to remove sensitive data

hael · Nov 16, 2020 · 31403cf · 31403cf
commit 31403cf
Show file tree

Hide file tree

Showing 764 changed files with 885,577 additions and 0 deletions.
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,43 @@
+*.[oa]
+*.oo
+*.mod
+*~
+fort.*
+*.spi
+*.dat
+*.img
+*.hed
+*.mrc
+*.bin
+*.log
+*.swp
+.emanlog
+.DS_Store
+SIMPLE_UNIT*
+*.hed
+*.spi
+Makefile_macros
+junk*
+*.dSYM
+bin/
+lib/
+build*
+obj/
+add2.bashrc
+add2.tcshrc
+simple_user_input.pm
+doc/html/
+# Latex derived
+*.dvi
+*.ps
+*.spl
+*.bbl
+*.blg
+*.aux
+*.out
+*.pdf
+*.synctex.gz
+*.toc
+*.orig
+/node_modules
+/dist
diff --git a/CMakeFiles/cmake.check_cache b/CMakeFiles/cmake.check_cache
@@ -0,0 +1 @@
+# This file is generated by cmake for dependency checking of the CMakeCache.txt file
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -0,0 +1,267 @@
+cmake_minimum_required(VERSION 3.2 FATAL_ERROR)
+set(CMAKE_MODULE_PATH "${CMAKE_SOURCE_DIR}/cmake" "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+include(FortranOverride)
+project(SIMPLE Fortran)
+
+set(PROJECT_BRIEF "SIMPLE is a program package for cryo-EM image processing (https://simplecryoem.com)")
+
+#################################################################
+#
+# VERSION
+#
+#################################################################
+set(SIMPLE_VERSION_MAJOR 3)
+set(SIMPLE_VERSION_MINOR 0)
+set(SIMPLE_VERSION_PATCH 0)
+set(SIMPLE_VERSION "${SIMPLE_VERSION_MAJOR}.${SIMPLE_VERSION_MINOR}.${SIMPLE_VERSION_PATCH}")
+
+#################################################################
+#
+# OPTIONS
+#
+#################################################################
+option(USE_OPENMP  "Use OpenMP for parallelization - debugging may disable OpemMP" ON )
+option(USE_MPI     "Use OpenMPI for parallelization - in developement" OFF )
+option(USE_OPENACC "Use OpenACC for auto GPU parallelization - debugging may disable OpenMP" OFF)
+option(USE_CUDA    "GPU NVIDIA - in development" OFF)
+option(USE_LIBTIFF "Use libtiff" ON)
+option(${PROJECT_NAME}_BUILD_TESTS "Build the test examples" ON)
+option(BUILD_SHARED_LIBS "Build the simple library as shared or static (default)" OFF)
+option(BUILD_DOCS "Enable the generation of PDF manuals and doxygen API documentation" OFF)
+option(USE_SYSTEM_JPEG_SQLite "Compile libjpeg9 and sqlite3 from source (default) or use system libraries." OFF)
+option(GUI "Install the GUI" ON)
+# We probably don't want these to run on every build.
