Adding docker

.devcontainer/Dockerfile

@@ -0,0 +1,18 @@
+FROM mcr.microsoft.com/devcontainers/cpp:1-ubuntu-24.04
+
+ARG REINSTALL_CMAKE_VERSION_FROM_SOURCE="none"
+
+# Optionally install the cmake for vcpkg
+COPY ./reinstall-cmake.sh /tmp/
+
+RUN if [ "${REINSTALL_CMAKE_VERSION_FROM_SOURCE}" != "none" ]; then \
+        chmod +x /tmp/reinstall-cmake.sh && /tmp/reinstall-cmake.sh ${REINSTALL_CMAKE_VERSION_FROM_SOURCE}; \
+    fi \
+    && rm -f /tmp/reinstall-cmake.sh
+
+# [Optional] Uncomment this section to install additional vcpkg ports.
+# RUN su vscode -c "${VCPKG_ROOT}/vcpkg install <your-port-name-here>"
+
+# [Optional] Uncomment this section to install additional packages.
+# RUN apt-get update && export DEBIAN_FRONTEND=noninteractive \
+#     && apt-get -y install --no-install-recommends <your-package-list-here>

.devcontainer/devcontainer.json

@@ -0,0 +1,30 @@
+// For format details, see https://aka.ms/devcontainer.json. For config options, see the
+// README at: https://github.com/devcontainers/templates/tree/main/src/cpp
+{
+	"name": "C++",
+	"build": {
+		"dockerfile": "Dockerfile"
+	},
+
+	// Features to add to the dev container. More info: https://containers.dev/features.
+	// "features": {},
+
+	// Use 'forwardPorts' to make a list of ports inside the container available locally.
+	// "forwardPorts": [],
+
+	// Use 'postCreateCommand' to run commands after the container is created.
+	// "postCreateCommand": "gcc -v",
+
+	// Configure tool-specific properties.
+	// "customizations": {},
+
+	// Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root.
+	"remoteUser": "root",
+	"customizations": {
+		"vscode": {
+			"extensions": [
+				"ms-vscode.makefile-tools"
+			]
+		}
+	}
+}

.devcontainer/reinstall-cmake.sh

@@ -0,0 +1,59 @@
+#!/usr/bin/env bash
+#-------------------------------------------------------------------------------------------------------------
+# Copyright (c) Microsoft Corporation. All rights reserved.
+# Licensed under the MIT License. See https://go.microsoft.com/fwlink/?linkid=2090316 for license information.
+#-------------------------------------------------------------------------------------------------------------
+#
+set -e
+
+CMAKE_VERSION=${1:-"none"}
+
+if [ "${CMAKE_VERSION}" = "none" ]; then
+    echo "No CMake version specified, skipping CMake reinstallation"
+    exit 0
+fi
+
+# Cleanup temporary directory and associated files when exiting the script.
+cleanup() {
+    EXIT_CODE=$?
+    set +e
+    if [[ -n "${TMP_DIR}" ]]; then
+        echo "Executing cleanup of tmp files"
+        rm -Rf "${TMP_DIR}"
+    fi
+    exit $EXIT_CODE
+}
+trap cleanup EXIT
+
+
+echo "Installing CMake..."
+apt-get -y purge --auto-remove cmake
+mkdir -p /opt/cmake
+
+architecture=$(dpkg --print-architecture)
+case "${architecture}" in
+    arm64)
+        ARCH=aarch64 ;;
+    amd64)
+        ARCH=x86_64 ;;
+    *)
+        echo "Unsupported architecture ${architecture}."
+        exit 1
+        ;;
+esac
+
+CMAKE_BINARY_NAME="cmake-${CMAKE_VERSION}-linux-${ARCH}.sh"
+CMAKE_CHECKSUM_NAME="cmake-${CMAKE_VERSION}-SHA-256.txt"
+TMP_DIR=$(mktemp -d -t cmake-XXXXXXXXXX)
+
+echo "${TMP_DIR}"
+cd "${TMP_DIR}"
+
+curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_BINARY_NAME}" -O
+curl -sSL "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/${CMAKE_CHECKSUM_NAME}" -O
+
+sha256sum -c --ignore-missing "${CMAKE_CHECKSUM_NAME}"
+sh "${TMP_DIR}/${CMAKE_BINARY_NAME}" --prefix=/opt/cmake --skip-license
+
+ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake
+ln -s /opt/cmake/bin/ctest /usr/local/bin/ctest

