Merge branch 'master' into master

Author: anandrdbz

.github/Dockerfile

@@ -7,38 +7,82 @@ ARG CXX_COMPILER
 ARG FC_COMPILER
 ARG COMPILER_PATH
 ARG COMPILER_LD_LIBRARY_PATH
+ARG AFAR_VERSION
+ARG OLCF_AFAR_ROOT=""
+
+ENV DEBIAN_FRONTEND=noninteractive
+ENV TZ=UTC
 
 RUN apt-get update -y && \
-    apt-get install -y software-properties-common ca-certificates gnupg && \
+    apt-get install -y software-properties-common ca-certificates gnupg wget && \
     add-apt-repository ppa:deadsnakes/ppa && \
     apt-get update -y && \
-    if [ "$TARGET" != "gpu" ]; then \
+    if [ "$TARGET" = "cpu" ]; then \
         apt-get install -y \
             build-essential git make cmake gcc g++ gfortran bc \
             python3.12 python3.12-venv python3-pip \
             openmpi-bin libopenmpi-dev libfftw3-dev \
             mpich libmpich-dev; \
-    else \
+    elif [ "$TARGET" = "gpu" ]; then \
         apt-get install -y \
             build-essential git make cmake bc \
             python3.12 python3.12-venv python3-pip \
             libfftw3-dev \
             openmpi-bin libopenmpi-dev; \
+    elif [ "$TARGET" = "amd" ]; then \
+        apt-get install -y \
+            build-essential git make gcc g++ gfortran bc \
+            python3.12 python3.12-venv python3-pip \
+            libfftw3-dev libnuma1 libdrm2 libdrm-amdgpu1; \
     fi && \
     update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.12 2 && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
+# AMD: download AFAR, install cmake 3.28 (Ubuntu 22.04 ships 3.22 which doesn't
+# recognize amdflang as LLVMFlang), then build MPICH with amdflang so the
+# generated mpi.mod is compiler-compatible.
+RUN if [ "$TARGET" = "amd" ] && [ -n "$AFAR_VERSION" ]; then \
+        OLCF_AFAR_ROOT="/opt/${AFAR_VERSION}" && \
+        wget -q "https://repo.radeon.com/rocm/misc/flang/${AFAR_VERSION}-ubuntu.tar.bz2" -O /tmp/afar.tar.bz2 && \
+        tar -xjf /tmp/afar.tar.bz2 -C /opt/ && \
+        rm /tmp/afar.tar.bz2 && \
+        CMAKE_VER=3.28.6 && \
+        wget -q "https://github.com/Kitware/CMake/releases/download/v${CMAKE_VER}/cmake-${CMAKE_VER}-linux-x86_64.sh" \
+            -O /tmp/cmake-install.sh && \
+        chmod +x /tmp/cmake-install.sh && \
+        /tmp/cmake-install.sh --prefix=/usr/local --skip-license --exclude-subdir && \
+        rm /tmp/cmake-install.sh && \
+        printf '#!/bin/bash\nargs=()\nwhile [ "$#" -gt 0 ]; do\n    if [ "$1" = "-soname" ]; then\n        args+=("-Wl,-soname,$2"); shift 2\n    else\n        args+=("$1"); shift\n    fi\ndone\nexec '"${OLCF_AFAR_ROOT}"'/bin/amdflang "${args[@]}"\n' \
+            > /usr/local/bin/amdflang-ld-wrap && \
+        chmod +x /usr/local/bin/amdflang-ld-wrap && \
+        MPICH_VER=3.4.3 && \
+        wget -q "https://www.mpich.org/static/downloads/${MPICH_VER}/mpich-${MPICH_VER}.tar.gz" \
+            -O /tmp/mpich.tar.gz && \
+        mkdir -p /tmp/mpich-src && \
+        tar -xzf /tmp/mpich.tar.gz -C /tmp/mpich-src --strip-components=1 && \
+        cd /tmp/mpich-src && \
+        FC=/usr/local/bin/amdflang-ld-wrap CC=gcc CXX=g++ \
+            ./configure --prefix=/opt/mpich --enable-shared --disable-static \
+            --with-device=ch3 2>&1 && \
+        make -j$(nproc) 2>&1 && \
+        make install 2>&1 && \
+        cd / && \
+        rm -rf /tmp/mpich-src /tmp/mpich.tar.gz; \
+    fi
+
 ENV OMPI_ALLOW_RUN_AS_ROOT=1
 ENV OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
+ENV HYDRA_LAUNCHER=fork
 ENV PATH="/opt/MFC:$PATH"
 