+option(COVERALLS "Generate coveralls data" OFF) #coveralls.io
+OPTION(USE_CODE_COVERAGE "Added code coverage flags" OFF)
+OPTION(USE_PROFILING "enable symbol generation without debug support" OFF)
+option(USE_LINK_TIME_OPTIMISATION "Enable link-time optimisation" OFF)
+
+#################################################################
+#
+# SET default flags
+#
+#################################################################
+# Add our local modules to the module path
+#set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules/")
+
+set(EXTRA_LIBS "")
+set(NUM_JOBS 1)
+include(ProcessorCount)
+ProcessorCount(NUM_JOBS)
+
+set(BUILD_NAME "${CMAKE_Fortran_COMPILER_ID}_${CMAKE_BUILD_TYPE}" CACHE STRING "Build name with compiler, type and FFT backend ")
+set(CMAKE_Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
+
+############################################################
+# Define the main targets
+############################################################
+# Have the .mod files placed in the lib folder
+include_directories(${CMAKE_Fortran_MODULE_DIRECTORY})
+set(EXECUTABLE_OUTPUT_DIRECTORY "${CMAKE_INSTALL_BINDIR}")
+set(LIBRARY_OUTPUT_DIRECTORY "${CMAKE_INSTALL_LIBDIR}")
+set(SCRIPTS_OUTPUT_DIRECTORY "${CMAKE_INSTALL_PREFIX}/scripts")
+
+# Define the executable names
+set(SIMPLE_EXE simple_exec)
+set(SINGLE_EXE single_exec)
+set(SIMPLE_PRIVATE_EXE simple_private_exec)
+set(QUANT_EXE quant_exec)
+# Define the library name lib<name>.so
+set(SIMPLELIB "SIMPLE${${PROJECT_NAME}_VERSION}")
+
+# Define some directories
+include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src/inc)
+include_directories(${CMAKE_BINARY_DIR}/lib/simple)
+include_directories(${CMAKE_CURRENT_BINARY_DIR})
+
+#################################################################
+# INCLUDES
+#################################################################
+# include(CMakeAddFortranSubdirectory)
+include(CheckIncludeFiles)
+include(SimpleFortranOptions)
+
+############################################################
+#
+# Add definition macros unique to compilation
+#
+############################################################
+add_definitions("-DBUILD_NAME=\"${BUILD_NAME}\"")
+add_definitions(" -D__FILENAME__='\"$(notdir $<)\"' ")
+# use _DEBUG since DEBUG or debug is used as a variable in some files
+# _DEBUG is defined by Intel Fortran on Windows
+if(CMAKE_BUILD_TYPE STREQUAL "DEBUG")
+  add_definitions("-D_DEBUG")
+endif()
+
+
+#   cmake_add_fortran_subdirectory(
+#    ${SRC}                  # name of subdirectory
+#    PROJECT libSIMPLE       # project name in subdir top CMakeLists.txt
+#    ARCHIVE_DIR ${LIB}      # dir where project places .lib files
+#    RUNTIME_DIR ${LIB}      # dir where project places .dll files
+#    LIBRARIES <lib>         # names of library targets to import
+#    LINK_LIBRARIES          # link interface libraries for LIBRARIES
+#     [LINK_LIBS ${FFTW_LIBRARIES} <dep>...]...
+#    CMAKE_COMMAND_LINE ...  # extra command line flags to pass to cmake
+#    NO_EXTERNAL_INSTALL     # skip installation of external project
+#    )
+
+
+#################################################################
+#
+# CREATE libSIMPLE<VERSION>
+#
+#################################################################
+add_subdirectory(src lib)
+list(APPEND EXTRA_LIBS
+  ${SIMPLELIB}
+  ${CMAKE_THREAD_LIBS_INIT}
+  ${EXTRA_LIBS})
+link_directories(lib)
+message(STATUS " EXTRA_LIBS  ${EXTRA_LIBS}")
+
+
+#################################################################
+#
+# ADD SCRIPTS
+#
+#################################################################
+# The script folder contains some handy perl scripts for running SIMPLE
+add_subdirectory(scripts)
+
+
+#################################################################
+#
+# INSTALL GUI
+#
+#################################################################
+if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/gui)
+  add_subdirectory(gui ${CMAKE_INSTALL_BINDIR}/gui)
+endif()
+
+
+
+#################################################################
+#
+# STATIC LIBRARIES
+#
+#################################################################
