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

@@ -53,34 +53,17 @@ jobs:
         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
-        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
+      - name: Make dependency installer executable
+        run: chmod +x ./scripts/install_dependencies.sh
 
-      - name: Setup Ubuntu (Intel)
-        if:   matrix.os == 'ubuntu' && matrix.intel == true
-        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
+      - name: Run dependency installer
+        run: ./scripts/install_dependencies.sh
 
+      - name: Verify dependency installation
+        run: |
+          cmake --version
+          gcc --version
+          python3 --version
 
       - name: Build
         run:  |
@@ -135,4 +118,4 @@ 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

@@ -126,7 +126,7 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
             $<$<COMPILE_LANGUAGE:Fortran>:-fprofile-arcs>
             $<$<COMPILE_LANGUAGE:Fortran>:-ftest-coverage>
             $<$<COMPILE_LANGUAGE:Fortran>:-O1>
-	    )
+        )
 
         add_link_options(
             $<$<COMPILE_LANGUAGE:Fortran>:-lgcov>
@@ -148,7 +148,7 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
             -Wunderflow
             -Wrealloc-lhs
             -Wsurprising
-	    )
+        )
     endif()
 
     if (CMAKE_Fortran_COMPILER_VERSION VERSION_GREATER 10)
@@ -195,7 +195,7 @@ elseif ((CMAKE_Fortran_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_Fortran_COMPILER_
     add_compile_options(
         $<$<COMPILE_LANGUAGE:Fortran>:-Mfreeform>
         $<$<COMPILE_LANGUAGE:Fortran>:-cpp>
-	    $<$<COMPILE_LANGUAGE:Fortran>:-Minfo=inline>
+        $<$<COMPILE_LANGUAGE:Fortran>:-Minfo=inline>
         $<$<COMPILE_LANGUAGE:Fortran>:-Minfo=accel>
     )
 
