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CMakeLists.txt
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CMakeLists.txt
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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<module>.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_FLUID TRUE) #FLUID is not required for relion
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()