+# Try to search first static libraries
+if(NOT ${BUILD_SHARED_LIBS})
+  set(CMAKE_FIND_LIBRARY_SUFFIXES "${CMAKE_FIND_LIBRARY_SUFFIXES} .a")
+endif()
+
+#################################################################
+#
+# Add a distclean target to the Makefile
+#
+#################################################################
+add_custom_target(distclean
+  COMMAND ${CMAKE_COMMAND} -P ${CMAKE_SOURCE_DIR}/cmake/distclean.cmake
+  )
+
+# here we save a version file
+set(VERSION_FILE "${CMAKE_INSTALL_LIBDIR}/simple/CMake/${PROJECT_NAME}ConfigVersion.cmake")
+configure_file( "${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules/ProjectConfigVersion.cmake.in" ${VERSION_FILE} @ONLY )
+
+# modules / depends
+FILE(GLOB_RECURSE SIMPLE_CMAKE_FILES
+  LIST_DIRECTORIES false
+  RELATIVE ${CMAKE_SOURCE_DIR} "*.cmake" )
+list(REMOVE_DUPLICATES SIMPLE_CMAKE_FILES)
+INSTALL(
+  FILES ${SIMPLE_CMAKE_FILES}
+  DESTINATION "${CMAKE_INSTALL_LIBDIR}/simple/CMake"
+  CONFIGURATIONS DEBUG
+  COMPONENT dev)
+
+message( STATUS "Set runtime variables ")
+if(NOT BUILD_SHARED_LIBS)
+  configure_file( "${CMAKE_CURRENT_SOURCE_DIR}/scripts/add2.bashrc.template"  ${CMAKE_CURRENT_BINARY_DIR}/add2.bashrc @ONLY )
+  configure_file( "${CMAKE_CURRENT_SOURCE_DIR}/scripts/add2.tcshrc.template"  ${CMAKE_CURRENT_BINARY_DIR}/add2.tcshrc @ONLY )
+else()
+  configure_file( "${CMAKE_CURRENT_SOURCE_DIR}/scripts/add2.bashrc.sharedtemplate"  ${CMAKE_CURRENT_BINARY_DIR}/add2.bashrc @ONLY )
+  configure_file( "${CMAKE_CURRENT_SOURCE_DIR}/scripts/add2.tcshrc.sharedtemplate"  ${CMAKE_CURRENT_BINARY_DIR}/add2.tcshrc @ONLY )
+endif()
+install(FILES  ${CMAKE_CURRENT_BINARY_DIR}/add2.bashrc ${CMAKE_CURRENT_BINARY_DIR}/add2.tcshrc
+  DESTINATION ${CMAKE_INSTALL_PREFIX}
+  CONFIGURATIONS DEBUG|RELEASE
+  PERMISSIONS   OWNER_READ OWNER_WRITE GROUP_READ GROUP_WRITE WORLD_READ WORLD_WRITE
+  )
+
+if(${BUILD_DOCS})
+
+  #
+  # User manual and tutorial
+  #
+  add_subdirectory(doc)
+
+  #
+  # Doxygen
+  #
+  option(ENABLE_DOXYGEN "Enable a 'make docs' target for Doxygen documentation" ON)
+  if (ENABLE_DOXYGEN)
+    add_custom_target(doc
+      ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile
+      WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+      COMMENT "Generating API documentation with Doxygen" VERBATIM
+      )
+    include(UseDoxygen OPTIONAL)
+    # add_doxygen(
+    #     docs
+    #     INPUT
+    #         "${CMAKE_SOURCE_DIR}/src"
+    #     STRIP_FROM_PATH
+    #         "${CMAKE_SOURCE_DIR}/src/inc"
+    #     STRIP_FROM_INC_PATH
+    #         "${CMAKE_SOURCE_DIR}/src/inc"
+    #     EXCLUDE_PATTERNS
+    #         */gnufor2/*
+    #     EXCLUDE_SYMBOLS
+    #         *debug*
+    #         *verbose*
+    #     ALL
+    # )
+  endif()
+endif()
+
+
+if(VERBOSE) #only for the fool-hardy
+  OPTION(USE_FAST_MATH_OPTIMISATION "Optimize code for fastmath. " OFF)
+  OPTION(USE_PROFILE_OPTIMISATION "Optimize code for PFO. (GNU: -fpfo )" OFF)
+  OPTION(USE_AUTO_PARALLELISE "Optimize code for parallel systems. [Intel and PGI only]" OFF)
+  OPTION(USE_AGGRESSIVE_OPTIMISATION "Flags for aggressive optimization level. Unroll all loops and inline functions."  OFF)
+  option(CPACK_GENERATOR "Enable build of distribution packages using CPack" TGZ)
+
+  #
+  # CPack
+  #
+  option(CPACK_GENERATOR "Enable build of distribution packages using CPack" OFF)
+  include(SimplePackage)
+  ## Debugging CMAKE
+  include(CMakeGraphVizOptions)
+endif()
+
+#################################################################
+# CTest
+#################################################################
+enable_testing()
+# emulate GNU Autotools `make check`
+add_custom_target(check COMMAND ${CMAKE_CTEST_COMMAND})
+
+#################################################################
+#
+# ADD PRODUCTION EXECUTABLES
+#
+#################################################################
+# The source for the SIMPLE binary and have it placed in the bin folder
+add_subdirectory(production bin)
+
+#only for debugging
+if(VERBOSE)
+  include(GenericLogging)
+endif()
+
+# Add message at end of installation
+add_subdirectory(${CMAKE_SOURCE_DIR}/cmake/PostInstall)