFT_LIBRARY} STREQUAL "FFTW2")
- message(FATAL_ERROR "FFTW2 can't be used with threads. Try fftw3 or mkl.")
- endif()
-endif(GMX_THREADS)
+else(GMX_THREAD_MPI)
+ tmpi_get_source_list(THREAD_MPI_SRC NOMPI)
+endif(GMX_THREAD_MPI)
if(GMX_OPENMM)
set(CUDA_BUILD_EMULATION OFF)
find_package(OpenMM)
endif(GMX_OPENMM)
+
+if(GMX_GPU)
+ if(GMX_DOUBLE)
+ message(WARNING "GPU acceleration is not available in double precision, disabled!")
+ set(GMX_GPU OFF CACHE BOOL "Enable GPU acceleration" FORCE)
+ endif()
+endif(GMX_GPU)
+
+if(GMX_GPU)
+
+ # We support CUDA >=v3.2 on *nix, but <= v4.1 doesn't work with MSVC
+ if(MSVC)
+ find_package(CUDA 4.1)
+ else()
+ find_package(CUDA 3.2)
+ endif()
+
+ if (NOT EXISTS ${CUDA_TOOLKIT_ROOT_DIR})
+ message(FATAL_ERROR "
+ mdrun supports native GPU acceleration on NVIDIA hardware with compute
+ capability >=2.0. This requires the NVIDIA CUDA library, which was not
+ found; the location can be hinted by setting CUDA_TOOLKIT_ROOT_DIR as
+ a CMake option (It does not work as an environment variable).
+ The typical location would be /usr/local/cuda.
+
+ CPU or GPU acceleration can be selected at runtime, but if you are
+ sure you can not make use of GPU acceleration, disable it by setting
+ the CMake variable GMX_GPU=OFF.")
+ endif()
+
+ if(NOT GMX_OPENMP)
+ message(WARNING "
+ In order to use GPU acceleration efficiently, mdrun requires OpenMP multithreading.
+ Without OpenMP only a single CPU core per GPU can be used which is suboptimal.
+ Note that with MPI multiple processes can be forced to use a single GPU, but this
+ typically inefficient. Note that you need to set both C and C++ compilers that
+ support OpenMP (CC and CXX environment variables, respectively) when using GPUs.")
+ endif()
+
+ include(gmxManageNvccConfig)
+
+ # Check whether we can use atomic operations needed for polling wait for GPU
+ # (to avoid the cudaStreamSynchronize + ECC bug).
+ # With thread-MPI testing atomics has already been carried out, but without
+ # thread-MPI we need to invoke the atomics test independently.
+ if (NOT GMX_THREAD_MPI)
+ set(TEST_TMPI_ATOMICS_ONLY ON CACHE INTERNAL
+ "Test only the atomic operations of thread-MPI.")
+ include(ThreadMPI)
+ endif()
+
+ # Version info (semicolon used as line separator) for nvcc.
+ get_nvcc_version_info()
+
+endif()
+# Annoyingly enough, FindCUDA leaves a few variables behind as non-advanced.
+# We need to mark these advanced outside the conditional, otherwise, if the user
+# tuns GMX_GPU=OFF after a failed cmake pass, these variables will be left behind.
+mark_as_advanced(CUDA_BUILD_CUBIN CUDA_BUILD_EMULATION CUDA_SDK_ROOT_DIR CUDA_VERBOSE_BUILD)
+
if(APPLE)
find_library(ACCELERATE_FRAMEWORK Accelerate)
list(APPEND GMX_EXTRA_LIBRARIES ${ACCELERATE_FRAMEWORK})
set(GMX_CYGWIN 1)
endif(CYGWIN)
+if(WIN32 AND NOT CYGWIN)
+ set(GMX_NATIVE_WINDOWS 1)
+endif()
+
# only bother with finding git and using version.h if the source is a git repo
if(EXISTS "${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
- # fund or the version is too small, we can't generate version information.
- find_package(Git 1.5.3)
- # this should at some point become VERSION_LESS
- if(NOT Git_FOUND OR Git_VERSION STRLESS "1.5.3")
- message("No compatible git version found, won't be able to generate proper development version information.")
