Getting prepared for the new version of Cadmium

CMakeLists.txt

@@ -13,6 +13,12 @@ project(cadmium)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/bin)
 
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release)
+endif()
+set(CMAKE_CXX_FLAGS_DEBUG "-g")
+set(CMAKE_CXX_FLAGS_RELEASE "-O3")
+
 add_library(cadmium INTERFACE)
 target_include_directories(cadmium INTERFACE include/ json/include)
 
@@ -31,8 +37,26 @@ foreach(exampleSrc ${Examples})
     add_example(${exampleSrc})
 endforeach(exampleSrc)
 
+if(APPLE)
+    # Apple Clang does not pack OpenMP. We must install it via HomeBrew and link it manually
+    if(CMAKE_C_COMPILER_ID MATCHES "Clang\$")
+        set(OpenMP_C_FLAGS "-Xpreprocessor -fopenmp")
+        set(OpenMP_C_LIB_NAMES "omp")
+        set(OpenMP_omp_LIBRARY omp)
+    endif()
+    if(CMAKE_CXX_COMPILER_ID MATCHES "Clang\$")
+        set(OpenMP_CXX_FLAGS "-Xpreprocessor -fopenmp")
+        set(OpenMP_CXX_LIB_NAMES "omp")
+        set(OpenMP_omp_LIBRARY omp)
+    endif()
+endif()
 find_package(OpenMP)
 if(OpenMP_CXX_FOUND)
+    if (APPLE)
+        # HomeBrew leaves a symlink to the installed version of OpenMP in these directories
+        include_directories("/usr/local/opt/libomp/include")
+        link_directories("/usr/local/opt/libomp/lib")
+    endif()
     FILE(GLOB Examples RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} example/*/parallel_main_*.cpp)
     foreach(exampleSrc ${Examples})
         add_example(${exampleSrc})

Doxyfile

@@ -1,6 +1,6 @@
 #
 # SPDX-License-Identifier: MIT
-# Copyright (c) 2021-present Román Cárdenas Rodríguez
+# Copyright (c) 2022-present Román Cárdenas Rodríguez
 # ARSLab - Carleton University
 #
 

build.sh

@@ -1,16 +1,67 @@
+#! /bin/bash
 #
 # SPDX-License-Identifier: MIT
 # Copyright (c) 2022-present jsoulier
-# ARSLab - Carleton University
 # Copyright (c) 2022-present Román Cárdenas Rodríguez
+# Copyright (c) 2025-present Sasisekhar
 # ARSLab - Carleton University
 #
 
+#Function to install deps depending on OS
+install_deps() {
+  if command -v apt >/dev/null 2>&1; then
+    echo "Detected apt (Debian/Ubuntu)"
+    sudo apt update
+    sudo apt install -y build-essential make cmake git
+
+  elif command -v dnf >/dev/null 2>&1; then
+    echo "Detected dnf (Fedora)"
+    sudo dnf group install -y development-tools
+    sudo dnf install -y gcc gcc-c++ make cmake git boost-devel
+
+  else
+    echo "No supported package manager found."
+    echo "Please install build tools, make, cmake, and git manually."
+    exit 1
+  fi
+}
+
+# Function to add the CADMIUM variable to the environment
+add_cadmium_env() {
+  # Check if CADMIUM is already set in .bashrc
+  if ! grep -Fxq "export CADMIUM=$(pwd)" ~/.bashrc; then
+    echo "export CADMIUM=$(pwd)" >> ~/.bashrc
+    echo "The CADMIUM variable has been set to $(pwd) in ~/.bashrc."
+  else
+    echo "The CADMIUM variable is already set in ~/.bashrc."
+  fi
+
+  # Source the updated .bashrc
+  source ~/.bashrc
+}
+
+
 echo Downloading all the dependencies...
-git submodule update --init --recursive
+install_deps
+git pull
+git submodule update --init --recursive --progress
 mkdir build
 cd build || exit
 cmake ..
 cmake --build .
 cd ..
 echo Compilation done. All the examples are in the bin folder
+
+cd include
+# Prompt the user for confirmation
+echo "Do you want to add cadmium ($(pwd)) as an environment variable? (yes/no)"
+read -r response
+
+# Check the response and take action
+if [[ "$response" =~ ^[Yy][Ee][Ss]$ || "$response" =~ ^[Yy]$ ]]; then
+  add_cadmium_env
+elif [[ "$response" =~ ^[Nn][Oo]$ || "$response" =~ ^[Nn]$ ]]; then
+  echo "Operation canceled. The $(pwd) was not added to PATH."
+else
+  echo "Invalid response. Please run the script again and respond with 'yes' or 'no'."
+fi

