Add and use jemalloc lib (#90)

* Add and use jemalloc lib

* Add autoconf

* Silence macro redefinition warning

environment/os/centos-7.sh

@@ -46,6 +46,7 @@ MEMGRAPH_BUILD_DEPS=(
     rpm-build rpmlint # for RPM package building
     doxygen graphviz # source documentation generators
     which mono-complete dotnet-sdk-3.1 golang nodejs zip unzip java-11-openjdk-devel # for driver tests
+    autoconf # for jemalloc code generation
 )
 list() {
     echo "$1"

environment/os/centos-8.sh

@@ -45,6 +45,7 @@ MEMGRAPH_BUILD_DEPS=(
     doxygen graphviz # source documentation generators
     which mono-complete dotnet-sdk-3.1 nodejs golang zip unzip java-11-openjdk-devel # for driver tests
     sbcl # for custom Lisp C++ preprocessing
+    autoconf # for jemalloc code generation
 )
 list() {
     echo "$1"

environment/os/debian-10.sh

@@ -43,6 +43,7 @@ MEMGRAPH_BUILD_DEPS=(
     doxygen graphviz # source documentation generators
     mono-runtime mono-mcs zip unzip default-jdk-headless # for driver tests
     dotnet-sdk-3.1 golang nodejs npm
+    autoconf # for jemalloc code generation
 )
 list() {
     echo "$1"

environment/os/debian-9.sh

@@ -41,6 +41,7 @@ MEMGRAPH_BUILD_DEPS=(
     sbcl # for custom Lisp C++ preprocessing
     doxygen graphviz # source documentation generators
     mono-runtime mono-mcs nodejs zip unzip default-jdk-headless # for driver tests
+    autoconf # for jemalloc code generation
 )
 list() {
     echo "$1"

environment/os/ubuntu-18.04.sh

@@ -42,6 +42,7 @@ MEMGRAPH_BUILD_DEPS=(
     sbcl # custom Lisp C++ preprocessing
     doxygen graphviz # source documentation generators
     mono-runtime mono-mcs nodejs zip unzip default-jdk-headless # driver tests
+    autoconf # for jemalloc code generation
 )
 list() {
     echo "$1"

environment/os/ubuntu-20.04.sh

@@ -43,6 +43,7 @@ MEMGRAPH_BUILD_DEPS=(
     doxygen graphviz # source documentation generators
     mono-runtime mono-mcs zip unzip default-jdk-headless # for driver tests
     dotnet-sdk-3.1 golang nodejs npm
+    autoconf # for jemalloc code generation
 )
 list() {
     echo "$1"

libs/.gitignore

@@ -4,3 +4,4 @@
 !cleanup.sh
 !CMakeLists.txt
 !__main.cpp
+!jemalloc.cmake

libs/CMakeLists.txt

@@ -8,6 +8,8 @@ if (NPROC EQUAL 0)
   set(NPROC 1)
 endif()
 
+set(LIB_DIR ${CMAKE_CURRENT_SOURCE_DIR})
+
 # convenience functions
 function(import_header_library name include_dir)
   add_library(${name} INTERFACE IMPORTED GLOBAL)
@@ -212,3 +214,5 @@ import_external_library(spdlog STATIC
   ${CMAKE_CURRENT_SOURCE_DIR}/spdlog/${CMAKE_INSTALL_LIBDIR}/libspdlog.a
   ${CMAKE_CURRENT_SOURCE_DIR}/spdlog/include
   BUILD_COMMAND $(MAKE) spdlog)
+
+include(jemalloc.cmake)