- set(USE_VERSION_H OFF)
+ # 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()
endif()
else()
set(USE_VERSION_H OFF)
endif()
-if (GMX_DLOPEN)
- list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS})
- set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
-else(GMX_DLOPEN)
- set(PKG_DL_LIBS)
-endif (GMX_DLOPEN)
-
########################################################################
# Generate development version info for cache
########################################################################
add_definitions( -DHAVE_CONFIG_H )
include_directories(${CMAKE_BINARY_DIR}/src)
+include_directories(${CMAKE_BINARY_DIR}/include)
include_directories(${CMAKE_SOURCE_DIR}/include)
-include(gmxCheckBuildUserTime)
-gmx_check_build_user_time(BUILD_TIME BUILD_USER BUILD_MACHINE)
+include(gmxTestInlineASM)
+gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
+
+include(gmxSetBuildInformation)
+gmx_set_build_information()
+if(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
+ # The timestep counter headers do not include config.h
+ add_definitions(-DHAVE_RDTSCP)
+endif(BUILD_CPU_FEATURES MATCHES "rdtscp" AND NOT GMX_DISTRIBUTABLE_BUILD)
include(gmxTestFloatFormat)
gmx_test_float_format(GMX_FLOAT_FORMAT_IEEE754
gmx_test_large_files(GMX_LARGEFILES)
include(gmxTestSignal)
-gmx_test_retsigtype(RETSIGTYPE)
gmx_test_sigusr1(HAVE_SIGUSR1)
include(gmxTestInline)
gmx_test_inline(INLINE_KEYWORD)
include(gmxTestRestrict)
-gmx_test_inline(RESTRICT_KEYWORD)
+gmx_test_restrict(RESTRICT_KEYWORD)
include(gmxTestPipes)
gmx_test_pipes(HAVE_PIPES)
gmx_test__isfinite(HAVE__ISFINITE)
gmx_test__finite(HAVE__FINITE)
-include(gmxTestInlineASM)
-gmx_test_inline_asm_gcc_x86(GMX_X86_GCC_INLINE_ASM)
-gmx_test_inline_asm_msvc_x86(GMX_X86_MSVC_INLINE_ASM)
-
-# turn on SSE if supported with reasonable defaults.
-if (${GMX_ACCELERATION} STREQUAL "auto" AND NOT GMX_OPENMM)
- if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(i.86|x86|x64|x86_64|AMD64|amd64)" OR CYGWIN)
-
- set(GMX_ACCELERATION "SSE" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran" FORCE)
-
- # Determine the assembler/compiler to use
- else()
- set(GMX_ACCELERATION "none" CACHE STRING "Accelerated kernels. Pick one of: auto, none, SSE, BlueGene, Power6, ia64, altivec, fortran" FORCE)
- endif()
-endif (${GMX_ACCELERATION} STREQUAL "auto" AND NOT GMX_OPENMM)
-
include(gmxTestXDR)
gmx_test_xdr(GMX_SYSTEM_XDR)
if(NOT GMX_SYSTEM_XDR)
endif(NOT GMX_SYSTEM_XDR)
# Process nonbonded accelerated kernels settings
-string(TOUPPER ${GMX_ACCELERATION} ${GMX_ACCELERATION})
-if(${GMX_ACCELERATION} STREQUAL "NONE")
- # nothing to do
-elseif(${GMX_ACCELERATION} STREQUAL "SSE")
-
- if (GMX_64_BIT)
- set(GMX_X86_64_ASM ON CACHE BOOL "Add SSE assembly files for x86_64" FORCE)
- else (GMX_64_BIT)
- set(GMX_IA32_ASM ON CACHE BOOL "Add SSE assembly files for i386" FORCE)
- endif (GMX_64_BIT)
-
- if( WIN32 AND NOT CYGWIN )
- option(GMX_ASM_USEASM_NASM "Use Nasm for assembly instead of compiler (necessary on windows)" ON)
- else()
- option(GMX_ASM_USEASM_NASM "Use Nasm for assembly instead of compiler (necessary on windows)" OFF)
+string(TOUPPER ${GMX_CPU_ACCELERATION} ${GMX_CPU_ACCELERATION})
+if(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
+ # nothing to do
+elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE2")
+
+ GMX_TEST_CFLAG(GNU_SSE2_CFLAG "-msse2" GROMACS_C_FLAGS)
+ if(NOT GNU_SSE2_CFLAG)
+ 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()
+
+ # We dont warn for lacking SSE2 flag support, since that is probably standard today.