 COPY ../ /opt/MFC
 
 ENV CC=${CC_COMPILER}
 ENV CXX=${CXX_COMPILER}
 ENV FC=${FC_COMPILER}
-ENV PATH="${COMPILER_PATH}:$PATH"
-ENV LD_LIBRARY_PATH="${COMPILER_LD_LIBRARY_PATH}:${LD_LIBRARY_PATH:-}"
+ENV OLCF_AFAR_ROOT=${OLCF_AFAR_ROOT}
+ENV PATH="${COMPILER_PATH}:/opt/mpich/bin:$PATH"
+ENV LD_LIBRARY_PATH="${COMPILER_LD_LIBRARY_PATH}:/opt/mpich/lib:${LD_LIBRARY_PATH:-}"
 
 # Pre-install numpy into the venv before mfc.sh runs, as it's required at
 # build time by several dependencies (pandas, cantera, matplotlib, etc.) that
@@ -50,14 +94,18 @@ RUN python3.12 -m venv /opt/MFC/build/venv && \
 RUN echo "TARGET=$TARGET CC=$CC_COMPILER FC=$FC_COMPILER" && \
     cd /opt/MFC && \
     if [ "$TARGET" = "gpu" ]; then \
-      ./mfc.sh build --gpu -j $(nproc); \
+      ./mfc.sh build --gpu acc -j $(nproc); \
+    elif [ "$TARGET" = "amd" ]; then \
+      ./mfc.sh build --gpu mp -j $(nproc); \
     else \
       ./mfc.sh build -j $(nproc); \
     fi
 
 RUN cd /opt/MFC && \
     if [ "$TARGET" = "gpu" ]; then \
-      ./mfc.sh test -a --dry-run --gpu -j $(nproc); \
+      ./mfc.sh test -a --dry-run --gpu acc -j $(nproc); \
+    elif [ "$TARGET" = "amd" ]; then \
+      ./mfc.sh test -a --dry-run --gpu mp -j $(nproc); \
     else \
       ./mfc.sh test -a --dry-run -j $(nproc); \
     fi

.github/file-filter.yml

@@ -30,6 +30,8 @@ yml: &yml
   - '.github/workflows/bench.yml'
   - '.github/workflows/test.yml'
   - '.github/workflows/formatting.yml'
+  - '.github/workflows/fp-stability.yml'
+  - '.github/workflows/convergence.yml'
 
 checkall: &checkall
   - *fortran_src

.github/workflows/convergence.yml

@@ -4,15 +4,36 @@ on:
   push:
     branches: [master]
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
   workflow_dispatch:
 
 env:
   OMPI_MCA_rmaps_base_oversubscribe: 1
 
 jobs:
+  file-changes:
+    name: Detect File Changes
+    runs-on: ubuntu-latest
+    outputs:
+      checkall: ${{ steps.changes.outputs.checkall }}
+    steps:
+      - name: Clone
+        uses: actions/checkout@v4
+
+      - name: Detect Changes
+        uses: dorny/paths-filter@v3
+        id: changes
+        with:
+          filters: ".github/file-filter.yml"
+
   convergence:
     name: "Convergence"
     runs-on: ubuntu-latest
+    needs: [file-changes]
+    if: >-
+      !cancelled() &&
+      needs.file-changes.result == 'success' &&
+      (needs.file-changes.outputs.checkall == 'true' || github.event_name == 'workflow_dispatch')
     timeout-minutes: 240
 
     steps:

