Merge tag '1.0.1'

grc-iit · Jun 7, 2024 · af91b48 · af91b48
2 parents bc39458 + 6573d45
commit af91b48
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diff --git a/.gitmodules b/.gitmodules
diff --git a/CI/docker/chornolog.dockerfile b/CI/docker/chornolog.dockerfile
@@ -0,0 +1,33 @@
+# Use scs-lab/base:1.0 as base image
+FROM spack/ubuntu-jammy:latest as coeus-builder
+ENV DOCKER_TAG=0.2
+
+# What we want to install and how we want to install it
+# is specified in a manifest file (spack.yaml)
+RUN mkdir /opt/spack-environment \
+&&  (echo "spack:" \
+&&   echo "  specs:" \
+&&   echo "  - [email protected]" \
+&&   echo "  - [email protected]~fortran +verbs +argobots ^[email protected] fabrics=mlx,rxd,rxm,shm,sockets,tcp,udp,verbs" \
+&&   echo "  - [email protected] ^[email protected] fabrics=mlx,rxd,rxm,shm,sockets,tcp,udp,verbs" \
+&&   echo "  - [email protected] ^[email protected] fabrics=mlx,rxd,rxm,shm,sockets,tcp,udp,verbs" \
+&&   echo "  - [email protected]~boostsys ^[email protected] fabrics=mlx,rxd,rxm,shm,sockets,tcp,udp,verbs" \
+&&   echo "  - [email protected]" \
+&&   echo "  concretizer:" \
+&&   echo "    unify: true" \
+&&   echo "  config:" \
+&&   echo "    install_tree: /opt/software" \
+&&   echo "  view: /opt/view") > /opt/spack-environment/spack.yaml
+
+# Install the software, remove unnecessary deps
+RUN cd /opt/spack-environment && spack env activate . && spack install --fail-fast && spack gc -y
+
+FROM ubuntu:22.04
+ENV DEBIAN_FRONTEND="noninteractive"
+
+RUN apt-get update -y && apt-get upgrade -y
+RUN apt-get install -y pkg-config cmake build-essential environment-modules gfortran git python3 gdb
+
+COPY --from=coeus-builder /opt/spack-environment /opt/spack-environment
+COPY --from=coeus-builder /opt/software /opt/software
+COPY --from=coeus-builder /opt/view /usr
diff --git a/CI/docker/chronolog-ssh.dockerfile b/CI/docker/chronolog-ssh.dockerfile
@@ -0,0 +1,15 @@
+FROM scslab/chronolog:0.1
+ENV DEBIAN_FRONTEND="noninteractive"
+
+RUN apt-get install -y openssh-server sudo
+
+RUN passwd -d root
+
+RUN mkdir /var/run/sshd
+RUN sed -i'' -e's/^#PermitRootLogin prohibit-password$/PermitRootLogin yes/' /etc/ssh/sshd_config \
+        && sed -i'' -e's/^#PasswordAuthentication yes$/PasswordAuthentication yes/' /etc/ssh/sshd_config \
+        && sed -i'' -e's/^#PermitEmptyPasswords no$/PermitEmptyPasswords yes/' /etc/ssh/sshd_config \
+        && sed -i'' -e's/^UsePAM yes/UsePAM no/' /etc/ssh/sshd_config
+
+EXPOSE 22
+CMD ["/usr/bin/sudo", "/usr/sbin/sshd", "-D"]
diff --git a/CI/enviroment/loads b/CI/enviroment/loads
@@ -30,8 +30,6 @@ module load boost-1.77.0-gcc-9.3.0-hdotzut
 module load bzip2-1.0.8-gcc-9.3.0-gk3mz66
 # [email protected]%[email protected]+optimize+pic+shared arch=linux-ubuntu20.04-zen2
 module load zlib-1.2.11-gcc-9.3.0-whj3n7m
-# [email protected]%[email protected]~bz2+lz4+shared~snappy+static~tbb+zlib~zstd patches=9a8833a arch=linux-ubuntu20.04-zen2
-module load rocksdb-6.20.3-gcc-9.3.0-hqiuiit
 # [email protected]%[email protected]~ipo build_type=RelWithDebInfo arch=linux-ubuntu20.04-zen2
 module load gflags-2.2.2-gcc-9.3.0-ox4tyrq
 # [email protected]%[email protected] libs=shared,static arch=linux-ubuntu20.04-zen2