+
+ # Only test the include after we have tried to add the correct flag for SSE2 support
+ check_include_file(emmintrin.h HAVE_EMMINTRIN_H ${GROMACS_C_FLAGS})
+
+ if(NOT HAVE_EMMINTRIN_H)
+ message(FATAL_ERROR "Cannot find emmintrin.h, which is required for SSE2 intrinsics support.")
+ endif(NOT HAVE_EMMINTRIN_H)
+
+ set(GMX_CPU_ACCELERATION_X86_SSE2 1)
+ # The user should not be able to set this orthogonally to the acceleration
+ set(GMX_X86_SSE2 1)
+ if (NOT ACCELERATION_QUIETLY)
+ message(STATUS "Enabling SSE2 Gromacs acceleration, and it will help compiler optimization.")
endif()
- mark_as_advanced(GMX_ASM_USEASM_NASM)
-
- if (NOT GMX_64_BIT)
- # for 32-bit compiles, we might need to turn on sse
- CHECK_C_COMPILER_FLAG("-msse2" XFLAGS_SSE)
- if (XFLAGS_SSE)
- set(GROMACS_C_FLAGS "-msse2 ${GROMACS_C_FLAGS}")
- endif (XFLAGS_SSE)
- CHECK_CXX_COMPILER_FLAG("-msse2" XXFLAGS_SSE)
- if (XXFLAGS_SSE)
- set(GROMACS_CXX_FLAGS "-msse2 ${GROMACS_CXX_FLAGS}")
- endif (XXFLAGS_SSE)
- endif (NOT GMX_64_BIT)
-
- if(GMX_IA32_ASM)
- if(GMX_DOUBLE)
- set(GMX_IA32_SSE2 1)
- else()
- set(GMX_IA32_SSE 1)
- endif()
- elseif(GMX_X86_64_ASM)
- if(GMX_DOUBLE)
- set(GMX_X86_64_SSE2 1)
- else()
- set(GMX_X86_64_SSE 1)
- endif()
+
+elseif(${GMX_CPU_ACCELERATION} STREQUAL "SSE4.1")
+
+ GMX_TEST_CFLAG(GNU_SSE4_CFLAG "-msse4.1" GROMACS_C_FLAGS)
+ if (NOT GNU_SSE4_CFLAG)
+ GMX_TEST_CFLAG(MSVC_SSE4_CFLAG "/arch:SSE4.1" GROMACS_C_FLAGS)
+ endif(NOT GNU_SSE4_CFLAG)
+ if (NOT GNU_SSE4_CFLAG AND NOT MSVC_SSE4_CFLAG)
+ 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_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()
+
+ # This must come after we have added the -msse4.1 flag on some platforms.
+ check_include_file(smmintrin.h HAVE_SMMINTRIN_H ${GROMACS_C_FLAGS})
+
+ if(NOT HAVE_SMMINTRIN_H)
+ message(FATAL_ERROR "Cannot find smmintrin.h, which is required for SSE4.1 intrinsics support.")
+ endif(NOT HAVE_SMMINTRIN_H)
+
+ set(GMX_CPU_ACCELERATION_X86_SSE4_1 1)
+ # The user should not be able to set this orthogonally to the acceleration
+ set(GMX_X86_SSE4_1 1)
+ set(GMX_X86_SSE2 1)
+ if (NOT ACCELERATION_QUIETLY)
+ message(STATUS "Enabling SSE4.1 Gromacs acceleration, and it will help compiler optimization.")
+ endif()
+
+elseif(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA" OR ${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
+
+ # Set the AVX compiler flag for both these choices!
+
+ GMX_TEST_CFLAG(GNU_AVX_CFLAG "-mavx" GROMACS_C_FLAGS)
+ if (NOT GNU_AVX_CFLAG)
+ GMX_TEST_CFLAG(MSVC_AVX_CFLAG "/arch:AVX" GROMACS_C_FLAGS)
+ endif (NOT GNU_AVX_CFLAG)
+ if (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
+ message(WARNING "No C AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
+ endif (NOT GNU_AVX_CFLAG AND NOT MSVC_AVX_CFLAG)
+
+ if (CMAKE_CXX_COMPILER_LOADED)
+ GMX_TEST_CXXFLAG(GNU_AVX_CXXFLAG "-mavx" GROMACS_CXX_FLAGS)
+ if (NOT GNU_AVX_CXXFLAG)
+ GMX_TEST_CXXFLAG(MSVC_AVX_CXXFLAG "/arch:AVX" GROMACS_CXX_FLAGS)
+ endif (NOT GNU_AVX_CXXFLAG)
+ if (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
+ message(WARNING "No C++ AVX flag found. Consider a newer compiler, or try SSE4.1 (lower performance).")