@@ -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 +1,206 @@
+#!/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
+
+SUDO=${SUDO:-sudo}
+CI_INTEL=${CI_INTEL:-false}
+
+log() { echo ">>> $*"; }
+
+# Guarded append to GITHUB_ENV (safe when running locally)
+append_to_github_env() {
+    local line="$1"
+    if [[ -n "${GITHUB_ENV:-}" ]]; then
+        printf '%s\n' "$line" >> "$GITHUB_ENV"
+    else
+        printf '%s\n' "$line"
+    fi
+}
+
+verify_tool() {
+    local t="$1"
+    if command -v "$t" >/dev/null 2>&1; then
+        "$t" --version 2>&1 | head -n1 || true
+    else
+        echo "$t not found"
+    fi
+}
+
+# macOS / Homebrew
+install_macos() {
+    log "Detected macOS"
+
+    if ! command -v brew >/dev/null 2>&1; then
+        log "Homebrew not found. Please install Homebrew first."
+        return 1
+    fi
+
+    export PATH="/opt/homebrew/bin:/opt/homebrew/sbin:$PATH"
+    brew update
+    brew upgrade || true
+
+    pkgs=(coreutils python fftw hdf5 gcc@15 boost open-mpi lapack cmake protobuf)
+
+    for pkg in "${pkgs[@]}"; do
+        # Use brew list to detect installed formulae (correct for lib-only formulae)
+        if ! brew list --formula | grep -q "^${pkg%%@*}$"; then
+            log "Installing ${pkg}..."
+            brew install "${pkg}" || brew reinstall "${pkg}" || log "Failed to install ${pkg} (continuing)"
+        else
+            log "${pkg} already installed"
+        fi
+    done
+
+    # Attempt to fix common Homebrew linking quirks
+    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
+
+    # Export useful environment vars in GH Actions only (guarded)
+    append_to_github_env "FC=gfortran-15"
+    append_to_github_env "BOOST_INCLUDE=/opt/homebrew/include/"
+
+    log "Verifying installations..."
+    # Use guarded verification so script doesn't exit on set -e for these checks
+    if ! verify_tool cmake >/dev/null 2>&1; then echo "cmake not found"; fi
+    if ! verify_tool gcc >/dev/null 2>&1; then echo "gcc not found"; fi
+    if ! verify_tool gfortran >/dev/null 2>&1; then echo "gfortran not found"; fi
+    if ! verify_tool python3 >/dev/null 2>&1; then echo "python3 not found"; fi
+    if ! verify_tool mpirun >/dev/null 2>&1; then echo "mpirun not found"; fi
+
+    if brew list --formula | grep -q "^fftw$"; then
+        echo "FFTW library found"
+    else
+        echo "FFTW library not found"
+    fi
+
+    log "macOS dependencies installed successfully."
+}
+
+# Debian / Ubuntu
+install_debian() {
+    log "Detected Debian/Ubuntu"
+
+    $SUDO apt-get update -y
+    $SUDO apt-get install -y build-essential wget tar cmake python3 python3-dev pkg-config
+
+    if [[ "${CI_INTEL}" == "true" ]]; then
+        log "Intel OneAPI: adding repo with signed-by keyring (secure method)"
+        # download key and install to /etc/apt/keyrings (modern secure approach)
+        wget -q https://apt.repos.intel.com/intel-gpg-keys/GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB -O /tmp/intel-pubkey.PUB
+        $SUDO mkdir -p /etc/apt/keyrings
+        $SUDO install -m 0644 /tmp/intel-pubkey.PUB /etc/apt/keyrings/intel-archive-keyring.gpg
+        echo "deb [signed-by=/etc/apt/keyrings/intel-archive-keyring.gpg] https://apt.repos.intel.com/oneapi all main" | $SUDO tee /etc/apt/sources.list.d/oneapi.list > /dev/null
+        $SUDO apt-get update -y
+        $SUDO apt-get install -y intel-oneapi-compiler-fortran intel-oneapi-mpi intel-oneapi-mpi-devel || log "Intel packages failed; continuing"
+
+        # capture environment changes made by Intel setvars.sh and append only deltas to GITHUB_ENV
+        if [[ -f /opt/intel/oneapi/setvars.sh ]]; then
+            env > /tmp/env_before
+            source /opt/intel/oneapi/setvars.sh || log "sourcing Intel setvars.sh failed"
+            if [[ -n "${GITHUB_ENV:-}" ]]; then
+                # append only newly added / changed env vars
+                diff --unchanged-line-format="" --old-line-format="" --new-line-format="%L" <(sort /tmp/env_before) <(env | sort) >> "$GITHUB_ENV" || true
+            fi
+            rm -f /tmp/env_before
+        fi
+    fi
+
+    # Install common dev packages including fftw/openmpi/protobuf/boost
+    $SUDO apt-get install -y libfftw3-dev libopenmpi-dev openmpi-bin libprotobuf-dev protobuf-compiler libboost-all-dev
+
+    log "Verifying installations..."
+    if ! verify_tool cmake >/dev/null 2>&1; then echo "cmake not found"; fi
+    if ! verify_tool gfortran >/dev/null 2>&1; then echo "gfortran not found"; fi
+    if ! verify_tool python3 >/dev/null 2>&1; then echo "python3 not found"; fi
+    if ! verify_tool mpirun >/dev/null 2>&1; then echo "mpirun not found"; fi
+    if ! ldconfig -p | grep -q libfftw3; then echo "FFTW library not found"; fi
+}
+
+# RHEL / CentOS
+install_rhel() {
+    log "Detected RHEL/CentOS"
+
+    pkgs="tar wget make cmake3 gcc gcc-c++ python3-devel openmpi openmpi-devel fftw fftw-devel protobuf protobuf-devel boost-devel"
+    $SUDO yum install -y $pkgs || $SUDO dnf install -y $pkgs || log "yum/dnf install failed"
+
+    log "Verifying installations..."
+    if command -v cmake3 >/dev/null 2>&1; then
+        verify_tool cmake3
+    elif command -v cmake >/dev/null 2>&1; then
+        verify_tool cmake
+    else
+        echo "cmake not found"
+    fi
+
+    if ! verify_tool gfortran >/dev/null 2>&1; then echo "gfortran not found"; fi
+    if ! verify_tool python3 >/dev/null 2>&1; then echo "python3 not found"; fi
+    if ! verify_tool mpirun >/dev/null 2>&1; then echo "mpirun not found"; fi
+    if ! ldconfig -p | grep -q libfftw3; then echo "FFTW library not found"; fi
+}
+
+# Boost compile check
+boost_check() {
+    log "Verifying Boost by compiling a tiny program..."
+    cat <<'EOF' > /tmp/boost_check.cpp
+#include <boost/version.hpp>
+#include <iostream>
+int main(){ std::cout << "Boost version: " << BOOST_LIB_VERSION << std::endl; return 0;}
+EOF
+
+    # Try pkg-config first (if available)
+    if command -v pkg-config >/dev/null 2>&1 && pkg-config --exists boost; then
+        g++ /tmp/boost_check.cpp -o /tmp/boost_check $(pkg-config --cflags --libs boost) || true
+    else
+        # Try a plain compile (system include path), fallback to /opt/homebrew/include
+        if g++ /tmp/boost_check.cpp -o /tmp/boost_check 2>/dev/null; then
+            true
+        else
+            if [[ -d /opt/homebrew/include ]]; then
+                g++ -I/opt/homebrew/include /tmp/boost_check.cpp -o /tmp/boost_check || true
+            else
+                log "Could not compile boost_check; boost include path unknown"
+            fi
+        fi
+    fi
+
+    if [[ -x /tmp/boost_check ]]; then
+        /tmp/boost_check || true
+    else
+        log "boost_check binary not available"
+    fi
+}
+
+# Main entry
+main() {
+    case "$(uname -s)" in
+        Darwin)
+            install_macos
+            ;;
+        *)
+            if [[ -f /etc/debian_version ]]; then
+                install_debian
+            elif [[ -f /etc/redhat-release ]] || [[ -f /etc/centos-release ]]; then
+                install_rhel
+            else
+                log "Unsupported OS: $OSTYPE"
+                return 1
+            fi
+            ;;
+    esac
+
+    boost_check
+    log "Done."
+}
+
+main "$@"