Merge pull request #299 from LLNL/release/v0.27

Release/v0.27

.gitlab-ci.yml

@@ -37,7 +37,7 @@ install_boost:
  script:
  - echo "=== build section ==="
  - module load gcc/${GCC_VERSION}
- - spack load boost@${BOOST_VERSION} arch=$(spack arch)
+ - spack load --first boost@${BOOST_VERSION} arch=$(spack arch)
  - export METALL_TEST_DIR="/dev/shm/metall_test-${CI_CONCURRENT_ID}-${CI_PIPELINE_IID}"
  - srun -N1 -ppdebug bash ./scripts/CI/build_and_test.sh
 

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.12)
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 include(FetchContent)
 
@@ -17,7 +17,7 @@ endif()
 # Metall general configuration
 # -------------------------------------------------------------------------------- #
 project(Metall
- VERSION 0.26
+ VERSION 0.27
  DESCRIPTION "A persistent memory allocator for data-centric analytics"
  HOMEPAGE_URL "https://github.com/LLNL/metall")
 
@@ -82,33 +82,20 @@ option(JUST_INSTALL_METALL_HEADER "Just install Metall header files (do not buil
 option(BUILD_UTILITY "Build utility programs" OFF)
 option(BUILD_DOC "Build API documentation" OFF)
 option(BUILD_C "Build C examples and libraries" OFF)
-option(VERBOSE_SYSTEM_SUPPORT_WARNING "Show compile time warning regarding system support" OFF)
-option(DISABLE_FREE_FILE_SPACE "Disable freeing file space" OFF)
-option(DISABLE_SMALL_OBJECT_CACHE "Disable small object cache" OFF)
 option(BUILD_EXAMPLE "Build the examples" OFF)
-option(BUILD_BENCH "Build the benchmark" OFF)
 option(BUILD_TEST "Build the test" OFF)
 option(RUN_LARGE_SCALE_TEST "Run large scale tests" OFF)
 option(RUN_BUILD_AND_TEST_WITH_CI "Perform build and basic test with CI" OFF)
-option(BUILD_VERIFICATION "Build verification directory" OFF)
-option(USE_SORTED_BIN "Use VM space aware algorithm in the bin directory" OFF)
-
-set(DEFAULT_VM_RESERVE_SIZE "0" CACHE STRING
- "Set the default VM reserve size (use the internally defined value if 0 is specified)")
-set(MAX_SEGMENT_SIZE "0" CACHE STRING
- "Set the max segment size (use the internally defined value if 0 is specified)")
-set(INITIAL_SEGMENT_SIZE "0" CACHE STRING
- "Set the initial segment size (use the internally defined value if 0 is specified)")
+option(BUILD_BENCH "Build the benchmark" OFF)
+option(BUILD_VERIFICATION "Build verification programs" OFF)
+set(COMPILER_DEFS "" CACHE STRING "A list of Metall compile definitions to be added to all targets")
 
 # ---------- Experimental options ---------- #
-option(USE_ANONYMOUS_NEW_MAP "Use the anonymous map when creating a new map region" OFF)
 set(UMAP_ROOT "" CACHE PATH "UMap installed root directory")
 
 option(ONLY_DOWNLOAD_GTEST "Only downloading Google Test" OFF)
 option(SKIP_DOWNLOAD_GTEST "Skip downloading Google Test" OFF)
 option(BUILD_NUMA "Build programs that require the NUMA policy library (numa.h)" OFF)
-set(FREE_SMALL_OBJECT_SIZE_HINT "0" CACHE STRING
- "Try to free the associated pages and file space when objects equal to or larger than that is deallocated")
 
