Dependency installer for macOS, Debian/Ubuntu, and RedHat/CentOS

.gitattributes

@@ -1,2 +1,5 @@
-/tests/**/* linguist-generated=true
-/toolchain/mechanisms/* linguist-generated=true
+*.fpp text eol=lf
+*.f90 text eol=lf
+*.sh text eol=lf
+/tests/**/* linguist-generated=true
+/toolchain/mechanisms/* linguist-generated=true

.github/workflows/test.yml

@@ -48,39 +48,21 @@ jobs:
       - name: Clone
         uses: actions/checkout@v4
 
-      - name: Set up Python 3.13
-        uses: actions/setup-python@v5
-        with:
-          python-version: '3.13'
-
-      - name: Setup MacOS
-        if:   matrix.os == 'macos'
-        run:  |
-          brew update
-          brew upgrade
-          brew install coreutils python fftw hdf5 gcc@15 boost open-mpi lapack
-          echo "FC=gfortran-15" >> $GITHUB_ENV
-          echo "BOOST_INCLUDE=/opt/homebrew/include/" >> $GITHUB_ENV
-
-      - name: Setup Ubuntu
-        if:   matrix.os == 'ubuntu' && matrix.intel == false
+      - name: Install Dependencies (Unified Script)
         run: |
-           sudo apt update -y
-           sudo apt install -y cmake gcc g++ python3 python3-dev hdf5-tools \
-                    libfftw3-dev libhdf5-dev openmpi-bin libopenmpi-dev \
-                    libblas-dev liblapack-dev
+          chmod +x ./scripts/install_dependencies.sh
+          ./scripts/install_dependencies.sh
 
-      - name: Setup Ubuntu (Intel)
-        if:   matrix.os == 'ubuntu' && matrix.intel == true
+      - name: Verify dependency installation
         run: |
-          wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
-          sudo add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
-          sudo apt-get update
-          sudo apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-mpi intel-oneapi-mpi-devel
-          source /opt/intel/oneapi/setvars.sh
-          printenv >> $GITHUB_ENV
+          cmake --version
+          gcc --version
+          python3 --version
 
+      - name: Set up Python 3.13
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.13'
 
       - name: Build
         run:  |
@@ -135,4 +117,4 @@ jobs:
         if:   matrix.lbl == 'frontier'
         with:
           name: logs-${{ strategy.job-index }}-${{ matrix.device }}
-          path: test-${{ matrix.device }}.out
+          path: test-${{ matrix.device }}.out

CMakeLists.txt

@@ -715,3 +715,12 @@ site_name(SITE_NAME)
 configure_file(
     "${CMAKE_CURRENT_SOURCE_DIR}/toolchain/cmake/configuration.cmake.in"
     "${CMAKE_CURRENT_BINARY_DIR}/configuration.txt")
+
+# -------------------------
+# Small dependency-check executable (used by CI to verify deps like Boost)
+find_package(Boost REQUIRED)
+add_executable(dependency_check examples/dependency_check/dependency_check.cpp)
+# make sure compiler sees Boost headers
+target_include_directories(dependency_check PRIVATE ${Boost_INCLUDE_DIRS})
+# don't force any link libraries: we use Boost header macros only
+# -------------------------