+ endif (NOT GNU_AVX_CXXFLAG AND NOT MSVC_AVX_CXXFLAG)
+ endif()
+
+ # Set the FMA4 flags (MSVC doesn't require any)
+ if(${GMX_CPU_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 try SSE4.1 (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 try SSE4.1 (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 ${GROMACS_C_FLAGS})
+
+ if(NOT HAVE_IMMINTRIN_H)
+ message(FATAL_ERROR "Cannot find immintrin.h, which is required for AVX intrinsics support. Consider switching compiler.")
+ endif(NOT HAVE_IMMINTRIN_H)
+
+ if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_256")
+ try_compile(TEST_AVX ${CMAKE_BINARY_DIR}
+ "${CMAKE_SOURCE_DIR}/cmake/TestAVX.c"
+ COMPILE_DEFINITIONS "${GROMACS_C_FLAGS}")
+ if(NOT TEST_AVX)
+ message(FATAL_ERROR "Cannot compile AVX intrinsics. Consider switching compiler.")
+ endif()
+ endif()
+
+ # 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 ${GROMACS_C_FLAGS})
+
+ # The user should not be able to set this orthogonally to the acceleration
+ set(GMX_X86_SSE4_1 1)
+ set(GMX_X86_SSE2 1)
+
+ # But just enable one of the choices internally...
+ if(${GMX_CPU_ACCELERATION} STREQUAL "AVX_128_FMA")
+ set(GMX_CPU_ACCELERATION_X86_AVX_128_FMA 1)
+ set(GMX_X86_AVX_128_FMA 1)
+ if (NOT ACCELERATION_QUIETLY)
+ message(STATUS "Enabling 128-bit AVX Gromacs acceleration (with fused-multiply add), and it will help compiler optimization.")
+ endif()
+ else()
+ # If we are not doing AVX_128, it must be AVX_256...
+ set(GMX_CPU_ACCELERATION_X86_AVX_256 1)
+ set(GMX_X86_AVX_256 1)
+ if (NOT ACCELERATION_QUIETLY)
+ message(STATUS "Enabling 256-bit AVX Gromacs acceleration, and it will help compiler optimization.")
+ endif()
endif()
-# if(HAVE_PMMINTRIN_H)
-# set(GMX_SSE3 1)
-# endif(HAVE_PMMINTRIN_H)
-# if(HAVE_SMMINTRIN_H)
-# set(GMX_SSE4_1 1)
-# endif(HAVE_SMMINTRIN_H)
-
-elseif(${GMX_ACCELERATION} STREQUAL "FORTRAN")
- set(GMX_FORTRAN 1)
- #these are switch on by default sometimes
- set(GMX_IA32_ASM 0)
- set(GMX_GMX_X86_64_ASM 0)
-elseif(${GMX_ACCELERATION} STREQUAL "BLUEGENE")
-# GMX_ACCELERATION=BlueGene should be set in the Toolchain-BlueGene?-???.cmake file
- message(STATUS "Configuring for BlueGene")
+elseif(${GMX_CPU_ACCELERATION} STREQUAL "FORTRAN")
+
+# Fortran is temporarily disabled while we push in nbNxN kernels.
+# We need to fake it a bit here to avoid jenkins build errors!