example/celldevs_benchmark/benchmark_config.json

@@ -1,16 +1,21 @@
 {
   "scenario": {
-    "shape": [50, 50], "origin": [-24, -24]
+    "shape": [50, 50], "origin": [0, 0]
   },
   "cells": {
     "default": {
       "delay": "inertial",
-      "cell_type": "benchmark",
+      "model": "benchmark",
       "state": {"digit": 0},
       "neighborhood": [
         {"type": "von_neumann", "vicinity": 0.25, "range": 1},
         {"type": "relative", "vicinity": 1, "neighbors": [[0, 0]]}
       ]
     }
-  }
+  },
+  "viewer": [{
+    "colors": [[0, 0, 0], [255, 0, 0]],
+    "breaks": [0, 0.5, 1],
+    "field": "digit"
+}]
 }

example/celldevs_benchmark/include/benchmark_grid_cell.hpp

@@ -1,18 +1,17 @@
 /**
  * SPDX-License-Identifier: MIT
  * Copyright (c) 2022-present Guillermo Trabes
- * ARSLab - Carleton University
- * Copyright (c) 2022-present Román Cárdenas Rodríguez
- * ARSLab - Carleton University
+ * Copyright (c) 2023-present Román Cárdenas Rodríguez
+ * ArSLab - Carleton University
  */
 
 #ifndef CADMIUM_EXAMPLE_CELLDEVS_BENCHMARK_CELL_HPP_
 #define CADMIUM_EXAMPLE_CELLDEVS_BENCHMARK_CELL_HPP_
 
 #include <cmath>
 #include <nlohmann/json.hpp>
-#include <cadmium/celldevs/grid/cell.hpp>
-#include <cadmium/celldevs/grid/config.hpp>
+#include <cadmium/modeling/celldevs/grid/cell.hpp>
+#include <cadmium/modeling/celldevs/grid/config.hpp>
 #include "state.hpp"
 
 namespace cadmium::celldevs::example::benchmark {

example/celldevs_benchmark/main_grid_benchmark.cpp

@@ -1,14 +1,14 @@
 /**
  * SPDX-License-Identifier: MIT
  * Copyright (c) 2022-present Guillermo Trabes
- * ARSLab - Carleton University
  * Copyright (c) 2022-present Román Cárdenas Rodríguez
+ * Copyright (c) 2025-present Sasisekhar
  * ARSLab - Carleton University
  */
 
-#include <cadmium/celldevs/grid/coupled.hpp>
-#include <cadmium/core/logger/csv.hpp>
-#include <cadmium/core/simulation/root_coordinator.hpp>
+#include <cadmium/modeling/celldevs/grid/coupled.hpp>
+#include <cadmium/simulation/logger/csv.hpp>
+#include <cadmium/simulation/root_coordinator.hpp>
 #include <chrono>
 #include <fstream>
 #include <string>
@@ -43,8 +43,7 @@ int main(int argc, char ** argv) {
 
