cmake_minimum_required(VERSION 2.8 FATAL_ERROR) #if(POLICY CMP0048) # cmake_policy(SET CMP0048 NEW) #endif() project(Relion) # Use new policy for OS X @rpath if(POLICY CMP0042) cmake_policy(SET CMP0042 NEW) endif() # Add the path to the additional Find.cmake files # which are included with the distributed RLEION-code list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake) add_definitions(-DINSTALL_LIBRARY_DIR=${CMAKE_INSTALL_PREFIX}/lib/) add_definitions(-DSOURCE_DIR=${CMAKE_SOURCE_DIR}/src/) if(MDT_TYPE_CHECK) message(" DEVELOPER MODE: MetaDataTable type check is enabled.") add_definitions(-DMETADATA_TABLE_TYPE_CHECK) endif() # message(STATUS "INSTALL_LIBRARY_DIR set to ${CMAKE_INSTALL_PREFIX}/lib/") # message(STATUS "SOURCE_DIR set to ${CMAKE_SOURCE_DIR}/src/") # ------------------------------------------------------------------RPATH SETTINGS-- if(NOT APPLE) # use, i.e. don't skip the full RPATH for the build tree SET(CMAKE_SKIP_BUILD_RPATH FALSE) # when building, don't use the install RPATH already # (but later on when installing) SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") # add the automatically determined parts of the RPATH # which point to directories outside the build tree to the install RPATH SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) # the RPATH to be used when installing, but only if it's not a system directory LIST(FIND CMAKE_PLATFORM_IMPLICIT_LINK_DIRECTORIES "${CMAKE_INSTALL_PREFIX}/lib" isSystemDir) IF("${isSystemDir}" STREQUAL "-1") SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") ENDIF("${isSystemDir}" STREQUAL "-1") endif(NOT APPLE) # ---------------------------------------------------------SET SPECIFIC BUILD TYPE-- if(NOT ${CMAKE_BUILD_TYPE} STREQUAL "") string( TOLOWER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_LOWER ) if( ( NOT ${CMAKE_BUILD_TYPE_LOWER} STREQUAL "none" ) AND ( NOT ${CMAKE_BUILD_TYPE_LOWER} STREQUAL "release" ) AND ( NOT ${CMAKE_BUILD_TYPE_LOWER} STREQUAL "debug" ) AND ( NOT ${CMAKE_BUILD_TYPE_LOWER} STREQUAL "relwithdebinfo" ) AND ( NOT ${CMAKE_BUILD_TYPE_LOWER} STREQUAL "profiling" ) AND ( NOT ${CMAKE_BUILD_TYPE_LOWER} STREQUAL "benchmarking" ) ) message( FATAL_ERROR "CMAKE_BUILD_TYPE : '${CMAKE_BUILD_TYPE}' is not a valid build type. " "Valid options are: 'None', 'Release', 'Debug', 'RelWithDebInfo', and 'Profiling'." ) endif() message(STATUS "BUILD TYPE set to '${CMAKE_BUILD_TYPE}'") SET(CMAKE_BUILD_TYPE ${CMAKE_BUILD_TYPE} CACHE STRING "Choose the type of build, options are: 'None', 'Release', 'Debug', 'RelWithDebInfo', and 'Profiling'.") else() SET(CMAKE_BUILD_TYPE "Release") message(STATUS "BUILD TYPE set to the default type: '${CMAKE_BUILD_TYPE}'") string( TOLOWER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_LOWER ) endif() # ------------------OPTIONS WHICH ARE NEEDED TO SET BUILD-TYPES (COMPILATION FLAGS)-- # ------------------------------------------------------------------------CUDA-ARCH-- if(NOT DEFINED CUDA_ARCH) message(STATUS "Setting fallback CUDA_ARCH=35") set(CUDARCH "-arch=sm_35") else(NOT DEFINED CUDA_ARCH) message(STATUS "Using provided CUDA_ARCH=${CUDA_ARCH}") set(CUDARCH "-arch=sm_${CUDA_ARCH}") endif(NOT DEFINED CUDA_ARCH) # -------------------------------------------------------------------FURTHER OPTIONS-- # CUDA on by default, so check for CPU-accelration request and possible conflicting dual-request option(ALTCPU "Enable Accelerated CPU version" OFF) if(ALTCPU) option(CUDA "Enable CUDA GPU acceleration" OFF) if(ALTCPU AND CUDA) message(FATAL_ERROR "You cannot build with both CUDA=ON and ALTCPU=ON. Please choose one and rerun CMAKE") endif() else() option(CUDA "Enable CUDA GPU acceleration" ON) endif() option(DoublePrec_CPU "DoublePrec_CPU" ON) option(DoublePrec_ACC "Accelerated Code use double-precision" OFF) option(MKLFFT "Use MKL rather than FFTW for FFT" OFF) option(CudaTexture "CudaTexture" ON) option(ALLOW_CTF_IN_SAGD "Allow CTF-modulation in SAGD, as specified in Claim 1 of patent US10,282,513B2" ON) if(ALLOW_CTF_IN_SAGD) message(STATUS "ALLOW_CTF_IN_SAGD enabled - This build of RELION allows modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2") else() message(STATUS "ALLOW_CTF_IN_SAGD disabled - This build of RELION does not allow modulation of particle images by a contrast transfer function inside stochastic average gradient descent, as specified in Claim 1 of patent US10,282,513B2") endif() if(ALTCPU) message(STATUS "ALTCPU enabled - Building CPU-accelerated version of RELION") endif() if(CUDA) message(STATUS "CUDA enabled - Building CUDA-accelerated version of RELION") endif() if(CUDA OR ALTCPU) add_definitions(-DACC_CUDA=2 -DACC_CPU=1) endif() # -----------------------------------------------DOUBLE PRECISION (CUDA-CODE) OR NOT-- if(DoublePrec_CPU) message(STATUS "Setting cpu precision to double") else(DoublePrec_CPU) message(STATUS "Setting cpu precision to single") add_definitions(-DRELION_SINGLE_PRECISION) endif(DoublePrec_CPU) if(DoublePrec_ACC) message(STATUS "Setting accelerated code precision to double") add_definitions(-DACC_DOUBLE_PRECISION) set(CudaTexture FALSE) else(DoublePrec_ACC) message(STATUS "Setting accelerated code precision to single") endif(DoublePrec_ACC) # ----------------------------------------------------------INCLUDE ALL BUILD TYPES-- #This *has* to be AFTER project() include(${CMAKE_SOURCE_DIR}/cmake/BuildTypes.cmake) if(CUDA) # -----------------------------------------------------------------------------CUDA-- # DOC: http://www.cmake.org/cmake/help/v3.0/module/FindCUDA.html FIND_PACKAGE(CUDA) endif() if(CUDA_FOUND) message(STATUS "Using cuda wrapper to compile....") if( (NOT ${CUDA_VERSION} VERSION_LESS "7.5") AND (NOT DoublePrec_ACC) ) message(STATUS "Cuda version is >= 7.5 and single-precision build, enable double usage warning.") set(WARN_DBL "--ptxas-options=-warn-double-usage") # cuda>=7.5 elseif( ${CUDA_VERSION} VERSION_LESS "7.0") message(WARNING "Cuda version is less than 7.0, so relion will be compiled without GPU support.") set(CUDA OFF) endif() if(CUDA) add_definitions(-DCUDA) endif() else(CUDA_FOUND) message(STATUS "Using non-cuda