+# add_definitions(-DGMX_FORTRAN)
+
+elseif(${GMX_CPU_ACCELERATION} STREQUAL "BLUEGENE")
+# GMX_CPU_ACCELERATION=BlueGene should be set in the Toolchain-BlueGene?-???.cmake file
+ if (NOT ACCELERATION_QUIETLY)
+ message(STATUS "Configuring for BlueGene")
+ endif()
set(GMX_BLUEGENE 1)
if (${CMAKE_SYSTEM_NAME} STREQUAL "BlueGeneL")
set(SHARED_LIBS_DEFAULT OFF CACHE BOOL "Shared libraries not compatible with BlueGene/L, disabled!" FORCE)
set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on BlueGene" FORCE)
set(GMX_POWERPC_INVSQRT ON CACHE BOOL "Use hardware reciprocal square root on BlueGene" FORCE)
set(GMX_X11 OFF CACHE BOOL "X11 not compatible with BlueGene, disabled!" FORCE)
- set(GMX_THREADS OFF CACHE BOOL "Threads not compatible with BlueGene, disabled!" FORCE)
+ set(GMX_THREAD_MPI OFF CACHE BOOL "Thread-MPI not compatible with BlueGene, disabled!" FORCE)
set(GMX_MPI ON CACHE BOOL "Use MPI on BlueGene" FORCE)
# Access to /etc/passwd is not available on the back end of BlueGene,
# despite being detected by CMake. This can cause linker warnings
# The automatic testing for endianness does not work for the BlueGene cross-compiler
set(GMX_IEEE754_BIG_ENDIAN_BYTE_ORDER 1 CACHE INTERNAL "BlueGene has big endian FP byte order (by default)" FORCE)
set(GMX_IEEE754_BIG_ENDIAN_WORD_ORDER 1 CACHE INTERNAL "BlueGene has big endian FP word order (by default)" FORCE)
-elseif(${GMX_ACCELERATION} STREQUAL "POWER6")
+elseif(${GMX_CPU_ACCELERATION} STREQUAL "POWER6")
set(GMX_POWER6 1)
set(GMX_SOFTWARE_INVSQRT OFF CACHE BOOL "Do not use software reciprocal square root on Power6" FORCE)
set(GMX_POWERPC_INVSQRT ON CACHE BOOL "Use hardware reciprocal square root on Power6" FORCE)
-elseif(${GMX_ACCELERATION} STREQUAL "IA64")
- set(GMX_IA64_ASM 1)
- set(DISABLE_WATERWATER_NLIST 1)
- set(DISABLE_WATER_NLIST 1)
-elseif(${GMX_ACCELERATION} STREQUAL "ALTIVEC")
- check_include_files(altivec.h HAVE_ALTIVEC_H)
- if(HAVE_ALTIVEC_H)
- set(GMX_PPC_ALTIVEC 1)
- endif(HAVE_ALTIVEC_H)
-else(${GMX_ACCELERATION} STREQUAL "NONE")
- MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_ACCELERATION}. Pick one of auto, none, SSE, Fortran, BlueGene, Power6, ia64, altivec")
-endif(${GMX_ACCELERATION} STREQUAL "NONE")
+else(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
+ MESSAGE(FATAL_ERROR "Unrecognized option for accelerated kernels: ${GMX_CPU_ACCELERATION}. Pick one of None, SSE2, SSE4.1, AVX_128_FMA, AVX_256, Fortran, BlueGene, Power6")
+endif(${GMX_CPU_ACCELERATION} STREQUAL "NONE")
+set(ACCELERATION_QUIETLY TRUE CACHE INTERNAL "")
if(GMX_FORTRAN OR GMX_POWER6)
- if (GMX_THREADS)
- message(FATAL_ERROR "FORTRAN/POWER6 is incompatible with threads and only provides a speed-up on certain IBM compilers. Disable FORTRAN (or threads if you really want to use FORTRAN kernels).")
- endif(GMX_THREADS)
+ if (GMX_THREAD_MPI)
+ message(FATAL_ERROR "FORTRAN/POWER6 is incompatible with thread-MPI and only provides a speed-up on certain IBM compilers. Disable FORTRAN (or threads if you really want to use FORTRAN kernels).")
+ endif(GMX_THREAD_MPI)
enable_language(Fortran)
include(FortranCInterface)
discover_fortran_mangling(prefix isupper suffix extra_under_score found)
set(PKG_FFT "")
set(PKG_FFT_LIBS "")
if(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
-# MESSAGE(STATUS "Using external FFT library - fftw3")
if(GMX_DOUBLE)
- find_package(FFTW3 REQUIRED)
- include_directories(${FFTW3_INCLUDE_DIR})
- set(FFT_LIBRARIES ${FFTW3_LIBRARIES})
- set(PKG_FFT "fftw3")
+ set(FFTW fftw)
else(GMX_DOUBLE)
- find_package(FFTW3F REQUIRED)
- include_directories(${FFTW3F_INCLUDE_DIR})
- set(FFT_LIBRARIES ${FFTW3F_LIBRARIES})
- set(PKG_FFT "fftw3f")
+ set(FFTW fftwf)
endif(GMX_DOUBLE)
-
- if(NOT FFTW3_FOUND AND NOT FFTW3F_FOUND)
- MESSAGE(FATAL_ERROR "Cannot find fftw3 (with correct precision). Fix it, choose another FFT library, or use the Gromacs built-in fftpack (slower)!")
