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Commit ddb1bdb6 authored by Pilar Cossio's avatar Pilar Cossio
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removed unnecessary files

parent 00616fca
Pipeline #4750 failed with stage
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CMakeLists.txt deleted 100644 → 0
View file @ 00616fca
cmake_minimum_required(VERSION 2.6)
project(BioEM)
###Set up options
option (USE_CUDA "Build BioEM with CUDA support" OFF)
option (USE_OPENMP "Build BioEM with OpenMP support" ON)
option (USE_MPI "Build BioEM with MPI support" ON)
option (PRINT_CMAKE_VARIABLES "List all CMAKE Variables" OFF)
option (CUDA_FORCE_GCC "Force GCC as host compiler for CUDA part (If standard host compiler is incompatible with CUDA)" ON)
###Set up general variables
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
include_directories(include)
set (BIOEM_ICC_FLAGS "-xHost -O3 -fno-alias -fno-fnalias -unroll -g0 -ipo")
set (BIOEM_GCC_FLAGS "-O3 -march=native -fweb -mfpmath=sse -frename-registers -minline-all-stringops -ftracer -funroll-loops -fpeel-loops -fprefetch-loop-arrays -ffast-math -ggdb")
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_ICC_FLAGS}")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${BIOEM_GCC_FLAGS}")
endif()
set (BIOEM_SOURCE_FILES "bioem.cpp" "main.cpp" "map.cpp" "model.cpp" "param.cpp" "timer.cpp")
###Find Required Packages
find_package(PkgConfig)
if (PKG_CONFIG_FOUND)
pkg_check_modules(FFTW fftw3)
endif()
if (NOT FFTW_FOUND)
find_package(FFTW 3 REQUIRED)
endif()
include_directories(${FFTW_INCLUDE_DIRS})
find_package(Boost 1.43 REQUIRED)
include_directories(${Boost_INCLUDE_DIRS})
###Find Optional Packages
###Find CUDA
set (BIOEM_CUDA_STATUS "Disabled")
if (INCLUDE_CUDA)
set (BIOEM_CUDA_STATUS "Not Found")
find_package(CUDA)
endif()
if (CUDA_FOUND)
if (CUDA_FORCE_GCC)
cmake_minimum_required(VERSION 2.8.10.1)
#Use GCC as host compiler for CUDA even though host compiler for other files is not GCC
set (CUDA_HOST_COMPILER gcc)
endif()
set(CUDA_NVCC_FLAGS "${CUDA_NVCC_FLAGS};--use_fast_math;-ftz=true;-O4;-Xptxas -O4")
# list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_13,code=sm_13")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_20")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_20,code=sm_21")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_30,code=sm_30")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_35,code=sm_35")
list(APPEND CUDA_NVCC_FLAGS "-gencode=arch=compute_52,code=sm_52")
add_definitions(-DWITH_CUDA)
set (BIOEM_CUDA_STATUS "Found")
endif()
###Find OpenMP
set (BIOEM_OPENMP_STATUS "Disabled")
if (INCLUDE_OPENMP)
set (BIOEM_OPENMP_STATUS "Not Found")
find_package(OpenMP)
endif()
if(OPENMP_FOUND)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
add_definitions(-DWITH_OPENMP)
set (BIOEM_OPENMP_STATUS "Found")
endif()
###Find MPI
set (BIOEM_MPI_STATUS "Disabled")
if (INCLUDE_MPI)
set (BIOEM_MPI_STATUS "Not Found")
find_package(MPI)
endif()
if (MPI_FOUND)
include_directories(${MPI_INCLUDE_PATH})
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${MPI_COMPILE_FLAGS} ${MPI_LINK_FLAGS}")
add_definitions(-DWITH_MPI)
set (BIOEM_MPI_STATUS "Found")
endif()
###Build Executable
if (CUDA_FOUND)
set(BIOEM_TMP_CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS})
if (CUDA_FORCE_GCC)
#Hack to use GCC flags for GCC host compiler during NVCC compilation, although host compiler is in fact not GCC for other files
set(CMAKE_CXX_FLAGS ${BIOEM_GCC_FLAGS})
endif()
cuda_add_executable(bioEM ${BIOEM_SOURCE_FILES} bioem_cuda.cu)
set(CMAKE_CXX_FLAGS ${BIOEM_TMP_CMAKE_CXX_FLAGS})
else()
add_executable(bioEM ${BIOEM_SOURCE_FILES})
endif()
#Additional CXX Flags not used by CUDA compiler
#Additional CXX Flags not used by CUDA compiler
if ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11 -Wall -pedantic")
else()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-vla -Wno-long-long -Wall -pedantic")
endif()
###Add Libraries
if (CUDA_FOUND)
cuda_add_cufft_to_target(bioEM)
#set(CUDA_LIBRARIES "/afs/ipp/.cs/cuda/6.5-gtx9/amd64_sles11/lib64/stubs/libcuda.so")
#cuda_add_library()
target_link_libraries(bioEM ${CUDA_CUDA_LIBRARY})
# target_link_libraries(bioEM ${CUDA_LIBRARIES})
endif()
if (FFTWF_LIBRARIES)
target_link_libraries(bioEM ${FFTWF_LIBRARIES})
else()
target_link_libraries(bioEM -L${FFTW_LIBDIR} -lfftw3 -lfftw3f)
endif()
target_link_libraries(bioEM -L${Boost_LIBRARY_DIRS} -lboost_program_options)
if (MPI_FOUND)
target_link_libraries(bioEM ${MPI_LIBRARIES})
endif()
###Show Status
message(STATUS "Build Status")
message(STATUS "FFTW library: ${FFTW_LIBDIR}")
message(STATUS "Boost directory: ${Boost_LIBRARY_DIRS}")
message(STATUS "FFTW includedir: ${FFTW_INCLUDEDIR}")
message(STATUS "CUDA libraries: ${CUDA_CUDA_LIBRARY}")
message(STATUS "CUDART libraries: ${CUDA_LIBRARIES}")
message(STATUS "CUDA: ${BIOEM_CUDA_STATUS}")
message(STATUS "OpenMP: ${BIOEM_OPENMP_STATUS}")
message(STATUS "MPI: ${BIOEM_MPI_STATUS}")
if (PRINT_CMAKE_VARIABLES)
get_cmake_property(_variableNames VARIABLES)
foreach (_variableName ${_variableNames})
message(STATUS "${_variableName}=${${_variableName}}")
endforeach()
endif()
Manual/CTF_PSF_Manual.eps deleted 100644 → 0
View file @ 00616fca
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/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef/.notdef
<