.github/workflows/deploy-tap.yml

@@ -28,6 +28,9 @@ jobs:
     permissions:
       contents: write
       pull-requests: write
+    environment:
+      name: homebrew
+      url: https://github.com/MFlowCode/homebrew-mfc
     steps:
       - name: Checkout MFC repository
         uses: actions/checkout@v4

.github/workflows/docker.yml

@@ -3,11 +3,17 @@ name: Containerization
 on:
   release:
     types: [published]
+  schedule:
+    - cron: '0 0 * * 0'
   workflow_dispatch:
     inputs:
       tag:
         description: 'tag to containerize'
-        required: true
+        required: false
+
+permissions:
+  contents: read
+  packages: write
 
 concurrency:
   group: Containerization
@@ -18,9 +24,11 @@ jobs:
     strategy:
       matrix:
         config:
-            - { name: 'cpu', runner: 'ubuntu-22.04',         base_image: 'ubuntu:22.04' }
-            - { name: 'gpu', runner: 'ubuntu-22.04',         base_image: 'nvcr.io/nvidia/nvhpc:23.11-devel-cuda_multi-ubuntu22.04' }
-            - { name: 'gpu', runner: 'ubuntu-22.04-arm',     base_image: 'nvcr.io/nvidia/nvhpc:23.11-devel-cuda_multi-ubuntu22.04' }
+            - { name: 'cpu',  tag: 'cpu',       runner: 'ubuntu-22.04',     base_image: 'ubuntu:22.04' }
+            - { name: 'cpu',  tag: 'cpu',       runner: 'ubuntu-22.04-arm', base_image: 'ubuntu:22.04' }
+            - { name: 'gpu',  tag: 'gpu-nvidia', runner: 'ubuntu-22.04',     base_image: 'nvcr.io/nvidia/nvhpc:24.5-devel-cuda_multi-ubuntu22.04', compiler_arch: 'Linux_x86_64' }
+            - { name: 'gpu',  tag: 'gpu-nvidia', runner: 'ubuntu-22.04-arm', base_image: 'nvcr.io/nvidia/nvhpc:24.5-devel-cuda_multi-ubuntu22.04', compiler_arch: 'Linux_aarch64' }
+            - { name: 'amd',  tag: 'gpu-amd',   runner: 'ubuntu-22.04',     base_image: 'ubuntu:22.04' }
     runs-on: ${{ matrix.config.runner }}
     outputs:
       tag: ${{ steps.clone.outputs.tag }}
@@ -36,25 +44,37 @@ jobs:
           docker-images: true
           swap-storage: true
 
-      - name: Login
+      - name: Login to Docker Hub
         uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
 
+      - name: Login to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
       - name: Setup Buildx
         uses: docker/setup-buildx-action@v3
 
-      - name: Setup QEMU
-        uses: docker/setup-qemu-action@v3
-
       - name: Clone
         id: clone
         run: |
-          TAG="${{ github.event.inputs.tag || github.ref_name }}"
+          if [ "${{ github.event_name }}" = "schedule" ]; then
+            BRANCH="master"
+            TAG="nightly"
+          else
+            BRANCH="${{ github.event.inputs.tag || github.ref_name }}"
+            TAG=$(echo "$BRANCH" | tr '/' '-')
+          fi
           echo "tag=$TAG" >> $GITHUB_OUTPUT
           echo "TAG=$TAG" >> $GITHUB_ENV
-          git clone --branch "$TAG" --depth 1 ${{ github.server_url }}/${{ github.repository }}.git mfc
+          OWNER="${{ github.repository_owner }}"
+          echo "GH_REGISTRY=ghcr.io/${OWNER,,}/mfc" >> $GITHUB_ENV
+          git clone --branch "$BRANCH" --depth 1 ${{ github.server_url }}/${{ github.repository }}.git mfc
 