 	modelGenerated = std::chrono::high_resolution_clock::now();
 	auto rootCoordinator = cadmium::RootCoordinator(model);
-	auto logger = std::make_shared<cadmium::CSVLogger>("grid_log.csv", ";");
-	rootCoordinator.setLogger(logger);
+	rootCoordinator.setLogger<cadmium::CSVLogger>("grid_benchmark_log.csv", ";");
 	rootCoordinator.start();
 	auto engineStarted = std::chrono::high_resolution_clock::now();
 	std::cout << "Engine creation time: " << std::chrono::duration_cast<std::chrono::duration<double, std::ratio<1>>>(engineStarted - modelGenerated).count() << " seconds" << std::endl;

example/celldevs_sir/asymm_config.json

@@ -2,7 +2,7 @@
   "cells": {
     "default": {
       "delay": "inertial",
-      "cell_type": "SIR",
+      "model": "SIR",
       "state": {"p": 200, "s": 1, "i": 0, "r": 0},
       "config": {"rec": 0.2, "susc": 0.8, "vir": 0.4}
     },

example/celldevs_sir/grid_config.json

@@ -5,7 +5,7 @@
   "cells": {
     "default": {
       "delay": "inertial",
-      "cell_type": "SIR",
+      "model": "SIR",
       "state": {"p": 100, "s": 1, "i": 0, "r": 0},
       "config": {"rec": 0.2, "susc": 0.8, "vir": 0.4},
       "neighborhood": [

example/celldevs_sir/include/asymm_sir_cell.hpp

@@ -9,8 +9,8 @@
 
 #include <cmath>
 #include <nlohmann/json.hpp>
-#include <cadmium/celldevs/asymm/cell.hpp>
-#include <cadmium/celldevs/asymm/config.hpp>
+#include <cadmium/modeling/celldevs/asymm/cell.hpp>
+#include <cadmium/modeling/celldevs/asymm/config.hpp>
 #include "state.hpp"
 
  namespace cadmium::celldevs::example::sir {

example/celldevs_sir/include/grid_sir_cell.hpp

@@ -9,8 +9,8 @@
 
 #include <cmath>
 #include <nlohmann/json.hpp>
-#include <cadmium/celldevs/grid/cell.hpp>
-#include <cadmium/celldevs/grid/config.hpp>
+#include <cadmium/modeling/celldevs/grid/cell.hpp>
+#include <cadmium/modeling/celldevs/grid/config.hpp>
 #include "state.hpp"
 
 namespace cadmium::celldevs::example::sir {

example/celldevs_sir/main_asymm_sir.cpp

@@ -4,9 +4,9 @@
  * ARSLab - Carleton University
  */
 
-#include <cadmium/celldevs/asymm/coupled.hpp>
-#include <cadmium/core/logger/csv.hpp>
-#include <cadmium/core/simulation/root_coordinator.hpp>
+#include <cadmium/modeling/celldevs/asymm/coupled.hpp>
+#include <cadmium/simulation/logger/csv.hpp>
+#include <cadmium/simulation/root_coordinator.hpp>
 #include <fstream>
 #include <string>
 #include "asymm_sir_cell.hpp"
@@ -31,13 +31,23 @@ int main(int argc, char ** argv) {
 	}
 	std::string configFilePath = argv[1];
 	double simTime = (argc > 2)? atof(argv[2]) : 500;
+    auto paramsProcessed = std::chrono::high_resolution_clock::now();
 