scripts/install_dependencies.sh

@@ -0,0 +1,153 @@
+#!/bin/bash
+# A solution for consolidating dependency installation commands for different operating systems (for macOS, Debian/Ubuntu, RedHat/CentOS)
+# Allows minimal repetition in command installations in multiple CI workflow files.
+# CI logs on which commands are being run.
+
+# Instructions:
+# 1. Run this command: chmod +x ./scripts/install_dependencies.sh
+# 2. Run the installer: ./scripts/install_dependencies.sh
+
+set -euo pipefail  
+set -x
+export DEBIAN_FRONTEND=noninteractive
+
+OS="$(uname -s)"
+echo "Installing dependencies for $OS OS"
+
+if command -v sudo >/dev/null 2>&1; then
+    SUDO="sudo"
+else
+    SUDO=""
+fi
+
+# macOS
+# if [[ "$OSTYPE" == "darwin"* ]]; then
+#     # Use Homebrew for macOS package management
+#     echo "Detected macOS."
+#     export PATH="/opt/homebrew/bin:/opt/homebrew/sbin:$PATH"
+#     brew update
+
+#     # Packages to install
+#     declare -A packages
+#     packages=(
+#         ["cmake"]="cmake"
+#         ["gcc"]="gcc"
+#         ["python3"]="[email protected]"
+#         ["boost"]="boost"
+#         ["protobuf"]="protobuf"
+#     )
+
+#     # Install missing packages
+#     for exe in "${!packages[@]}"; do
+#         formula="${packages[$exe]}"
+#         if ! command -v "$exe" >/dev/null 2>&1; then
+#             echo "Installing $formula..."
+#             brew install --verbose "$formula"
+#         else
+#             echo "$exe already installed"
+#         fi
+#     done
+
+#     # Verification
+#     echo "Verifying installations..."
+#     which cmake; cmake --version
+#     which gcc; gcc --version
+#     which python3; python3 --version
+#     brew list boost || echo "boost not found"
+#     brew list protobuf || echo "protobuf not found"
+
+#     echo "macOS dependencies installed successfully."
+# macOS
+if [[ "$OSTYPE" == "darwin"* ]]; then
+    echo "Detected macOS."
+    export PATH="/opt/homebrew/bin:/opt/homebrew/sbin:$PATH"
+    brew update
+    brew upgrade || true
+
+    # Install required packages (mirrors workflow setup)
+    pkgs=(coreutils python fftw hdf5 gcc@15 boost open-mpi lapack cmake protobuf)
+
+    for pkg in "${pkgs[@]}"; do
+        if ! brew list "$pkg" >/dev/null 2>&1; then
+            echo "Installing $pkg..."
+            brew install "$pkg" || brew reinstall "$pkg"
+        else
+            echo "$pkg already installed."
+        fi
+    done
+
+    # Fix potential linking issues for Homebrew-installed libraries
+    brew link --overwrite python || true
+    brew link --overwrite boost || true
+    brew link --overwrite hdf5 || true
+    brew link --overwrite cmake || true
+    brew link --overwrite protobuf || true
+
+    # Environment setup
+    echo "FC=gfortran-15" >> "$GITHUB_ENV"
+    echo "BOOST_INCLUDE=/opt/homebrew/include/" >> "$GITHUB_ENV"
+
+    echo "macOS dependencies installed successfully."
+
+# Debian/Ubuntu
+elif [[ -f /etc/debian_version ]]; then
+    echo "Detected Debian/Ubuntu"
+
+    # Install all required packages (this time with openmpi and fftw)
+    if [[ "${CI_INTEL:-false}" == "true" ]]; then
+        echo "Intel OneAPI environment detected. Installing Intel compilers and MPI..."
+        wget https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        $SUDO apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
+        $SUDO add-apt-repository "deb https://apt.repos.intel.com/oneapi all main"
+        $SUDO apt-get update
+        $SUDO apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-mpi intel-oneapi-mpi-devel
+        source /opt/intel/oneapi/setvars.sh
+        if [[ -n "${GITHUB_ENV:-}" ]]; then
+            echo "source /opt/intel/oneapi/setvars.sh" >> "$GITHUB_ENV"
+        fi
+        printenv >> "$GITHUB_ENV"
+        echo "Intel OneAPI installation completed."
+    else
+        echo "Standard GNU environment detected. Installing open-source toolchain..."
+        $SUDO apt-get update -y
+        pkgs="tar wget make cmake gcc g++ python3 python3-dev openmpi-bin libopenmpi-dev fftw3 libfftw3-dev protobuf-compiler libboost-all-dev"
+        $SUDO apt-get install -y $pkgs
+
+        # Verification
+        echo "Verifying installations..."
+        cmake --version || echo "cmake not found"
+        gcc --version || echo "gcc not found"
+        python3 --version || echo "python3 not found"
+        mpirun --version || echo "mpirun not found"
+        ldconfig -p | grep -q libfftw3 || echo "FFTW library not found"
+
+        echo "Linux (GNU) dependencies installed successfully."
+    fi
+
+# RedHat/CentOS
+elif [[ -f /etc/redhat-release ]]; then
+    echo "Detected RedHat/CentOS"
+    $SUDO yum install -y epel-release
+
+    # Install all required packages (this time with openmpi and fftw)
+    pkgs="tar wget make cmake3 gcc gcc-c++ python3 openmpi fftw protobuf boost-devel"
+    $SUDO yum install -y $pkgs
+
+    # Verification
+    echo "Verifying installations..."
+    cmake3 --version || echo "cmake3 not found"
+    gcc --version || echo "gcc not found"
+    python3 --version || echo "python3 not found"
+    mpirun --version || echo "mpirun not found"
+    rpm -q fftw || echo "FFTW library not found"
+
+    echo "RedHat/CentOS dependencies installed successfully."
+
+
+# If Unsupported OS
+else
+    echo "Unsupported OS: $OSTYPE"
+    exit 1
+fi
+
+echo "Dependencies installed successfully."