       - name: Stage
         run: |
@@ -71,16 +91,13 @@ jobs:
           cp -r mfc/.git /mnt/share/.git
           cp mfc/.github/Dockerfile /mnt/share/
           cp mfc/.github/.dockerignore /mnt/share/
-          docker buildx create --name mfcbuilder --driver docker-container --use
 
       - name: Build and push image (cpu)
         if: ${{ matrix.config.name == 'cpu' }}
         uses: docker/build-push-action@v6
         with:
-          builder: mfcbuilder
           context: /mnt/share
           file: /mnt/share/Dockerfile
-          platforms: linux/amd64,linux/arm64
           build-args: |
             BASE_IMAGE=${{ matrix.config.base_image }}
             TARGET=${{ matrix.config.name }}
@@ -89,7 +106,11 @@ jobs:
             FC_COMPILER=${{ 'gfortran' }}
             COMPILER_PATH=${{ '/usr/bin' }}
             COMPILER_LD_LIBRARY_PATH=${{ '/usr/lib' }}
-          tags: ${{ secrets.DOCKERHUB_USERNAME }}/mfc:${{ env.TAG }}-${{ matrix.config.name }}
+          labels: |
+            org.opencontainers.image.source=https://github.com/${{ github.repository }}
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/mfc:${{ env.TAG }}-${{ matrix.config.tag }}-${{ matrix.config.runner }}
+            ${{ env.GH_REGISTRY }}:${{ env.TAG }}-${{ matrix.config.tag }}-${{ matrix.config.runner }}
           push: true
 
       - name: Build and push image (gpu)
@@ -105,28 +126,95 @@ jobs:
             CC_COMPILER=${{ 'nvc' }}
             CXX_COMPILER=${{ 'nvc++' }}
             FC_COMPILER=${{ 'nvfortran' }}
-            COMPILER_PATH=${{ '/opt/nvidia/hpc_sdk/Linux_x86_64/compilers/bin' }}
-            COMPILER_LD_LIBRARY_PATH=${{ '/opt/nvidia/hpc_sdk/Linux_x86_64/compilers/lib' }}
-          tags: ${{ secrets.DOCKERHUB_USERNAME }}/mfc:${{ env.TAG }}-${{ matrix.config.name }}-${{ matrix.config.runner}}
+            COMPILER_PATH=/opt/nvidia/hpc_sdk/${{ matrix.config.compiler_arch }}/compilers/bin
+            COMPILER_LD_LIBRARY_PATH=/opt/nvidia/hpc_sdk/${{ matrix.config.compiler_arch }}/compilers/lib
+          labels: |
+            org.opencontainers.image.source=https://github.com/${{ github.repository }}
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/mfc:${{ env.TAG }}-${{ matrix.config.tag }}-${{ matrix.config.runner }}
+            ${{ env.GH_REGISTRY }}:${{ env.TAG }}-${{ matrix.config.tag }}-${{ matrix.config.runner }}
+          push: true
+
+      - name: Set AMD AFAR vars
+        if: ${{ matrix.config.name == 'amd' }}
+        run: |
+          AFAR=rocm-afar-8873-drop-22.2.0
+          ROOT="/opt/${AFAR}"
+          echo "AFAR_VERSION=${AFAR}"      >> $GITHUB_ENV
+          echo "AFAR_ROOT=${ROOT}"         >> $GITHUB_ENV
+
+      - name: Build and push image (amd)
+        if: ${{ matrix.config.name == 'amd' }}
+        uses: docker/build-push-action@v6
+        with:
+          context: /mnt/share
+          file: /mnt/share/Dockerfile
+          build-args: |
+            BASE_IMAGE=${{ matrix.config.base_image }}
+            TARGET=amd
+            AFAR_VERSION=${{ env.AFAR_VERSION }}
+            OLCF_AFAR_ROOT=${{ env.AFAR_ROOT }}
+            CC_COMPILER=gcc
+            CXX_COMPILER=g++
+            FC_COMPILER=${{ env.AFAR_ROOT }}/bin/amdflang
+            COMPILER_PATH=${{ env.AFAR_ROOT }}/lib/llvm/bin:${{ env.AFAR_ROOT }}/bin
+            COMPILER_LD_LIBRARY_PATH=${{ env.AFAR_ROOT }}/lib:${{ env.AFAR_ROOT }}/lib/llvm/lib
+          labels: |
+            org.opencontainers.image.source=https://github.com/${{ github.repository }}
+          tags: |
+            ${{ secrets.DOCKERHUB_USERNAME }}/mfc:${{ env.TAG }}-gpu-amd-ubuntu-22.04
+            ${{ env.GH_REGISTRY }}:${{ env.TAG }}-gpu-amd-ubuntu-22.04
           push: true
 