 # -------------------------------------------------------------------------------- #
 
@@ -153,63 +140,6 @@ endif ()
 # -------------------------------------------------------------------------------- #
 # Executables
 # -------------------------------------------------------------------------------- #
-if (NOT CMAKE_BUILD_TYPE)
- set(CMAKE_BUILD_TYPE Release)
- message(STATUS "CMAKE_BUILD_TYPE is set as Release")
-endif ()
-
-# ---------- MPI ---------- #
-find_package(MPI)
-
-# ---------- Configure Metall ---------- #
-if (FREE_SMALL_OBJECT_SIZE_HINT GREATER 0)
- list(APPEND METALL_DEFS "METALL_FREE_SMALL_OBJECT_SIZE_HINT=${FREE_SMALL_OBJECT_SIZE_HINT}")
- message(STATUS "Try to free space for objects >= ${FREE_SMALL_OBJECT_SIZE_HINT} bytes")
-endif ()
-
-if (VERBOSE_SYSTEM_SUPPORT_WARNING)
- list(APPEND METALL_DEFS "METALL_VERBOSE_SYSTEM_SUPPORT_WARNING")
- message(STATUS "Show compile time warning regarding system support")
-endif ()
-
-if (DISABLE_FREE_FILE_SPACE)
- list(APPEND METALL_DEFS "METALL_DISABLE_FREE_FILE_SPACE")
- message(STATUS "Disable freeing file space in Metall")
-endif ()
-
-if (DISABLE_SMALL_OBJECT_CACHE)
- list(APPEND METALL_DEFS "METALL_DISABLE_OBJECT_CACHE")
- message(STATUS "Disable small object cache")
-endif ()
-
-if (DEFAULT_VM_RESERVE_SIZE GREATER 0)
- list(APPEND METALL_DEFS "METALL_DEFAULT_VM_RESERVE_SIZE=${DEFAULT_VM_RESERVE_SIZE}")
- message(STATUS "METALL_DEFAULT_VM_RESERVE_SIZE=${DEFAULT_VM_RESERVE_SIZE}")
-endif ()
-
-if (MAX_SEGMENT_SIZE GREATER 0)
- list(APPEND METALL_DEFS "METALL_MAX_SEGMENT_SIZE=${MAX_SEGMENT_SIZE}")
- message(STATUS "METALL_MAX_SEGMENT_SIZE=${MAX_SEGMENT_SIZE}")
-endif ()
-
-if (INITIAL_SEGMENT_SIZE GREATER 0)
- list(APPEND METALL_DEFS "METALL_INITIAL_SEGMENT_SIZE=${INITIAL_SEGMENT_SIZE}")
- message(STATUS "METALL_INITIAL_SEGMENT_SIZE=${INITIAL_SEGMENT_SIZE}")
-endif ()
-
-if (USE_SORTED_BIN)
- list(APPEND METALL_DEFS "METALL_USE_SORTED_BIN")
- message(STATUS "Use VM space aware algorithm in the bin directory")
-endif ()
-
-if (USE_ANONYMOUS_NEW_MAP)
- if (USE_ANONYMOUS_NEW_MAP AND UMAP_ROOT)
- message(FATAL_ERROR "USE_ANONYMOUS_NEW_MAP and UMAP_ROOT options cannot coexist")
- endif ()
-
- list(APPEND METALL_DEFS "METALL_USE_ANONYMOUS_NEW_MAP")
- message(STATUS "Use the anonymous map for new map region")
-endif ()
 
 # Requirements for GCC
 if (NOT RUN_BUILD_AND_TEST_WITH_CI)
@@ -220,6 +150,18 @@ if (NOT RUN_BUILD_AND_TEST_WITH_CI)
  endif ()
 endif ()
 
+# ---------- Metall Macros ---------- #
+foreach(X ${COMPILER_DEFS})
+ message(STATUS "Metall compile definition: ${X}")
+endforeach()
+
+
+# ---------- CMAKE_BUILD_TYPE ---------- #
+if (NOT CMAKE_BUILD_TYPE)
+ set(CMAKE_BUILD_TYPE Release)
+ message(STATUS "CMAKE_BUILD_TYPE is set as Release")
+endif ()
+
 
 # ---------- Threads ---------- #
 find_package(Threads REQUIRED)
@@ -304,8 +246,8 @@ function(common_setup_for_metall_executable name)
  # --------------------
 
  # ----- Compile Definitions ----- #
- foreach(X IN LISTS METALL_DEFS)
- target_compile_definitions(${name} PRIVATE ${X})
+ foreach(X ${COMPILER_DEFS})
+  target_compile_definitions(${name} PRIVATE ${X})
  endforeach()
  # --------------------
 
@@ -325,7 +267,7 @@ function(common_setup_for_metall_executable name)
  target_include_directories(${name} PRIVATE ${UMAP_ROOT}/include)
  if (LIBUMAP)
  target_link_libraries(${name} PRIVATE ${LIBUMAP})
- target_compile_definitions(${name} PRIVATE METALL_USE_UMAP)
+ target_compile_definitions(${name} PRIVATE "METALL_USE_UMAP")
  endif ()
  endif ()
  # --------------------

bench/adjacency_list/CMakeLists.txt

@@ -1,32 +1,19 @@
-find_package(OpenMP)
-if (NOT OpenMP_CXX_FOUND)
- MESSAGE(STATUS "OpenMP is not found. Use single thread in adjacency_list.")
-endif ()
+include(setup_omp)
 