 	auto model = std::make_shared<AsymmCellDEVSCoupled<SIRState, double>>("sir", addAsymmCell, configFilePath);
 	model->buildModel();
+    auto modelGenerated = std::chrono::high_resolution_clock::now();
+    std::cout << "Model creation time: " << std::chrono::duration_cast<std::chrono::duration<double, std::ratio<1>>>( modelGenerated - paramsProcessed).count() << " seconds" << std::endl;
+
+    modelGenerated = std::chrono::high_resolution_clock::now();
 	auto rootCoordinator = cadmium::RootCoordinator(model);
-	auto logger = std::make_shared<cadmium::CSVLogger>("asymm_log.csv", ";");
-	rootCoordinator.setLogger(logger);
+	rootCoordinator.setLogger<cadmium::CSVLogger>("log_asymm_sir.csv", ";");
 	rootCoordinator.start();
-	rootCoordinator.simulate(simTime);
+    auto engineStarted = std::chrono::high_resolution_clock::now();
+    std::cout << "Engine creation time: " << std::chrono::duration_cast<std::chrono::duration<double, std::ratio<1>>>(engineStarted - modelGenerated).count() << " seconds" << std::endl;
+
+    engineStarted = std::chrono::high_resolution_clock::now();
+    rootCoordinator.simulate(simTime);
+    auto simulationDone =  std::chrono::high_resolution_clock::now();
+    std::cout << "Simulation time: " << std::chrono::duration_cast<std::chrono::duration<double, std::ratio<1>>>(simulationDone - engineStarted).count() << " seconds" << std::endl;
 	rootCoordinator.stop();
 }

example/celldevs_sir/main_grid_sir.cpp

@@ -4,9 +4,9 @@
  * ARSLab - Carleton University
  */
 
-#include <cadmium/celldevs/grid/coupled.hpp>
-#include <cadmium/core/logger/csv.hpp>
-#include <cadmium/core/simulation/root_coordinator.hpp>
+#include <cadmium/modeling/celldevs/grid/coupled.hpp>
+#include <cadmium/simulation/logger/csv.hpp>
+#include <cadmium/simulation/root_coordinator.hpp>
 #include <chrono>
 #include <fstream>
 #include <string>
@@ -41,8 +41,7 @@ int main(int argc, char ** argv) {
 
 	modelGenerated = std::chrono::high_resolution_clock::now();
 	auto rootCoordinator = cadmium::RootCoordinator(model);
-	auto logger = std::make_shared<cadmium::CSVLogger>("grid_log.csv", ";");
-	rootCoordinator.setLogger(logger);
+	rootCoordinator.setLogger<cadmium::CSVLogger>("log_grid_sir.csv", ";");
 	rootCoordinator.start();
 	auto engineStarted = std::chrono::high_resolution_clock::now();
 	std::cout << "Engine creation time: " << std::chrono::duration_cast<std::chrono::duration<double, std::ratio<1>>>(engineStarted - modelGenerated).count() << " seconds" << std::endl;

example/celldevs_sir/parallel_main_asymm_sir.cpp

@@ -1,14 +1,13 @@
 /**
  * SPDX-License-Identifier: MIT
  * Copyright (c) 2022-present Guillermo Trabes
- * ARSLab - Carleton University
  * Copyright (c) 2022-present Román Cárdenas Rodríguez
  * ARSLab - Carleton University
  */
 
-#include <cadmium/celldevs/asymm/coupled.hpp>
-#include <cadmium/core/logger/csv.hpp>
-#include <cadmium/core/simulation/parallel_root_coordinator.hpp>
+#include <cadmium/modeling/celldevs/asymm/coupled.hpp>
+#include <cadmium/simulation/logger/csv.hpp>
+#include <cadmium/simulation/parallel_root_coordinator.hpp>
 #include <fstream>
 #include <string>
 #include "asymm_sir_cell.hpp"
@@ -37,8 +36,7 @@ int main(int argc, char ** argv) {
 	auto model = std::make_shared<AsymmCellDEVSCoupled<SIRState, double>>("sir", addAsymmCell, configFilePath);
 	model->buildModel();
 	auto rootCoordinator = cadmium::ParallelRootCoordinator(model);
-	auto logger = std::make_shared<cadmium::CSVLogger>("asymm_log.csv", ";");
-	rootCoordinator.setLogger(logger);
+	rootCoordinator.setLogger<cadmium::CSVLogger>("log_parallel_asymm_sir.csv", ";");
 	rootCoordinator.start();
 	rootCoordinator.simulate(simTime);
 	rootCoordinator.stop();

example/celldevs_sir/parallel_main_grid_sir.cpp

@@ -1,14 +1,13 @@
 /**
  * SPDX-License-Identifier: MIT
  * Copyright (c) 2022-present Guillermo Trabes
- * ARSLab - Carleton University
  * Copyright (c) 2022-present Román Cárdenas Rodríguez
  * ARSLab - Carleton University
  */
 