   manifests:
     runs-on: ubuntu-latest
     needs: Container
+    environment:
+      name: containers
+      url: https://hub.docker.com/r/sbryngelson/mfc
     steps:
-      - name: Login
+      - name: Login to Docker Hub
         uses: docker/login-action@v3
         with:
           username: ${{ secrets.DOCKERHUB_USERNAME }}
           password: ${{ secrets.DOCKERHUB_PASSWORD }}
 
+      - name: Login to GHCR
+        uses: docker/login-action@v3
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Setup Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Set GHCR registry (lowercase)
+        run: |
+          OWNER="${{ github.repository_owner }}"
+          echo "GH_REGISTRY=ghcr.io/${OWNER,,}/mfc" >> $GITHUB_ENV
+
       - name: Create and Push Manifest Lists
         env:
           TAG: ${{ needs.Container.outputs.tag }}
-          REGISTRY: ${{ secrets.DOCKERHUB_USERNAME }}/mfc
+          DH: ${{ secrets.DOCKERHUB_USERNAME }}/mfc
+        run: |
+          GH="${{ env.GH_REGISTRY }}"
+          for R in "$DH" "$GH"; do
+            docker buildx imagetools create -t $R:$TAG-cpu       $R:$TAG-cpu-ubuntu-22.04 $R:$TAG-cpu-ubuntu-22.04-arm
+            docker buildx imagetools create -t $R:$TAG-gpu-nvidia $R:$TAG-gpu-nvidia-ubuntu-22.04 $R:$TAG-gpu-nvidia-ubuntu-22.04-arm
+            docker buildx imagetools create -t $R:$TAG-gpu-amd   $R:$TAG-gpu-amd-ubuntu-22.04
+          done
+
+      - name: Update latest tags
+        if: github.event_name == 'release'
+        env:
+          TAG: ${{ needs.Container.outputs.tag }}
+          DH: ${{ secrets.DOCKERHUB_USERNAME }}/mfc
         run: |
-          docker buildx imagetools create -t $REGISTRY:latest-cpu $REGISTRY:$TAG-cpu
-          docker manifest create $REGISTRY:$TAG-gpu $REGISTRY:$TAG-gpu-ubuntu-22.04 $REGISTRY:$TAG-gpu-ubuntu-22.04-arm
-          docker manifest create $REGISTRY:latest-gpu $REGISTRY:$TAG-gpu-ubuntu-22.04 $REGISTRY:$TAG-gpu-ubuntu-22.04-arm
-          docker manifest push $REGISTRY:$TAG-gpu
-          docker manifest push $REGISTRY:latest-gpu
+          GH="${{ env.GH_REGISTRY }}"
+          for R in "$DH" "$GH"; do
+            docker buildx imagetools create -t $R:latest-cpu       $R:$TAG-cpu-ubuntu-22.04 $R:$TAG-cpu-ubuntu-22.04-arm
+            docker buildx imagetools create -t $R:latest-gpu-nvidia $R:$TAG-gpu-nvidia-ubuntu-22.04 $R:$TAG-gpu-nvidia-ubuntu-22.04-arm
+            docker buildx imagetools create -t $R:latest-gpu-amd   $R:$TAG-gpu-amd-ubuntu-22.04
+          done