compilation....") endif(CUDA_FOUND) # ------------------------------------------------------------------ALLOCATOR CHOICE-- option(CachedAlloc "CachedAlloc" ON) if(NOT CachedAlloc) add_definitions(-DCUDA_NO_CUSTOM_ALLOCATION) message(STATUS "Cached allocation is disabled.") endif(NOT CachedAlloc) option(CustomAllocMemGuards "CustomAllocMemGuards" OFF) if(CustomAllocMemGuards) add_definitions(-DCUSTOM_ALLOCATOR_MEMGUARD) message(STATUS "Abort on out of bound write.") endif(CustomAllocMemGuards) # -------------------------------------------------------------FORCE USE OF STL-LIBS-- option(CudaForceSTL "CudaForceSTL" OFF) if(CudaForceSTL) add_definitions(-DCUDA_FORCESTL) message(STATUS "Building cuda files wusing stl-libs for sort, min and max.") endif(CudaForceSTL) # ------------------------------------------------------------------------GUI OR NOT-- # Skip FLTK/X11-dependent binaries or not option(GUI "GUI" ON) if(NOT GUI) message(STATUS "Omitting GUI targets as per your request") endif() # ---------------------------------------------------------------------------TBB -- option(FORCE_OWN_TBB "FORCE_OWN_TBB" OFF) if (ALTCPU) if (FORCE_OWN_TBB) message(STATUS "Will ignore any potentially installed system TBB lib, as per your request.") include(${CMAKE_SOURCE_DIR}/cmake/BuildTBB.cmake) set(INSTALL_OWN_TBB 1) else(FORCE_OWN_TBB) find_package(TBB) if(TBB_FOUND) include_directories("${TBB_INCLUDE_DIRS}") message(STATUS "TBB_FOUND : ${TBB_FOUND}") message(STATUS "TBB_INCLUDE_DIRS : ${TBB_INCLUDE_DIRS}") message(STATUS "TBB_VERSION : ${TBB_VERSION}") message(STATUS "TBB_LIBRARIES : ${TBB_LIBRARIES}") else(TBB_FOUND) include(${CMAKE_SOURCE_DIR}/cmake/BuildTBB.cmake) set(INSTALL_OWN_TBB 1) endif(TBB_FOUND) endif(FORCE_OWN_TBB) endif(ALTCPU) # -------------------------------------------------------------------------------MPI-- find_package(MPI REQUIRED) if ("${MPI_CXX_INCLUDE_DIRS}" STREQUAL "") include_directories("${MPI_CXX_INCLUDE_PATH}") else() include_directories("${MPI_CXX_INCLUDE_DIRS}") endif() message(STATUS "MPI_INCLUDE_PATH : ${MPI_INCLUDE_PATH}") message(STATUS "MPI_LIBRARIES : ${MPI_LIBRARIES}") message(STATUS "MPI_CXX_INCLUDE_PATH : ${MPI_CXX_INCLUDE_PATH}") message(STATUS "MPI_CXX_LIBRARIES : ${MPI_CXX_LIBRARIES}") message(STATUS "CMAKE_C_COMPILER : ${CMAKE_C_COMPILER}") message(STATUS "CMAKE_CXX_COMPILER : ${CMAKE_CXX_COMPILER}") message(STATUS "MPI_C_COMPILER : ${MPI_C_COMPILER}") message(STATUS "MPI_CXX_COMPILER : ${MPI_CXX_COMPILER}") SET(CMAKE_C_COMPILER ${MPI_C_COMPILER}) SET(CMAKE_CXX_COMPILER ${MPI_CXX_COMPILER}) 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) # ----------------------------------------------------------Intel Compiler support -- # ---------------------------------- and build flags including MKL and TBB --------- message(STATUS "CMAKE_CXX_COMPILER_ID : ${CMAKE_CXX_COMPILER_ID}") if(MKLFFT) if (NOT "$ENV{MKLROOT}" STREQUAL "") include_directories("$ENV{MKLROOT}/include/fftw") message(STATUS "MKL FFTW wrapper header files: $ENV{MKLROOT}/include/fftw") else() message("COMPILATION MAY FAIL since no MKL FFTW wrapper header files could