libs/jemalloc.cmake

@@ -0,0 +1,52 @@
+set(JEMALLOC_DIR "${LIB_DIR}/jemalloc")
+
+set(JEMALLOC_SRCS
+    ${JEMALLOC_DIR}/src/arena.c
+    ${JEMALLOC_DIR}/src/background_thread.c
+    ${JEMALLOC_DIR}/src/base.c
+    ${JEMALLOC_DIR}/src/bin.c
+    ${JEMALLOC_DIR}/src/bitmap.c
+    ${JEMALLOC_DIR}/src/ckh.c
+    ${JEMALLOC_DIR}/src/ctl.c
+    ${JEMALLOC_DIR}/src/div.c
+    ${JEMALLOC_DIR}/src/extent.c
+    ${JEMALLOC_DIR}/src/extent_dss.c
+    ${JEMALLOC_DIR}/src/extent_mmap.c
+    ${JEMALLOC_DIR}/src/hash.c
+    ${JEMALLOC_DIR}/src/hook.c
+    ${JEMALLOC_DIR}/src/jemalloc.c
+    ${JEMALLOC_DIR}/src/large.c
+    ${JEMALLOC_DIR}/src/log.c
+    ${JEMALLOC_DIR}/src/malloc_io.c
+    ${JEMALLOC_DIR}/src/mutex.c
+    ${JEMALLOC_DIR}/src/mutex_pool.c
+    ${JEMALLOC_DIR}/src/nstime.c
+    ${JEMALLOC_DIR}/src/pages.c
+    ${JEMALLOC_DIR}/src/prng.c
+    ${JEMALLOC_DIR}/src/prof.c
+    ${JEMALLOC_DIR}/src/rtree.c
+    ${JEMALLOC_DIR}/src/sc.c
+    ${JEMALLOC_DIR}/src/stats.c
+    ${JEMALLOC_DIR}/src/sz.c
+    ${JEMALLOC_DIR}/src/tcache.c
+    ${JEMALLOC_DIR}/src/test_hooks.c
+    ${JEMALLOC_DIR}/src/ticker.c
+    ${JEMALLOC_DIR}/src/tsd.c
+    ${JEMALLOC_DIR}/src/witness.c
+    ${JEMALLOC_DIR}/src/safety_check.c
+)
+
+add_library(jemalloc ${JEMALLOC_SRCS})
+target_include_directories(jemalloc PUBLIC "${JEMALLOC_DIR}/include")
+
+target_compile_definitions(jemalloc PRIVATE -DJEMALLOC_NO_PRIVATE_NAMESPACE)
+
+if (CMAKE_BUILD_TYPE STREQUAL "DEBUG")
+    target_compile_definitions(jemalloc PRIVATE -DJEMALLOC_DEBUG=1 -DJEMALLOC_PROF=1)
+endif()
+
+target_compile_options(jemalloc PRIVATE -Wno-redundant-decls)
+# for RTLD_NEXT
+target_compile_options(jemalloc PRIVATE -D_GNU_SOURCE)
+
+set_property(TARGET jemalloc APPEND PROPERTY INTERFACE_COMPILE_DEFINITIONS USE_JEMALLOC=1)

libs/setup.sh

@@ -121,3 +121,22 @@ clone https://github.com/memgraph/pymgclient.git pymgclient $pymgclient_tag
 
 spdlog_tag="46d418164dd4cd9822cf8ca62a116a3f71569241" # (2020-12-01)
 clone https://github.com/gabime/spdlog spdlog $spdlog_tag
+
+jemalloc_tag="ea6b3e973b477b8061e0076bb257dbd7f3faa756" # (2021-02-11)
+clone https://github.com/jemalloc/jemalloc.git jemalloc $jemalloc_tag
+pushd jemalloc
+# ThreadPool select job randomly, and there can be some threads that had been
+# performed some memory heavy task before and will be inactive for some time,
+# but until it will became active again, the memory will not be freed since by
+# default each thread has it's own arena, but there should be not more then
+# 4*CPU arenas (see opt.nareans description).
+#
+# By enabling percpu_arena number of arenas limited to number of CPUs and hence
+# this problem should go away.
+#
+# muzzy_decay_ms -- use MADV_FREE when available on newer Linuxes, to
+# avoid spurious latencies and additional work associated with
+# MADV_DONTNEED. See
+# https://github.com/ClickHouse/ClickHouse/issues/11121 for motivation.
+./autogen.sh --with-malloc-conf="percpu_arena:percpu,oversize_threshold:0,muzzy_decay_ms:10000"
+popd