diff --git a/CI/enviroment/spack.lock b/CI/enviroment/spack.lock
@@ -16,10 +16,6 @@
     {
       "hash": "wtle6ecnkjzrxxjgdjyighedzjmua5kr",
       "spec": "boost"
-    },
-    {
-      "hash": "ggx2rpxnirkj2l2zfgxagqcmnsdjlgka",
-      "spec": "rocksdb"
     }
   ],
   "concrete_specs": {
@@ -1829,104 +1825,6 @@
       ],
       "hash": "hdotzutcx2a4pp5cmkbc3bw5g34xwu4x"
     },
-    "ggx2rpxnirkj2l2zfgxagqcmnsdjlgka": {
-      "name": "rocksdb",
-      "version": "6.20.3",
-      "arch": {
-        "platform": "linux",
-        "platform_os": "ubuntu20.04",
-        "target": {
-          "name": "zen2",
-          "vendor": "AuthenticAMD",
-          "features": [
-            "abm",
-            "aes",
-            "avx",
-            "avx2",
-            "bmi1",
-            "bmi2",
-            "clflushopt",
-            "clwb",
-            "clzero",
-            "cx16",
-            "f16c",
-            "fma",
-            "fsgsbase",
-            "mmx",
-            "movbe",
-            "pclmulqdq",
-            "popcnt",
-            "rdseed",
-            "sse",
-            "sse2",
-            "sse4_1",
-            "sse4_2",
-            "sse4a",
-            "ssse3",
-            "xsavec",
-            "xsaveopt"
-          ],
-          "generation": 0,
-          "parents": [
-            "zen"
-          ]
-        }
-      },
-      "compiler": {
-        "name": "gcc",
-        "version": "9.3.0"
-      },
-      "namespace": "builtin",
-      "parameters": {
-        "bz2": false,
-        "lz4": true,
-        "patches": [
-          "9a8833a09a0d6fb7b3fcf77e445b78ca86fb0a3638c1b9ef3716ff476eb6a82c"
-        ],
-        "shared": true,
-        "snappy": false,
-        "static": true,
-        "tbb": false,
-        "zlib": true,
-        "zstd": false,
-        "cflags": [],
-        "cppflags": [],
-        "cxxflags": [],
-        "fflags": [],
-        "ldflags": [],
-        "ldlibs": []
-      },
-      "patches": [
-        "9a8833a09a0d6fb7b3fcf77e445b78ca86fb0a3638c1b9ef3716ff476eb6a82c"
-      ],
-      "dependencies": [
-        {
-          "name": "gflags",
-          "build_hash": "vvjkbnwku7n6p2e5fjunybqwozblv7wp",
-          "type": [
-            "build",
-            "link"
-          ]
-        },
-        {
-          "name": "lz4",
-          "build_hash": "6m7dct2pygnn4iob47pdbhn6dxfhiryd",
-          "type": [
-            "build",
-            "link"
-          ]
-        },
-        {
-          "name": "zlib",
-          "build_hash": "whj3n7mok67wqtm5dofead56i6krevxc",
-          "type": [
-            "build",
-            "link"
-          ]
-        }
-      ],
-      "hash": "hqiuiit4ltk2mlp63bjfxrbobjeugjji"
-    },
     "vvjkbnwku7n6p2e5fjunybqwozblv7wp": {
       "name": "gflags",
       "version": "2.2.2",

diff --git a/CI/enviroment/spack.yaml b/CI/enviroment/spack.yaml
@@ -4,5 +4,5 @@
 # configuration settings.
 spack:
   # add package specs to the `specs` list
-  specs: [cmake, mpich~fortran, boost, rocksdb]
+  specs: [ cmake, mpich~fortran, boost ]
   view: true
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,17 +1,18 @@
-cmake_minimum_required(VERSION 3.17)
+cmake_minimum_required(VERSION 3.25)
 
 # Set a consistent MACOSX_RPATH default across all CMake versions.
 if(NOT DEFINED CMAKE_MACOSX_RPATH)
     set(CMAKE_MACOSX_RPATH 0)
 endif()
 
+
 project(ChronoLog LANGUAGES CXX)
 