 add_metall_executable(run_adj_list_bench_stl run_adj_list_bench_stl.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(run_adj_list_bench_stl PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(run_adj_list_bench_stl)
 
 add_metall_executable(run_adj_list_bench_bip run_adj_list_bench_bip.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(run_adj_list_bench_bip PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(run_adj_list_bench_bip)
 
 add_metall_executable(run_adj_list_bench_bip_extend run_adj_list_bench_bip_extend.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(run_adj_list_bench_bip_extend PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(run_adj_list_bench_bip_extend)
 
 add_metall_executable(run_adj_list_bench_metall run_adj_list_bench_metall.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(run_adj_list_bench_metall PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(run_adj_list_bench_metall)
 
 add_metall_executable(run_adj_list_bench_reflink_snapshot run_adj_list_bench_reflink_snapshot.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(run_adj_list_bench_reflink_snapshot PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(run_adj_list_bench_reflink_snapshot)
 
 if (MEMKIND_ROOT)
  add_metall_executable(run_adj_list_bench_pmem run_adj_list_bench_pmem.cpp)
@@ -39,9 +26,7 @@ if (MEMKIND_ROOT)
  message(FATAL_ERROR "Cannot find memkind library")
  endif ()
  endif ()
- if (OpenMP_CXX_FOUND)
- target_link_libraries(run_adj_list_bench_pmem PRIVATE OpenMP::OpenMP_CXX)
- endif ()
+ setup_omp_target(run_adj_list_bench_pmem)
 endif ()
 
 configure_file(run_bench.sh run_bench.sh COPYONLY)

bench/adjacency_list/edge_generator/CMakeLists.txt

@@ -1,4 +1,2 @@
 add_metall_executable(generate_rmat_edge_list generate_rmat_edge_list.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(generate_rmat_edge_list PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(generate_rmat_edge_list)

bench/adjacency_list/edge_generator/rmat_edge_generator.hpp

@@ -94,9 +94,9 @@ class rmat_edge_generator_iterator {
  const uint64_t mask = (1ULL << m_ptr_parent->m_vertex_scale) - 1;
  // Assume utility::hash is a good hash function
  m_current_edge.first =
- metall::utility::hash<uint64_t>()(m_current_edge.first) & mask;
+ metall::utility::hash<>()(m_current_edge.first) & mask;
  m_current_edge.second =
- metall::utility::hash<uint64_t>()(m_current_edge.second) & mask;
+ metall::utility::hash<>()(m_current_edge.second) & mask;
  }
  ++m_num_generated_edges;
  }

bench/adjacency_list/test/compare_key_value_lists.cpp

@@ -17,8 +17,8 @@
 using key_type = uint64_t;
 using value_type = uint64_t;
 using item_type = std::pair<key_type, value_type>;
-using table_type = std::unordered_map<item_type, std::size_t,
-  metall::utility::hash<item_type>>;
+using table_type =
+ std::unordered_map<item_type, std::size_t, metall::utility::hash<>>;
 
 void ingest_item(const std::string& file_name, table_type* table) {
  std::ifstream ifs(file_name);

bench/adjacency_list/test/test_large.sh

@@ -11,7 +11,6 @@ a=0.57
 b=0.19
 c=0.19
 seed=123
-e=$((2**$((${v}+4)))) # The number of edges to generate
 
 # The default path to store data.
 # This value is overwritten if '-d' option is specified
@@ -78,6 +77,8 @@ main() {
  ref_edge_dump_file1="${out_dir_path}/ref_edge_list1"
  ref_edge_dump_file2="${out_dir_path}/ref_edge_list2"
 
+ local e=$((2**$((${v}+4)))) # The number of edges to generate
+
  ./run_adj_list_bench_metall -o ${data_store_path} -d ${adj_list_dump_file} -s ${seed} -v ${v} -e ${e} -a ${a} -b ${b} -c ${c} -r 1 -u 1 -D ${ref_edge_dump_file1}
  check_program_exit_status
  echo ""

bench/bfs/CMakeLists.txt

@@ -1,21 +1,12 @@
-find_package(OpenMP)
-if (NOT OpenMP_CXX_FOUND)
- MESSAGE(STATUS "OpenMP is not found. Use single thread in BFS")
-endif()
+include(setup_omp)
 
 add_metall_executable(run_bfs_bench_metall run_bfs_bench_metall.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(run_bfs_bench_metall PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(run_bfs_bench_metall)
 
 add_metall_executable(run_bfs_bench_metall_multiple run_bfs_bench_metall_multiple.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(run_bfs_bench_metall_multiple PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(run_bfs_bench_metall_multiple)
 