- endif(NOT FFTW3_FOUND AND NOT FFTW3F_FOUND)
+ find_package(FFTW COMPONENTS ${FFTW})
+ string(TOUPPER "${FFTW}" FFTW)
+ set(PKG_FFT "${${FFTW}_PKG}")
+ include_directories(${${FFTW}_INCLUDE_DIRS})
+ set(FFT_LIBRARIES ${${FFTW}_LIBRARIES})
+ if(NOT ${FFTW}_FOUND)
+ MESSAGE(FATAL_ERROR "Cannot find FFTW3 (with correct precision - libfftw3f for single precision GROMACS or libfftw3 for double precision GROMACS). Fix it, choose another FFT library, or use the Gromacs built-in fftpack (slower)!")
+ endif(NOT ${FFTW}_FOUND)
set(GMX_FFT_FFTW3 1)
-elseif(${GMX_FFT_LIBRARY} STREQUAL "FFTW2")
-# MESSAGE(STATUS "Using external FFT library - fftw2")
- if(GMX_DOUBLE)
- find_package(FFTW2 REQUIRED)
- else(GMX_DOUBLE)
- find_package(FFTW2F REQUIRED)
- endif(GMX_DOUBLE)
+ if (NOT ${GMX_CPU_ACCELERATION} STREQUAL "NONE" AND NOT ${FFTW}_HAVE_SIMD)
+ message(WARNING "The fftw library found is compiled without SIMD support, which makes it slow. Consider recompiling it or contact your admin")
+ endif (NOT ${GMX_CPU_ACCELERATION} STREQUAL "NONE" AND NOT ${FFTW}_HAVE_SIMD)
- if(NOT FFTW2_FOUND)
- MESSAGE(FATAL_ERROR "Cannot find fftw2 (with correct precision). Fix it, choose another FFT library, or use the Gromacs built-in fftpack (slower)!")
- endif(NOT FFTW2_FOUND)
- include_directories(${FFTW2_INCLUDE_DIR})
- set(FFT_LIBRARIES ${FFTW2_LIBRARIES})
- set(PKG_FFT_LIBS ${FFTW2_LIBRARIES})
-
- if("${FFTW2_LIBRARIES}" MATCHES "dfftw")
- set(FFTW2_NAME_DFFTW 1)
- elseif("${FFTW2_LIBRARIES}" MATCHES "sfftw")
- set(FFTW2_NAME_SFFTW 1)
- else("${FFTW2_LIBRARIES}" MATCHES "dfftw")
- set(FFTW2_NAME_FFTW 1)
- endif("${FFTW2_LIBRARIES}" MATCHES "dfftw")
-
- set(GMX_FFT_FFTW2 1)
elseif(${GMX_FFT_LIBRARY} STREQUAL "MKL")
# MESSAGE(STATUS "Using external FFT library - Intel MKL")
find_package(MKL REQUIRED)
MESSAGE(STATUS "Using internal FFT library - fftpack")
set(GMX_FFT_FFTPACK 1)
else(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
- MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, fftw2, mkl, acml, fftpack")
+ MESSAGE(FATAL_ERROR "Invalid FFT library setting: ${GMX_FFT_LIBRARY}. Choose one of: fftw3, mkl, fftpack")
endif(${GMX_FFT_LIBRARY} STREQUAL "FFTW3")
+# enable threaded fftw3 if we've found it
+if(FFTW3_THREADS OR FFTW3F_THREADS)
+ add_definitions(-DFFT5D_FFTW_THREADS)
+endif()
+
+set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use external BLAS instead of built-in")
+set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use external LAPACK instead of built-in")
# MKL has BLAS/LAPACK routines
-if(HAVE_MKL OR ACCELERATE_FRAMEWORK)
- set(GMX_EXTERNAL_BLAS TRUE CACHE BOOL "Use external BLAS instead of built-in")
- set(GMX_EXTERNAL_LAPACK TRUE CACHE BOOL "Use external LAPACK instead of built-in")
-else(HAVE_MKL OR ACCELERATE_FRAMEWORK)