 #------------------------------------------------------------------------------
 # Version information
 #------------------------------------------------------------------------------
 set(CHRONOLOG_VERSION_MAJOR "0")
-set(CHRONOLOG_VERSION_MINOR "1")
+set(CHRONOLOG_VERSION_MINOR "7")
 set(CHRONOLOG_VERSION_PATCH "0")
 set(CHRONOLOG_PACKAGE "ChronoLog")
 set(CHRONOLOG_PACKAGE_NAME "CHRONOLOG")
@@ -24,6 +25,9 @@ set(CHRONOLOG_PACKAGE_TARNAME "${CHRONOLOG_PACKAGE}")
 #------------------------------------------------------------------------------
 # Setup install and output Directories
 #------------------------------------------------------------------------------
+#if(NOT CMAKE_INSTALL_PREFIX)
+set(CMAKE_INSTALL_PREFIX /home/$ENV{USER}/chronolog)
+#endif()
 if(NOT CHRONOLOG_INSTALL_BIN_DIR)
     set(CHRONOLOG_INSTALL_BIN_DIR ${CMAKE_INSTALL_PREFIX}/bin)
 endif()
@@ -42,8 +46,8 @@ endif()
 #------------------------------------------------------------------------------
 if("${CMAKE_SOURCE_DIR}" STREQUAL "${CMAKE_BINARY_DIR}")
     message(FATAL_ERROR
-            "ChronoLog requires an out of source build. "
-            "Please create a separate binary directory and run CMake there.")
+        "ChronoLog requires an out of source build. "
+        "Please create a separate binary directory and run CMake there.")
 endif()
 
 #------------------------------------------------------------------------------
@@ -84,27 +88,28 @@ option(CHRONOLOG_ENABLE_DOXYGEN "Enable Doxygen documentation generation." OFF)
 #    add_compile_options(-Wextra)
 #endif()
 
+#set(CMAKE_BUILD_TYPE "Debug")
 # Change some compilation flags depending on the build type
 if(CMAKE_BUILD_TYPE STREQUAL "Debug")
     message("Compiling ChronoLog in Debug Mode")
-#    add_compile_options(-g3)
+    #    add_compile_options(-g3)
     add_compile_options(-O0)
     #set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -O0")
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -O0 -g")
 
-    #if (HERMES_USE_ADDRESS_SANITIZER)
+    #if (CHRONOLOG_USE_ADDRESS_SANITIZER)
     #    add_compile_options(-fsanitize=address)
     #endif()
 
-    #if (HERMES_USE_THREAD_SANITIZER)
+    #if (CHRONOLOG_USE_THREAD_SANITIZER)
     #    add_compile_options(-fsanitize=thread)
     #endif()
 
-    #if (HERMES_USE_THREAD_SANITIZER AND HERMES_USE_ADDRESS_SANITIZER)
+    #if (CHRONOLOG_USE_THREAD_SANITIZER AND CHRONOLOG_USE_ADDRESS_SANITIZER)
     #    message(FATAL_ERROR "Cannont use -fsanitize=address and -fsanitize=thread "
     #            "at the same time")
     #endif()
-else()    
+else()
     message("Compiling ChronoLog in release Mode")
     add_compile_options(-O3 -lm)
     #add_compile_options(-Wno-switch-unreachable -Wno-return-type)
@@ -115,13 +120,13 @@ endif()
 #------------------------------------------------------------------------------
 if(CHRONOLOG_ENABLE_COVERAGE)
     if(NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
-        message(FATAL_ERROR  "Use code coverage with debug mode")
+        message(FATAL_ERROR "Use code coverage with debug mode")
     endif()
 endif()
 
 
 #------------------------------------------------------------------------------
-# Transform flags from boolean to meaningfull usages.
+# Transform flags from boolean to meaningful usages.
 #------------------------------------------------------------------------------
 if(BUILD_SHARED_LIBS)
     set(CHRONOLOG_LIBTYPE SHARED)
@@ -133,30 +138,22 @@ endif()
 #-----------------------------------------------------------------------------
 # Dependencies common to all subdirectories
 #-----------------------------------------------------------------------------
-find_package(MPI REQUIRED COMPONENTS CXX)
-find_package(Boost REQUIRED)
-find_package(Thallium REQUIRED)
-#find_library(ROCKSDB_LIB rocksdb)
-#if(NOT ROCKSDB_LIB)
-#    message(FATAL_ERROR "rocksdb is required")
-#else()
-#    find_path(ROCKDSB_INCLUDE rocksdb)
-#    MESSAGE(STATUS "Found rocksdb at: ${ROCKSDB_INCLUDE}")
-#endif()
+
+
 #-----------------------------------------------------------------------------
 # Coverage
 #-----------------------------------------------------------------------------
 if(CHRONOLOG_ENABLE_COVERAGE)
     set(COVERAGE_FLAGS "-fprofile-arcs -ftest-coverage" CACHE STRING
-            "Flags to the coverage program to perform coverage inspection")
+        "Flags to the coverage program to perform coverage inspection")
     mark_as_advanced(COVERAGE_FLAGS)
 