 add_metall_executable(run_bfs_bench_bip run_bfs_bench_bip.cpp)
-if (OpenMP_CXX_FOUND)
- target_link_libraries(run_bfs_bench_bip PRIVATE OpenMP::OpenMP_CXX)
-endif ()
+setup_omp_target(run_bfs_bench_bip)
 
 configure_file(run_bench.sh run_bench.sh COPYONLY)

bench/data_structure/multithread_adjacency_list.hpp

@@ -48,9 +48,10 @@ class multithread_adjacency_list {
 
  using key_table_allocator_type = container::scoped_allocator_adaptor<
  other_allocator_type<std::pair<const key_type, list_type>>>;
- using key_table_type = container::unordered_map<
- key_type, list_type, metall::utility::hash<key_type>,
- std::equal_to<key_type>, key_table_allocator_type>;
+ using key_table_type =
+ container::unordered_map<key_type, list_type, metall::utility::hash<>,
+ std::equal_to<key_type>,
+ key_table_allocator_type>;
 
  using bank_table_allocator_type =
  container::scoped_allocator_adaptor<other_allocator_type<key_table_type>>;
@@ -81,9 +82,9 @@ class multithread_adjacency_list {
  m_bank_table[bank_index(key)][key].emplace_back(std::move(value));
 #else
  m_bank_table[bank_index(key)][key].emplace_back(std::move(value));
-// m_bank_table[bank_index(key)].try_emplace(key,
-// list_allocator_type(m_bank_table.get_allocator()));
-// m_bank_table[bank_index(key)].at(key).emplace_back(std::move(value));
+ // m_bank_table[bank_index(key)].try_emplace(key,
+ // list_allocator_type(m_bank_table.get_allocator()));
+ // m_bank_table[bank_index(key)].at(key).emplace_back(std::move(value));
 #endif
 #else
  // MEMO: GCC does not work with STL Containers (tested with GCC 10.2.0 on

cmake/setup_mpi.cmake

@@ -0,0 +1,14 @@
+if (MPI_CXX_FOUND)
+ find_package(MPI)
+endif ()
+
+function(setup_mpi_target target)
+ if (MPI_CXX_FOUND)
+ target_link_libraries(${target} PRIVATE MPI::MPI_CXX)
+ if (${CMAKE_HOST_SYSTEM_NAME} MATCHES "Linux")
+ target_link_libraries(${target} PRIVATE rt)
+ endif ()
+ else ()
+ message(SEND_ERROR "MPI not found, ${target} will not be built")
+ endif ()
+endfunction()

cmake/setup_omp.cmake

@@ -0,0 +1,11 @@
+if (NOT OpenMP_CXX_FOUND)
+ find_package(OpenMP)
+endif ()
+
+function(setup_omp_target target)
+ if (OpenMP_CXX_FOUND)
+ target_link_libraries(${target} PUBLIC OpenMP::OpenMP_CXX)
+ else ()
+ message(WARNING "OpenMP not found, ${target} will not be built with OpenMP support")
+ endif ()
+endfunction()

docs/Doxyfile.in

@@ -38,7 +38,7 @@ PROJECT_NAME = "Metall"
 # could be handy for archiving the generated documentation or if some version
 # control system is used.
 
-PROJECT_NUMBER = v0.26
+PROJECT_NUMBER = v0.27
 
 # Using the PROJECT_BRIEF tag one can provide an optional one line description
 # for a project that appears at the top of each page and should give viewer a
@@ -835,8 +835,6 @@ INPUT = ../include/metall \
  ../include/metall/json \
  ../include/metall/container/experimental/jgraph \
  ../include/metall/utility \
- ../include/metall/detail/base_stl_allocator.hpp \
- ../include/metall/detail/utility/named_proxy.hpp \
  ../example/graph_data_structure \
  ../example/json
 
@@ -2139,7 +2137,7 @@ ENABLE_PREPROCESSING = YES
 # The default value is: NO.
 # This tag requires that the tag ENABLE_PREPROCESSING is set to YES.
 
-MACRO_EXPANSION = NO
+MACRO_EXPANSION = YES
 
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES then
 # the macro expansion is limited to the macros specified with the PREDEFINED and

docs/readthedocs/advanced_build/cmake.md

@@ -17,7 +17,7 @@ cmake build_doc # option; BUILD_DOC must be ON when running cmake
 
 ## Required
 
- - CMake 3.10 or more.
+ - CMake 3.12 or more.
  - GCC 8.1 or more.
  - Boost C++ Libraries 1.64 or more (build is not required; needs only their header files).