src/CMakeLists.txt

@@ -38,7 +38,7 @@ if (MG_ENTERPRISE)
 endif()
 
 set(MG_SINGLE_NODE_V2_LIBS stdc++fs Threads::Threads
-    telemetry_lib mg-query mg-communication)
+    telemetry_lib mg-query mg-communication mg-new-delete)
 if (MG_ENTERPRISE)
   # These are enterprise subsystems
   set(MG_SINGLE_NODE_V2_LIBS ${MG_SINGLE_NODE_V2_LIBS} mg-auth mg-audit)

src/utils/CMakeLists.txt

@@ -11,3 +11,6 @@ set(utils_src_files
 
 add_library(mg-utils STATIC ${utils_src_files})
 target_link_libraries(mg-utils stdc++fs Threads::Threads spdlog fmt gflags uuid)
+
+add_library(mg-new-delete STATIC new_delete.cpp)
+target_link_libraries(mg-new-delete jemalloc)

src/utils/new_delete.cpp

@@ -0,0 +1,58 @@
+#include <iostream>
+#include <new>
+
+#if USE_JEMALLOC
+#include <jemalloc/jemalloc.h>
+#else
+#include <cstdlib>
+#endif
+
+#include "utils/likely.hpp"
+
+namespace {
+void *newImpl(std::size_t size) {
+  auto *ptr = malloc(size);
+  if (LIKELY(ptr != nullptr)) {
+    return ptr;
+  }
+
+  throw std::bad_alloc{};
+}
+
+void *newNoExcept(const std::size_t size) noexcept { return malloc(size); }
+
+void deleteImpl(void *ptr) noexcept { free(ptr); }
+
+#if USE_JEMALLOC
+
+void deleteSized(void *ptr, const std::size_t size) noexcept {
+  if (UNLIKELY(ptr == nullptr)) {
+    return;
+  }
+
+  sdallocx(ptr, size, 0);
+}
+
+#else
+
+void deleteSized(void *ptr, const std::size_t /*unused*/) noexcept { free(ptr); }
+
+#endif
+
+}  // namespace
+
+void *operator new(std::size_t size) { return newImpl(size); }
+
+void *operator new[](std::size_t size) { return newImpl(size); }
+
+void *operator new(std::size_t size, const std::nothrow_t & /*unused*/) noexcept { return newNoExcept(size); }
+
+void *operator new[](std::size_t size, const std::nothrow_t & /*unused*/) noexcept { return newNoExcept(size); }
+
+void operator delete(void *ptr) noexcept { deleteImpl(ptr); }
+
+void operator delete[](void *ptr) noexcept { deleteImpl(ptr); }
+
+void operator delete(void *ptr, std::size_t size) noexcept { deleteSized(ptr, size); }
+
+void operator delete[](void *ptr, std::size_t size) noexcept { deleteSized(ptr, size); }

tests/unit/CMakeLists.txt

@@ -32,7 +32,7 @@ function(_add_unit_test test_cpp custom_main)
   # used to help create two targets of the same name even though CMake
   # requires unique logical target names
   set_target_properties(${target_name} PROPERTIES OUTPUT_NAME ${exec_name})
-  target_link_libraries(${target_name} mg-utils gtest gmock Threads::Threads)
+  target_link_libraries(${target_name} mg-utils mg-new-delete gtest gmock Threads::Threads dl)
   # register test
   if(TEST_COVERAGE)
     add_test(${target_name} env LLVM_PROFILE_FILE=${exec_name}.profraw ./${exec_name})