be found. Please make sure the MKLROOT environmental variable is set.") endif() add_definitions(-DMKLFFT) endif(MKLFFT) if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Intel" OR "${CMAKE_CXX_COMPILER}" MATCHES "icpx") # "Intel" is for classic Intel compiler and "IntelLLVM" is for oneAPI compiler which is supported from CMake 3.20 if(MKLFFT) if("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel") SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -qopenmp -mkl=parallel -limf ") else() # Intel oneAPI compiler SET(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fiopenmp -mkl=parallel -limf ") endif() endif(MKLFFT) if(ALTCPU) add_definitions(-DFAST_CENTERFFT) endif() else() if(MKLFFT) # For the time being, let's use the sequential version (as with FFTW) link_directories("$ENV{MKLROOT}/lib/intel64") SET(FFTW_LIBRARIES mkl_intel_lp64 mkl_sequential mkl_core) endif(MKLFFT) endif() if(ALTCPU) add_definitions(-DALTCPU) endif() if(ALLOW_CTF_IN_SAGD) add_definitions(-DALLOW_CTF_IN_SGD) endif() # ---------------------------------------------------------------USE TEXTURES OR NOT-- if(NOT CudaTexture OR ALTCPU) add_definitions(-DPROJECTOR_NO_TEXTURES) message(STATUS "Texture interpolation is omitted.") endif(NOT CudaTexture OR ALTCPU) # --------------------------------------------------------------------------X11/FLTK-- option(FORCE_OWN_FLTK "FORCE_OWN_FLTK" OFF) FIND_PACKAGE(X11) if(GUI) if(X11_FOUND) set(FLTK_SKIP_OPENGL TRUE) #OpenGL is not required for relion if(NOT FORCE_OWN_FLTK) FIND_PACKAGE(FLTK) if(FLTK_FOUND) message(STATUS "X11 and FLTK were found") message(STATUS "FLTK_LIBRARIES: ${FLTK_LIBRARIES}") else() message(STATUS "No FLTK installation was found") endif() endif(NOT FORCE_OWN_FLTK) if(NOT FLTK_FOUND) include(${CMAKE_SOURCE_DIR}/cmake/BuildFLTK.cmake) set(INSTALL_OWN_FLTK 1) endif(NOT FLTK_FOUND) else(X11_FOUND) message( STATUS "\n-- ------------------ YOU HAVE NO X11-LIBS ------------------") message( STATUS "CCmake found no X11-libs on your system, which are required for the GUI.") message( STATUS " You CAN add the flag -DGUI=OFF to avoid using X11" ) message(FATAL_ERROR "X11 is required for GUI.") endif(X11_FOUND) endif(GUI) # -------------------------------------------------------------------------------FFT-- if(NOT MKLFFT) option(FORCE_OWN_FFTW "FORCE_OWN_FFTW" OFF) option(AMDFFTW "Use AMD optimized version of FFTW. This needs a new version of GCC (>= 8.3 recommended)." OFF) set(FFTW_DOUBLE_REQUIRED TRUE) set(FFTW_SINGLE_REQUIRED TRUE) if(AMDFFTW) set(FORCE_OWN_FFTW ON) endif() if(NOT FORCE_OWN_FFTW) FIND_PACKAGE(FFTW COMPONENTS SINGLE DOUBLE) endif(NOT FORCE_OWN_FFTW) if(NOT FFTW_FOUND) include(${CMAKE_SOURCE_DIR}/cmake/BuildFFTW.cmake) endif(NOT FFTW_FOUND) endif(NOT MKLFFT) # ---------------------------------------------------------------------------SIN/COS-- include(CheckCXXSymbolExists) check_cxx_symbol_exists(sincos math.h HAVE_SINCOS) check_cxx_symbol_exists(__sincos math.h