memory mapped iitii

.gitignore

@@ -1,46 +1,7 @@
-# Prerequisites
-*.d
-
-# Compiled Object files
-*.slo
-*.lo
-*.o
-*.obj
-
-# Precompiled Headers
-*.gch
-*.pch
-
-# Compiled Dynamic libraries
-*.so
-*.dylib
-*.dll
-
-# Fortran module files
-*.mod
-*.smod
-
-# Compiled Static libraries
-*.lai
-*.la
-*.a
-*.lib
-
-# Executables
-*.exe
-*.out
-*.app
-.vscode
-
-# CMake
-CMakeCache.txt
-CMakeFiles
-test/Testing
-test/*.cmake
-test/DartConfiguration.tcl
-test/external
-test/Makefile
-test/test_iitii
-test/gnomad_benchmark
-test/variants.txt
-example
+\#*
+.#*
+*~
+build/
+bin/
+test/
+.gdb_history

CMakeLists.txt

@@ -0,0 +1,120 @@
+# Specify the minimum version for CMake
+
+cmake_minimum_required(VERSION 3.1)
+
+# Project's name
+project(iitii)
+# We build using c++14
+set(CMAKE_CXX_STANDARD 14)
+
+# Use all standard-compliant optimizations
+set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O3 -g")
+set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O3 -g")
+
+if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
+
+  # assumes clang build
+  # we can't reliably detect when we're using clang, so for the time being we assume
+  # TODO: can't we though?
+
+  # adapted from https://stackoverflow.com/questions/46414660/macos-cmake-and-openmp
+  # find_package(OpenMP) does not work reliably on macOS, so we do its work ourselves
+  set (OpenMP_C "${CMAKE_C_COMPILER}")
+  set (OpenMP_C_FLAGS " -Xpreprocessor -fopenmp -I/opt/local/include/libomp -I/usr/local/include -L/opt/local/lib/libomp -L/usr/local/lib")
+  set (OpenMP_C_LIB_NAMES "libomp" "libgomp" "libiomp5")
+  set (OpenMP_CXX "${CMAKE_CXX_COMPILER}")
+  set (OpenMP_CXX_FLAGS " -Xpreprocessor -fopenmp -I/opt/local/include/libomp -I/usr/local/include -L/opt/local/lib/libomp -L/usr/local/lib")
+  set (OpenMP_CXX_LIB_NAMES "libomp" "libgomp" "libiomp5")
+  set (OpenMP_libomp_LIBRARY "omp")
+  set (OpenMP_libgomp_LIBRARY "gomp")
+  set (OpenMP_libiomp5_LIBRARY "iomp5")
+
+  # and now add the OpenMP parameters to the compile flags
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")
+  set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS} -lomp")
+
+elseif (${CMAKE_SYSTEM_NAME} MATCHES "Linux")
+
+  find_package(OpenMP REQUIRED)
+
+  # add the flags it detects to the compile flags
+  set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS} -fopenmp")
+  set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS} -fopenmp")
+  set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
+
+endif()
+
+# Set the output folder where your program will be created
+set(CMAKE_BINARY_DIR ${CMAKE_SOURCE_DIR}/bin)
+set(EXECUTABLE_OUTPUT_PATH ${CMAKE_BINARY_DIR})
+set(LIBRARY_OUTPUT_PATH ${CMAKE_SOURCE_DIR}/lib)
+
+# The following folder will be included
+include_directories("${PROJECT_SOURCE_DIR}")
+
+# Add external projects
+include(${CMAKE_ROOT}/Modules/ExternalProject.cmake)
+
+# TODO: We're using INSTALL_DIR very wrong. We *should* be actually installing
+# the external projects into their prefixes and working with the installed
+# files. Instead we're building but not installing them and trying to work with
+# the non-installed build trees.
+# 
+# Hence the blanked out INSTALL_COMMANDs to suppress the install step.
+#
+# We need to NOT blank out UPDATE_COMMAND or we can never change the Git revision we point to.
+# The cost of this is that we have to re-configure on every build if we do update.
+
+# In-place Parallel Super Scalar Samplesort (IPS⁴o), header only
+ExternalProject_Add(ips4o
+  GIT_REPOSITORY "https://github.com/vgteam/ips4o.git"
+  GIT_TAG "22069381cc1bf2df07ee1ff47f6b6073fcfb4508"
+  UPDATE_COMMAND ""
+  INSTALL_COMMAND ""
+  BUILD_COMMAND ""
+  CONFIGURE_COMMAND "")
+ExternalProject_Get_property(ips4o SOURCE_DIR)
+set(ips4o_INCLUDE "${SOURCE_DIR}")
+
+# taywee's C++ args library, header only
+ExternalProject_Add(tayweeargs
+  GIT_REPOSITORY "https://github.com/Taywee/args.git"
+  GIT_TAG "3de44ec671db452cc0c4ef86399b108939768abb"
+  UPDATE_COMMAND ""
+  INSTALL_COMMAND "")
+ExternalProject_Get_property(tayweeargs SOURCE_DIR)
+set(tayweeargs_INCLUDE "${SOURCE_DIR}")
+
+ExternalProject_Add(mmap_allocator
+  GIT_REPOSITORY "https://github.com/ekg/mmap_allocator.git"
+  GIT_TAG "ed61daf094de1c2e1adbe8306287ad52da5f0264"
+  BUILD_IN_SOURCE TRUE
+  UPDATE_COMMAND ""
+  INSTALL_COMMAND ""
+  BUILD_COMMAND "make"
+  CONFIGURE_COMMAND "")
+ExternalProject_Get_property(mmap_allocator SOURCE_DIR)
+set(mmap_allocator_INCLUDE "${SOURCE_DIR}")
+
+set(CMAKE_BUILD_TYPE Debug)
+
+# set up our target executable and specify its dependencies and includes
+add_executable(iitii
+  ${CMAKE_SOURCE_DIR}/src/main.cpp
+  )
+add_dependencies(iitii ips4o tayweeargs mmap_allocator)
+target_include_directories(iitii PUBLIC
+  "${CMAKE_SOURCE_DIR}/src"
+  "${ips4o_INCLUDE}"
+  "${mmap_allocator_INCLUDE}"
+  "${tayweeargs_INCLUDE}")
+
+target_link_libraries(iitii
+  "${mmap_allocator_INCLUDE}/libmmap_allocator.a"
+  "-latomic")
+
+if (APPLE)
+elseif (TRUE)
+  set(CMAKE_EXE_LINKER_FLAGS "-static")
+endif()