     macro(set_coverage_flags target)
         set_target_properties(${target}
-                PROPERTIES
-                COMPILE_FLAGS ${COVERAGE_FLAGS}
-                LINK_FLAGS ${COVERAGE_FLAGS}
-                )
+            PROPERTIES
+            COMPILE_FLAGS ${COVERAGE_FLAGS}
+            LINK_FLAGS ${COVERAGE_FLAGS}
+        )
     endmacro()
 endif()
 
@@ -170,27 +167,27 @@ if(CHRONOLOG_ENABLE_DOXYGEN)
     include(UseDoxygenDoc)
 
     add_doxygen_doc(
-            BUILD_DIR
-            ${CMAKE_CURRENT_BINARY_DIR}/_build
-            DOXY_FILE
-            ${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in
-            TARGET_NAME
-            dox
-            COMMENT
-            "HTML documentation"
+        BUILD_DIR
+        ${CMAKE_CURRENT_BINARY_DIR}/_build
+        DOXY_FILE
+        ${CMAKE_CURRENT_SOURCE_DIR}/doc/Doxyfile.in
+        TARGET_NAME
+        dox
+        COMMENT
+        "HTML documentation"
     )
 endif()
 
 #-----------------------------------------------------------------------------
 # Linting
 #-----------------------------------------------------------------------------
 add_custom_target(lint COMMAND cpplint --recursive
-        --exclude=${CMAKE_CURRENT_SOURCE_DIR}/build
-        --exclude=${CMAKE_CURRENT_SOURCE_DIR}/cmake-build-debug
-        --exclude=${CMAKE_CURRENT_SOURCE_DIR}/external_libs
-        --exclude=${CMAKE_CURRENT_SOURCE_DIR}/doc
-        --exclude=${CMAKE_CURRENT_SOURCE_DIR}/CI
-        ${CMAKE_CURRENT_SOURCE_DIR} )
+    --exclude=${CMAKE_CURRENT_SOURCE_DIR}/build
+    --exclude=${CMAKE_CURRENT_SOURCE_DIR}/cmake-build-debug
+    --exclude=${CMAKE_CURRENT_SOURCE_DIR}/external_libs
+    --exclude=${CMAKE_CURRENT_SOURCE_DIR}/doc
+    --exclude=${CMAKE_CURRENT_SOURCE_DIR}/CI
+    ${CMAKE_CURRENT_SOURCE_DIR})
 
 #-----------------------------------------------------------------------------
 # Source
@@ -200,19 +197,18 @@ if(CHRONOLOG_BUILD_TESTING)
     include(CTest)
 endif()
 
-# External header only libraries
-add_subdirectory(external_libs)
-
-add_subdirectory(tools)
-
-# ChronoVisor
-add_subdirectory(ChronoAPI)
+# ChronoLog client library
+add_subdirectory(Client)
 
 # ChronoVisor
 add_subdirectory(ChronoVisor)
 
-# ChronoLog client library
-add_subdirectory(Client)
+# ChronoKeeper
+add_subdirectory(ChronoKeeper)
+add_subdirectory(ChronoGrapher)
+
+# ChronoStore
+add_subdirectory(ChronoStore)
 
 # custom
 add_custom_target(make_all cd ${CMAKE_BINARY_DIR} && make)
@@ -222,3 +218,8 @@ if(CHRONOLOG_BUILD_TESTING)
     enable_testing()
     add_subdirectory(test)
 endif()
+
+#if(CHRONOLOG_ENABLE_PYTHON_BINDINGS)
+message("Python binding enabled")
+add_subdirectory(python_client)
+#endif()