.vscode/c_cpp_properties.json

@@ -8,10 +8,10 @@
                 "include/epiworld"
             ],
             "defines": [],
-            "compilerPath": "/usr/bin/clang",
+            "compilerPath": "/usr/bin/g++",
             "cStandard": "gnu17",
             "cppStandard": "c++17",
-            "intelliSenseMode": "clang-x64"
+            "intelliSenseMode": "${default}"
         }
     ],
     "version": 4

.vscode/launch.json

@@ -2,16 +2,16 @@
     "version": "0.2.0",
     "configurations": [
         {
-            "name": "C/C++: clang++ build and debug active file",
+            "name": "C/C++: g++ build and debug active file",
             "type": "cppdbg",
             "request": "launch",
             "program": "${fileDirname}/${fileBasenameNoExtension}",
             "stopAtEntry": false,
             "cwd": "${fileDirname}",
             "environment": [],
             "externalConsole": false,
-            "MIMode": "lldb",
-            "preLaunchTask": "C/C++: clang++ build active file"
+            "MIMode": "gdb",
+            "preLaunchTask": "C/C++: g++ build active file"
         },
     ]
 }

.vscode/tasks.json

@@ -2,13 +2,13 @@
     "tasks": [
         {
             "type": "cppbuild",
-            "label": "C/C++: clang++ build active file",
-            "command": "/usr/bin/clang++",
+            "label": "C/C++: g++ build active file",
+            "command": "/usr/bin/g++",
             "args": [
-                "-fcolor-diagnostics",
-                "-fansi-escape-codes",
+                "-fdiagnostics-color=always",
                 "-g",
                 "${file}",
+                "-fopenmp",
                 "-o",
                 "${fileDirname}/${fileBasenameNoExtension}"
             ],

docker/Makefile

@@ -1,10 +1,11 @@
 DIR_UP := $(shell cd .. && pwd)
+CMD="podman"
 
 build:
-	docker build -t gvegayon/epiworld:latest .
+	${CMD} build -t gvegayon/epiworld:latest .
 
 run:
-	docker run -i --rm -v $(DIR_UP):/home -w /home gvegayon/epiworld:latest
+	${CMD} run -i --rm -v $(DIR_UP):/home -w /home gvegayon/epiworld:latest
 
 push:
-	docker push gvegayon/epiworld:latest
+	${CMD} push gvegayon/epiworld:latest

examples/06-sir-omp/Makefile

@@ -1,4 +1,4 @@
-CXX=clang++
+CXX=g++
 
 main.o: main.cpp
 	$(CXX) -std=c++11 -Wall -pedantic -g -O2 -ftree-vectorize -fopenmp main.cpp -o main.o

examples/06b-sir-omp/Makefile

@@ -1,4 +1,4 @@
-CXX=clang++
+CXX=g++
 main.o: main.cpp
 	$(CXX) -std=c++11 -Wall -pedantic -g -O2 -ftree-vectorize -fopenmp main.cpp -o main.o
 README.md: main.o

examples/06b-sir-omp/main.cpp

@@ -8,8 +8,8 @@ using namespace epiworld;
 
 int main(int argc, char * argv[]) {
 
-    auto nthreads = 2;
-    auto nsims    = 10;
+    auto nthreads = 4;
+    auto nsims    = 100;
     if (argc == 3)
     {
         nthreads = strtol(argv[1], nullptr, 0);
@@ -25,7 +25,7 @@ int main(int argc, char * argv[]) {
     );
 
     model.agents_from_adjlist(
-        rgraph_smallworld(10000, 4, .01, false, model)
+        rgraph_smallworld(100000, 4, .01, false, model)
     );
 
     auto sav = make_save_run<int>(std::string("%03lu-episim.txt"));