- set(GMX_EXTERNAL_BLAS FALSE CACHE BOOL "Use external BLAS instead of built-in")
- set(GMX_EXTERNAL_LAPACK FALSE CACHE BOOL "Use external LAPACK instead of built-in")
+if(NOT HAVE_MKL AND NOT ACCELERATE_FRAMEWORK)
if(GMX_EXTERNAL_BLAS)
- #FindBLAS needs Fortran
- enable_language(Fortran)
if (GMX_BLAS_USER)
list(APPEND GMX_EXTRA_LIBRARIES ${GMX_BLAS_USER})
else(GMX_BLAS_USER)
- find_package(BLAS REQUIRED)
- list(APPEND GMX_EXTRA_LIBRARIES ${BLAS_LIBRARIES})
+ set(BLAS_FIND_QUIETLY ON)
+ find_package(BLAS)
+ if (BLAS_FOUND)
+ list(APPEND GMX_EXTRA_LIBRARIES ${BLAS_LIBRARIES})
+ else()
+ MESSAGE(STATUS "Using internal BLAS library")
+ set(GMX_EXTERNAL_BLAS FALSE CACHE BOOL "Use external BLAS instead of built-in" FORCE)
+ endif()
endif(GMX_BLAS_USER)
endif(GMX_EXTERNAL_BLAS)
if(GMX_EXTERNAL_LAPACK)
- #FindLAPACK needs Fortran
- enable_language(Fortran)
- if (GMX_LAPACK_USER)
+ if (GMX_LAPACK_USER)
list(APPEND GMX_EXTRA_LIBRARIES ${GMX_LAPACK_USER})
- else(GMX_LAPACK_USER)
- find_package(LAPACK REQUIRED)
- list(APPEND GMX_EXTRA_LIBRARIES ${LAPACK_LIBRARIES})
+ else(GMX_LAPACK_USER)
+ set(LAPACK_FIND_QUIETLY ON)
+ find_package(LAPACK)
+ if (LAPACK_FOUND)
+ list(APPEND GMX_EXTRA_LIBRARIES ${LAPACK_LIBRARIES})
+ else()
+ MESSAGE(STATUS "Using internal LAPACK library")
+ set(GMX_EXTERNAL_LAPACK FALSE CACHE BOOL "Use external LAPACK instead of built-in" FORCE)
+ endif()
endif(GMX_LAPACK_USER)
endif(GMX_EXTERNAL_LAPACK)
-endif(HAVE_MKL OR ACCELERATE_FRAMEWORK)
+endif()
mark_as_advanced(GMX_EXTERNAL_LAPACK)
mark_as_advanced(GMX_EXTERNAL_BLAS)
+set(GMX_USE_PLUGINS OFF CACHE INTERNAL "Whether GROMACS will really try to compile support for VMD plugins")
+
+if(GMX_LOAD_PLUGINS)
+ if(CYGWIN OR NOT WIN32)
+ # Native Windows does not have, nor need dlopen
+ # Note that WIN32 is set with Cygwin, but Cygwin needs dlopen to use plug-ins
+ include(gmxTestdlopen)
+ gmx_test_dlopen(HAVE_DLOPEN)
+ endif()
+
+ # 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).")
+ endif()
+ if(NOT GMX_VMD_PLUGIN_PATH)
+ find_package(VMD)
+ endif()
+ set(GMX_USE_PLUGINS ON)
+ list(APPEND GMX_EXTRA_LIBRARIES ${CMAKE_DL_LIBS}) # magic cross-platform pre-set variable for dlopen library
+ set(PKG_DL_LIBS "-l${CMAKE_DL_LIBS}")
+ else()
+ set(PKG_DL_LIBS)
+ endif()
+endif(GMX_LOAD_PLUGINS)
+set(VMD_QUIETLY TRUE CACHE INTERNAL "")
+
+if(EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
+ if(NOT CMAKE_CROSSCOMPILING)
+ option(GMX_BUILD_MANPAGES "Build man pages" ON)
+ else()
+ message(STATUS "Building the man pages is not available when "
+ "cross-compiling the developer version from git")
+ endif()
+else()
+ #make sure source package contains all man pages
+ if(NOT EXISTS "${CMAKE_SOURCE_DIR}/man/man1/ngmx.1")
+ message(FATAL_ERROR "Man pages are missing from source package.")