HAVE___SINCOS) if(HAVE_SINCOS) add_definitions(-DHAVE_SINCOS) endif() if(HAVE___SINCOS) add_definitions(-DHAVE___SINCOS) endif() # ------------------------------------------------------------------------------TIFF-- find_package(TIFF REQUIRED) if(TIFF_FOUND) add_definitions(-DHAVE_TIFF) endif() find_package(ZLIB) find_package(PNG) if(PNG_FOUND) add_definitions(-DHAVE_PNG) endif() # ----------------------------------------------------------------------COPY SCRIPTS-- if(FORCE_OWN_FFTW) install(DIRECTORY external/fftw/lib/ DESTINATION lib FILES_MATCHING PATTERN "*") endif() list(APPEND RELION_SCRIPT_FILES star_printtable star_plottable star_loopheader star_datablock_stack star_datablock_singlefiles star_datablock_ctfdat qsub.csh) add_custom_target(copy_scripts ALL) foreach (SCRIPT_FILE ${RELION_SCRIPT_FILES}) add_custom_command(TARGET copy_scripts POST_BUILD COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_SOURCE_DIR}/scripts/${SCRIPT_FILE} ${CMAKE_BINARY_DIR}/bin/relion_${SCRIPT_FILE} ) endforeach() install( DIRECTORY ${CMAKE_BINARY_DIR}/bin DESTINATION ${CMAKE_INSTALL_PREFIX} USE_SOURCE_PERMISSIONS FILES_MATCHING PATTERN "*") # install fltk if we built our own version if(INSTALL_OWN_FLTK) install(DIRECTORY external/fltk/lib/ DESTINATION lib FILES_MATCHING PATTERN "*") endif() # -----------------------------------------------------------------RELION COMPONENTS-- option(BUILD_SHARED_LIBS "BUILD_SHARED_LIBS" OFF) message("BUILD_SHARED_LIBS = ${BUILD_SHARED_LIBS}") if(BUILD_SHARED_LIBS) message(STATUS "Building shared libs (smaller build size and binaries)") else() message(STATUS "Building static libs (larger build size and binaries)") endif() ADD_SUBDIRECTORY(src/apps) #message(STATUS "CUDA option = ${CUDA}") #message(STATUS "ALTCPU option = ${ALTCPU}") #message(STATUS "ALLOW_CTF_IN_SAGD option = ${ALLOW_CTF_IN_SAGD}") #message(STATUS "DoublePrec_CPU option = ${DoublePrec_CPU}") #message(STATUS "DoublePrec_ACC option = ${DoublePrec_ACC}") #message(STATUS "MKLFFT option = ${MKLFFT}") #message(STATUS "CudaTexture option = ${CudaTexture}") #get_directory_property( DirDefs COMPILE_DEFINITIONS ) #message(STATUS "COMPILE_DEFINITIONS = ${DirDefs}" ) #message(STATUS "CMAKE_C_FLAGS : ${CMAKE_C_FLAGS}") #message(STATUS "CMAKE_CXX_FLAGS : ${CMAKE_CXX_FLAGS}") #message(STATUS "CMAKE_C_COMPILER : ${CMAKE_C_COMPILER}") #message(STATUS "CMAKE_CXX_COMPILER : ${CMAKE_CXX_COMPILER}") #message(STATUS "MPI_C_COMPILER : ${MPI_C_COMPILER}") #message(STATUS "MPI_CXX_COMPILER : ${MPI_CXX_COMPILER}") #message(STATUS "CMAKE_EXE_LINKER_FLAGS : ${CMAKE_EXE_LINKER_FLAGS}") # -----------------------------------------------------------------------------TESTS-- # Include testing flag(s) as precomiler # definitions and include test directives #enable_testing() #include(${CMAKE_SOURCE_DIR}/tests/RelionTests.cmake) option(BUILD_TESTS "Build and configure tests" OFF) if(BUILD_TESTS) include(CTest) add_subdirectory(tests) endif() # ----------------------------------------------------------PRINT OUT ALL CMAKE VARS-- #get_cmake_property(_variableNames VARIABLES) #foreach (_variableName ${_variableNames}) # message(STATUS "${_variableName}=${${_variableName}}") #endforeach()