-#include <cadmium/celldevs/grid/coupled.hpp>
-#include <cadmium/core/logger/csv.hpp>
-#include <cadmium/core/simulation/parallel_root_coordinator.hpp>
+#include <cadmium/modeling/celldevs/grid/coupled.hpp>
+#include <cadmium/simulation/logger/csv.hpp>
+#include <cadmium/simulation/parallel_root_coordinator.hpp>
 #include <chrono>
 #include <fstream>
 #include <string>
@@ -43,8 +42,7 @@ int main(int argc, char ** argv) {
 
 	modelGenerated = std::chrono::high_resolution_clock::now();
 	auto rootCoordinator = cadmium::ParallelRootCoordinator(model);
-	auto logger = std::make_shared<cadmium::CSVLogger>("grid_log.csv", ";");
-	rootCoordinator.setLogger(logger);
+	rootCoordinator.setLogger<cadmium::CSVLogger>("grid_log.csv", ";");
 	rootCoordinator.start();
 	auto engineStarted = std::chrono::high_resolution_clock::now();
 	std::cout << "Engine creation time: " << std::chrono::duration_cast<std::chrono::duration<double, std::ratio<1>>>(engineStarted - modelGenerated).count() << " seconds" << std::endl;

example/devstone/include/devstone.hpp

@@ -9,8 +9,8 @@
 #ifndef CADMIUM_EXAMPLE_DEVSTONE_HPP_
 #define CADMIUM_EXAMPLE_DEVSTONE_HPP_
 
-#include <cadmium/core/modeling/coupled.hpp>
-#include <cadmium/core/simulation/root_coordinator.hpp>
+#include <cadmium/modeling/devs/coupled.hpp>
+#include <cadmium/simulation/root_coordinator.hpp>
 #include <memory>
 #include "devstone_coupled.hpp"
 

example/devstone/include/devstone_atomic.hpp

@@ -9,7 +9,7 @@
 #ifndef CADMIUM_EXAMPLE_DEVSTONE_ATOMIC_HPP_
 #define CADMIUM_EXAMPLE_DEVSTONE_ATOMIC_HPP_
 
-#include <cadmium/core/modeling/atomic.hpp>
+#include <cadmium/modeling/devs/atomic.hpp>
 #include <iostream>
 
 namespace cadmium::example::devstone {

example/devstone/include/devstone_coupled.hpp

@@ -9,8 +9,8 @@
 #ifndef CADMIUM_EXAMPLE_DEVSTONE_COUPLED_HPP_
 #define CADMIUM_EXAMPLE_DEVSTONE_COUPLED_HPP_
 
-#include <cadmium/core/modeling/coupled.hpp>
-#include <cadmium/core/simulation/root_coordinator.hpp>
+#include <cadmium/modeling/devs/coupled.hpp>
+#include <cadmium/simulation/root_coordinator.hpp>
 #include <memory>
 
 namespace cadmium::example::devstone {

example/devstone/include/devstone_generator.hpp

@@ -9,7 +9,7 @@
 #ifndef CADMIUM_EXAMPLE_DEVSTONE_GENERATOR_HPP_
 #define CADMIUM_EXAMPLE_DEVSTONE_GENERATOR_HPP_
 
-#include <cadmium/core/modeling/atomic.hpp>
+#include <cadmium/modeling/devs/atomic.hpp>
 #include <iostream>
 
 namespace cadmium::example::devstone {