+ endif()
+endif()
+mark_as_advanced(GMX_BUILD_MANPAGES)
+
# Math and thread libraries must often come after all others when linking...
if(HAVE_LIBM)
list(APPEND GMX_EXTRA_LIBRARIES m)
FORCE)
set(CMAKE_C_FLAGS "${GROMACS_C_FLAGS} ${CMAKE_C_FLAGS}" CACHE STRING
"Flags used by the compiler during all build types" FORCE)
- set(CMAKE_CXX_FLAGS "${GROMACS_CXX_FLAGS} ${CMAKE_CXX_FLAGS}" CACHE STRING
- "Flags used by the compiler during all build types" FORCE)
+ if (CMAKE_CXX_COMPILER_LOADED)
+ set(CMAKE_CXX_FLAGS "${GROMACS_CXX_FLAGS} ${CMAKE_CXX_FLAGS}" CACHE STRING
+ "Flags used by the compiler during all build types" FORCE)
+ endif()
set(CMAKE_EXE_LINKER_FLAGS
"${GROMACS_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS}"
- CACHE STRING "Linker flags" FORCE)
+ CACHE STRING "Linker flags for creating executables" FORCE)
+ set(CMAKE_SHARED_LINKER_FLAGS
+ "${GROMACS_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS}"
+ CACHE STRING "Linker flags for creating shared libraries" FORCE)
endif (NOT DEFINED GROMACS_C_FLAGS_SET)
+if(NOT GMX_OPENMP)
+ #Unset all OpenMP flags in case OpenMP was disabled either by the user
+ #or because it was only partially detected (e.g. only for C but not C++ compiler)
+ unset(OpenMP_C_FLAGS CACHE)
+ unset(OpenMP_CXX_FLAGS CACHE)
+ unset(OpenMP_LINKER_FLAGS CACHE)
+ unset(OpenMP_SHARED_LINKER_FLAGS)
+endif()
+
+######################################
+# Output compiler and CFLAGS used
+######################################
+get_compiler_info(C BUILD_C_COMPILER BUILD_CFLAGS)
+if (CMAKE_CXX_COMPILER_LOADED)
+ get_compiler_info(CXX BUILD_CXX_COMPILER BUILD_CXXFLAGS)
+endif ()
+
########################################################################
# Specify install locations and which subdirectories to process #
########################################################################
-if ( DEFINED GMXLIB )
- set(LIB_INSTALL_DIR "${CMAKE_INSTALL_PREFIX}/${GMXLIB}")
+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(LIB_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib)
+ set(GMX_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}/")
+endif()
+
+if ( NOT DEFINED GMXLIB )
+ set(GMXLIB lib)
endif()
-set(BIN_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/bin)
-set(DATA_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/gromacs)
-set(MAN_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/share/man)
-set(INCL_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/include)
+set(LIB_INSTALL_DIR "${GMX_INSTALL_PREFIX}${GMXLIB}")
+set(BIN_INSTALL_DIR ${GMX_INSTALL_PREFIX}bin)
+set(DATA_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/gromacs)
+set(MAN_INSTALL_DIR ${GMX_INSTALL_PREFIX}share/man)
+set(INCL_INSTALL_DIR ${GMX_INSTALL_PREFIX}include)
set(GMXLIBDIR ${DATA_INSTALL_DIR}/top)
if(NOT CMAKE_SYSTEM_NAME STREQUAL "Darwin")
set(CMAKE_SKIP_BUILD_RPATH FALSE)
set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE)
- set(CMAKE_INSTALL_RPATH "${LIB_INSTALL_DIR}")
+ set(CMAKE_INSTALL_RPATH "\\\$ORIGIN/../${GMXLIB}")
set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
endif()
+#COPYING file: Only necessary for binary distributions.
+#Simpler to always install.
+install(FILES COPYING DESTINATION ${DATA_INSTALL_DIR} COMPONENT data)
+
add_subdirectory(share)
add_subdirectory(include)
-add_subdirectory(man)
add_subdirectory(src)
add_subdirectory(scripts)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff