ecrc · mahmoudElkarargyBS · Oct 23, 2024 · Oct 29, 2024 · Nov 14, 2024 · Mar 18, 2025
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,26 @@
+stages:
+  - compile
+
+variables:
+  GIT_STRATEGY: clone
+  GIT_SUBMODULE_STRATEGY: normal
+  ARTIFACTS_NAME: "$CI_JOB_NAME-$CI_COMMIT_REF_SLUG"
+  ARTIFACTS_PATH: bin.tar
+
+.compile-job: &compile-job
+  stage: compile
+  artifacts:
+    when: on_success
+    name: $ARTIFACTS_NAME
+    expire_in: 1h
+    paths:
+      - bin.tar
+  script:
+    - echo -e "Script Arguments:\t $CONFIG_ARGS"
+
+compile:cpp:
+  <<: *compile-job
+  image: acai-oneapi
+  tags:
+    - acai-cpu
+
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -18,24 +18,41 @@ cmake_minimum_required(VERSION 3.20 FATAL_ERROR)
 cmake_policy(SET CMP0048 NEW)
 
 # Set project options
-option(USE_CUDA "Use Cuda, if available" false)
-option(USE_MPI "Use MPI, if available" false)
+option(USE_CUDA "Use CUDA, if available" OFF)
+option(USE_MPI "Use MPI, if available" OFF)
 option(BUILD_TESTS "Option to enable building tests" OFF)
 option(BUILD_HEAVY_TESTS "Option to enable building heavy tests, This may take a lot of time" OFF)
 option(BUILD_EXAMPLES "Option to enable building examples" ON)
 option(BUILD_DOCS "Build documentation in docs directory" ON)
 option(USE_R "Enable the use of R and Rcpp in the project" OFF)
 option(CREATE_PACKAGE "Enable a packaging system for distribution" OFF)
 
+# Declare the RUNTIME_TYPE variable with a default value
+set(RUNTIME_TYPE "starpu" CACHE STRING "Specify the runtime type (e.g., starpu or parsec)")
 # Cmake Module Paths
 set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake;${CMAKE_MODULE_PATH}")
-
 if (${BUILD_SHARED_LIBS})
     set(BLA_STATIC OFF)
 else ()
     set(BLA_STATIC ON)
 endif ()
 
+# Project Name and Version
+project(ExaGeoStatCPP VERSION 2.0.0 DESCRIPTION "ExaGeoStatCPP is a parallel high performance unified framework for geostatistics on manycore systems.")
+set(CMAKE_CXX_EXTENSIONS OFF)
+string(TOUPPER ${RUNTIME_TYPE} RUNTIME_TYPE)
+
+# Default path for default configuration json file
+add_definitions(
+        -DDEFAULT_CONFIGURATION_PATH="${PROJECT_SOURCE_DIR}/configurations/config.json"
+)
+
+if(RUNTIME_TYPE STREQUAL "PARSEC")
+    message(STATUS "MPI is required to be enabled in order to use PaRSEC")
+    set(USE_MPI ON)
+    set(USE_HICMA OFF)
+endif()
+
 # Select toolchain based on whether CUDA is enabled or not
 if (USE_CUDA)
     message("")
@@ -53,9 +70,6 @@ else ()
     include(toolchains/GccToolchain)
 endif ()
 
-# Project Name and Version
-project(ExaGeoStatCPP VERSION 1.0.0 DESCRIPTION "ExaGeoStatCPP is a parallel high performance unified framework for geostatistics on manycore systems.")
-
 # Show the current version of CMake.
 message(STATUS "CMAKE VERSION: ${CMAKE_VERSION}")
 # Enable C++ language
@@ -115,30 +129,46 @@ include(ImportHwloc)
 list(APPEND STARPU_COMPONENT_LIST "HWLOC")
 string(REPLACE ";" " " STARPU_COMPONENT_STRING "${STARPU_COMPONENT_LIST}")
 
-# ExaGeoStatCPP depends on StarPU runtime
+# ExaGeoStatCPP depends on NLOHMANN
 # -------------------------------
-include(ImportStarPu)
-
-# ExaGeoStatCPP depends on GSL
-# -------------------------------
-include(ImportGSL)
+include(ImportNlohmannJSON)
 
 # ExaGeoStatCPP depends on NLOPT
 # -------------------------------
 include(ImportNLOPT)
 
-# ExaGeoStatCPP depends on HiCMA
+# ExaGeoStatCPP depends on GSL
 # -------------------------------
-if (USE_HICMA)
-    add_definitions(-DUSE_HICMA=TRUE)
-    include(ImportHCore)
-    include(ImportStarsH)
-    include(ImportHiCMA)
-endif ()
+include(ImportGSL)
 
-# ExaGeoStatCPP depends on Chameleon
-# -------------------------------
-include(ImportChameleon)
+message("---------------------------------------- ${RUNTIME_TYPE}")
+if(RUNTIME_TYPE STREQUAL "STARPU")
+    message(STATUS "Using StarPU as the runtime")
+    # ExaGeoStatCPP depends on StarPU runtime
+    # -------------------------------
+    include(ImportStarPu)
+    # ExaGeoStatCPP depends on HiCMA
+    # -------------------------------
+    if (USE_HICMA)
+        add_definitions(-DUSE_HICMA=TRUE)
+        include(ImportHCore)
+        include(ImportStarsH)
+        include(ImportHiCMA)
+    endif ()
+    # ExaGeoStatCPP depends on Chameleon
+    # -------------------------------
+    include(ImportChameleon)
+
+elseif(RUNTIME_TYPE STREQUAL "PARSEC")
+    message(STATUS "Using PaRSEC as the runtime")
+    # ExaGeoStatCPP depends on StarPU runtime
+    # -------------------------------
+    include(ImportStarsH)
+    include(ImportHCore)
+    include(ImportHiCMAX)
+else()
+    message(FATAL_ERROR "Unknown RUNTIME_TYPE: ${RUNTIME_TYPE}. Supported values are 'STARPU' or 'PARSEC'.")
+endif()
 
 # ExaGeoStatCPP depends on LAPACK/BLASPP
 # -------------------------------
@@ -173,10 +203,16 @@ if (USE_R)
     endif ()
 endif ()
 
-
 # Add src Directory to expose added libraries
 add_subdirectory(src)
 
+# Define USE_STARPU or USE_RUNTIME based on the selected runtime
+if(RUNTIME_TYPE STREQUAL "STARPU")
+    target_compile_definitions(${PROJECT_NAME} PUBLIC DEFAULT_RUNTIME=1)
+elseif(RUNTIME_TYPE STREQUAL "PARSEC")
+    target_compile_definitions(${PROJECT_NAME} PUBLIC DEFAULT_RUNTIME=0)
+endif()
+
 # Creates a new INTERFACE library target named ${PROJECT_NAME}_INTERFACE.
 # The INTERFACE keyword specifies that this library will not be built, but instead will only be used for its properties.
 add_library(${PROJECT_NAME}_INTERFACE INTERFACE)
@@ -218,15 +254,22 @@ endif ()
 message(" \n \t ** Configurations of ExaGeoStatCPP and installation of dependence is done successfully ** ")
 message("\t - Export the following line to avoid re-install dependencies each time. -")
 message("\t ----------------------------------------------------------------------------------------------------------------------------------- ")
-message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/CHAMELEON/lib/pkgconfig:$PKG_CONFIG_PATH")
-message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/STARPU/lib/pkgconfig:$PKG_CONFIG_PATH")
+message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/NLOHMANN_JSON/share/pkgconfig:$PKG_CONFIG_PATH")
 message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/HWLOC/lib/pkgconfig:$PKG_CONFIG_PATH")
-message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/GSL/lib/pkgconfig:$PKG_CONFIG_PATH")
 message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/NLOPT/lib/pkgconfig:${CMAKE_INSTALL_PREFIX}/NLOPT/lib64/pkgconfig:$PKG_CONFIG_PATH")
-if(USE_HICMA)
+message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/GSL/lib/pkgconfig:$PKG_CONFIG_PATH")
+if(RUNTIME_TYPE STREQUAL "STARPU")
+    message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/STARPU/lib/pkgconfig:$PKG_CONFIG_PATH")
+    message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/CHAMELEON/lib/pkgconfig:$PKG_CONFIG_PATH")
+    if(USE_HICMA)
+        message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/STARSH/lib/pkgconfig:$PKG_CONFIG_PATH")
+        message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/HCORE/lib/pkgconfig:$PKG_CONFIG_PATH")
+        message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/HICMA/lib/pkgconfig:$PKG_CONFIG_PATH")
+    endif()
+elseif(RUNTIME_TYPE STREQUAL "PARSEC")
     message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/STARSH/lib/pkgconfig:$PKG_CONFIG_PATH")
     message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/HCORE/lib/pkgconfig:$PKG_CONFIG_PATH")
-    message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/HICMA/lib/pkgconfig:$PKG_CONFIG_PATH")
+    message("\t export PKG_CONFIG_PATH=${CMAKE_INSTALL_PREFIX}/HICMA-X/lib/pkgconfig:${CMAKE_INSTALL_PREFIX}/HICMA-X/lib64/pkgconfig:${CMAKE_INSTALL_PREFIX}/HICMA-X/lib64:$PKG_CONFIG_PATH")
 endif()
 message("\t ----------------------------------------------------------------------------------------------------------------------------------- \n")
 

diff --git a/README.md b/README.md
@@ -68,12 +68,12 @@ To build and run this software, you will need:
 ### C++ source code installation
 To install the `ExaGeoStatCPP` project locally (C++ version), run the following commands in your terminal:
 
-1. Clone the project from the remote gitHub repository into your local machine using the following command
+1. Clone the project repository to your local machine:
    ```bash
    git clone https://github.com/ecrc/ExaGeoStatCPP.git 
    ```
 
-2. Change your current directory by getting into the `ExaGeoStatCPP` project directory
+2. Navigate to the cloned directory:
    ```bash
    cd ExaGeoStatCPP
    ```
@@ -92,6 +92,7 @@ To install the `ExaGeoStatCPP` project locally (C++ version), run the following
    ```bash
    export PKG_CONFIG_PATH=$PWD/installdir/_deps/DEPENDENCY_NAME/lib/pkgconfig:$PKG_CONFIG_PATH
    ```
+   or copy/paste the output pkg-config paths from the configure step
 
 Now, you can use the pkg-config executable to collect compiler and linker flags for
 ExaGeoStatCPP.

diff --git a/USER_MANUAL.md b/USER_MANUAL.md
@@ -80,6 +80,7 @@
 * To enable packaging system for distribution, add `-p` disabled by default.
 * To enable showing code warnings, add `-w` disabled by default.
 * To manually set mkl as blas vendor, add `--use-mkl`. MKL is required as blas vendor and it's automatically detected but in some environments it need to be manually set.
+* To enable PaRSEC as a runtime system, add `--use=parsec`, StarPU by default.
 
 ## Building
 
@@ -98,7 +99,10 @@
 
 
 ## Arguments
-These are the arguments that you can specify when running any C++ example.
+These are the arguments that you can specify when running any C++ example. 
+**Please note that the arguments are not case-sensitive**, and you can use variations such as `-`, `_`, or capitalized forms for the same argument name. 
+For example, `MaxRank`, `max-rank`, `max_rank`, `Max_Rank` ,`Maxrank` , `MaxrAnk` and `Max-Rank` are all considered equivalent.
+
 * {Mandatory} To set the problem size (N)
 
         --N=<problem_size>
@@ -152,13 +156,13 @@ These are the arguments that you can specify when running any C++ example.
         --oub=<value:value:....:value>
 * {Optional} To set the initial theta
 
-        --itheta=<value:value:....:value>
+        --initial_theta=<value:value:....:value>
 * {Optional} To set the target theta
 
         --ttheta=<value:value:....:value>
 * {Optional} To set the estimated theta
 
-        --etheta=<value:value:....:value>
+        --estimated_theta=<value:value:....:value>
 * {Optional} To set the seed value, the default is 0
 
         --seed=<value>
@@ -223,10 +227,12 @@ These are the arguments that you can specify when running any C++ example.
 ### Provide Arguments
 
 To use any operations, you must initially supply the necessary arguments 
-to the operation via the Configurations module. There are two methods available
+to the operation via the Configurations module. 
+This program is configured by default through a json file of default values. You can either change the configuration arguments
+in the json file or provide them through command line. There are two methods available
 for setting your arguments:
 
-1. Provide your arguments with the command line.
+1. Provide your arguments with the command line, this overwrites the json configuration.
 ```c++
     // Create a new configuration object.
     Configurations configurations;

diff --git a/cmake/FindHICMA-X.cmake b/cmake/FindHICMA-X.cmake
@@ -0,0 +1,109 @@
+
+# Copyright (c) 2017-2024 King Abdullah University of Science and Technology,
+# All rights reserved.
+# ExaGeoStat is a software package, provided by King Abdullah University of Science and Technology (KAUST).
+
+# @file FindHICMA-X.cmake
+# @brief This is a CMakeLists file for finding HiCMA-X and link and include it's headers
+# @version 2.0.0
+# @author Mahmoud ElKarargy
+# @date 2024-09-28
+
+# Include pkg-config
+find_package(PkgConfig QUIET)
+
+# Try to find dplasma and parsec via pkg-config
+if(PKG_CONFIG_FOUND)
+    pkg_check_modules(DPLASMA_PKG dplasma)
+    pkg_check_modules(PARSEC_PKG parsec)
+    if(DPLASMA_PKG_FOUND AND PARSEC_PKG_FOUND)
+        # Try to find the HICMA-X or hicma-x path in the library directories
+        string(FIND "${PARSEC_PKG_LIBRARY_DIRS}" "HICMA-X" HICMA_X_START)
+        if(HICMA_X_START EQUAL -1)
+            string(FIND "${PARSEC_PKG_LIBRARY_DIRS}" "hicma-x" HICMA_X_START)
+        endif()
+        if(HICMA_X_START GREATER -1)
+            # Extract the full path to HICMA-X or hicma-x and set the include directory
+            string(REGEX MATCH "([^;]*(HICMA-X|hicma-x)[^;]*/lib)" HICMA_X_LIB_PATH "${PARSEC_PKG_LIBRARY_DIRS}")
+            get_filename_component(HICMA_X_ROOT "${HICMA_X_LIB_PATH}" DIRECTORY) # Go one level up
+            set(HICMA-X_INCLUDE_DIRS "${HICMA_X_ROOT}/include")  # Set the include path
+        endif()
+        # TODO: This is not generalized for the case of hicma installed manually
+        set(HICMA_X_SRC_DIR ${HICMA_X_ROOT}/hicma-x-src)
+        set(HICMA_X_BIN_DIR ${HICMA_X_ROOT}/bin)
+        set(HICMA-X_FOUND TRUE)
+        set(HICMA-X_LIBRARIES ${DPLASMA_PKG_LIBRARIES} ${PARSEC_PKG_LIBRARIES})
+        set(HICMA-X_LIBRARY_DIRS "${HICMA_X_LIB_PATH}")
+        # Add a search for lib64 directories and set HICMA-X_LIBRARY_DIRS_DEP
+        set(HICMA-X_LIBRARY_DIRS_DEP "${HICMA_X_LIB_PATH}64")
+
+        find_library(HICMA_PARSEC_LIB hicma_parsec PATHS ${HICMA-X_LIBRARY_DIRS_DEP})
+
+        if(HICMA_PARSEC_LIB)
+            list(APPEND HICMA-X_LIBRARIES ${HICMA_PARSEC_LIB})
+        else()
+            message(FATAL_ERROR "libhicma_parsec.so not found")
+        endif()
+
+    endif()
+endif()
+
+# Fallback: Manual search if pkg-config fails or HICMA-X path isn't set
+if(NOT HICMA-X_FOUND)
+    # Improved search to handle multiple possible paths and fallback for include directories
+    find_path(HICMA-X_INCLUDE_DIR
+            NAMES hicma.h
+            PATHS
+            ${CMAKE_CURRENT_LIST_DIR}/../hicma-x/include
+            /usr/local/include/hicma-x
+            /usr/local/include
+            /usr/include/hicma-x
+            /usr/include
+            DOC "Path to HICMA-X include directory"
+            )
+
+    # Search for the main HICMA-X library
+    find_library(HICMA-X_LIBRARY
+            NAMES hicma-x
+            PATHS
+            ${CMAKE_CURRENT_LIST_DIR}/../hicma-x/lib
+            /usr/local/lib
+            /usr/lib
+            DOC "Path to HICMA-X library"
+            )
+
+    # Search for the hicma_parsec library in the lib64 directory if it's not found in the standard lib
+    find_library(HICMA_PARSEC_LIB
+            NAMES hicma_parsec
+            PATHS
+            ${CMAKE_CURRENT_LIST_DIR}/../hicma-x/lib64
+            /usr/local/lib64
+            /usr/lib64
+            DOC "Path to HICMA-Parsec library"
+            )
+
+    # Check if both the include directory and libraries were found
+    if(HICMA-X_INCLUDE_DIR AND HICMA-X_LIBRARY AND HICMA_PARSEC_LIB)
+        set(HICMA-X_FOUND TRUE)
+        # Combine the found libraries
+        set(HICMA-X_LIBRARIES ${HICMA-X_LIBRARY} ${HICMA_PARSEC_LIB})
+        # Set the include directory
+        set(HICMA-X_INCLUDE_DIRS "${HICMA-X_INCLUDE_DIR}")
+        # Include both lib and lib64 directories
+        # TODO: This paths are not generalized, if the install is not with the same dir.
+        set(HICMA-X_LIBRARY_DIRS "${HICMA-X_LIBRARY}/lib")
+        set(HICMA-X_LIBRARY_DIRS_DEP "${HICMA-X_LIBRARY}/lib64")
+    else()
+        set(HICMA-X_FOUND FALSE)
+    endif()
+endif()
+
+# Mark the variables as advanced to keep the CMake GUI clean
+mark_as_advanced(HICMA-X_INCLUDE_DIR HICMA-X_LIBRARY HICMA_PARSEC_LIB)
+
+# Provide feedback on whether the library was found
+if(HICMA-X_FOUND)
+    message(STATUS "Found HICMA-X")
+else()
+    message("Could not find HICMA-X or its dependencies (dplasma, parsec)")
+endif()