Merge pull request #239 from NCAR/main

Release version 3.2.0
General solver, JIT solver, started GPU works

.dockerignore

@@ -1,9 +1,10 @@
-# blacklist all
+# ignore all
 *
 
-# whitelist things to copy
+# include things to copy
 !CMakeLists.txt
 !src/
+!docs/
 !libs/
 !test/
 !etc/

.github/workflows/clang_format.yml

@@ -0,0 +1,46 @@
+name: Clang-Format
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  format:
+    name: Run Clang-Format
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Install Clang-Format
+        run: sudo apt-get update && sudo apt-get install clang-format
+
+      - name: Check out code, run clang format, push changes
+        uses: actions/checkout@v3
+        with:
+          ref: ${{ github.head_ref }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Format code
+        run: |
+          find include -type f \( -name '*.hpp' -o -name '*.h' \) -exec clang-format -i --style=file {} +
+          find src -type f \( -name '*.cu' -o -name '*.hpp' -o -name '*.h' -o -name '*.cpp' \) -exec clang-format -i --style=file {} +
+          find test -type f \( -name '*.hpp' -o -name '*.h' -o -name '*.cpp' \) -exec clang-format -i --style=file {} +
+
+      - name: Commit and push changes
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "[email protected]"
+          git commit -am "Auto-format code using Clang-Format" || echo "No changes to commit"
+
+      - name: Push changes to main-formatting branch
+        run: |
+          git push origin HEAD:main-formatting
+
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v3
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          commit-message: "Auto-format code using Clang-Format"
+          title: "Auto-format code changes"
+          body: "This is an automated pull request to apply code formatting using Clang-Format."
+          branch: "main-formatting"

.github/workflows/gh_pages.yml

@@ -0,0 +1,125 @@
+# Build and deploy documentation to GitHub Pages
+name: GitHub Pages
+
+on: [ push, pull_request ]
+
+env:
+  DEFAULT_BRANCH: "release"
+
+jobs:
+  build-and-deploy:
+    name: Build and deploy to gh-pages
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+          lfs: true
+
+      - name: Debugging information
+        run: |
+          echo "github.ref:" ${{github.ref}}
+          echo "github.event_name:" ${{github.event_name}}
+          echo "github.head_ref:" ${{github.head_ref}}
+          echo "github.base_ref:" ${{github.base_ref}}
+          set -x
+          git rev-parse --abbrev-ref HEAD
+          git branch
+          git branch -a
+          git remote -v
+          python -V
+          pip list --not-required
+          pip list
+
+      # Clone and set up the old gh-pages branch
+      - name: Clone old gh-pages
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          set -x
+          git fetch
+          ( git branch gh-pages remotes/origin/gh-pages && git clone . --branch=gh-pages _gh-pages/ ) || mkdir _gh-pages
+          rm -rf _gh-pages/.git/
+          mkdir -p _gh-pages/branch/
+
+      # If a push and default branch, copy build to _gh-pages/ as the "main"
+      # deployment.
+      - name: Build and copy documentation (default branch)
+        if: |
+          contains(github.event_name, 'push') &&
+          contains(github.ref, env.DEFAULT_BRANCH)
+        run: |
+          set -x
+          mkdir -p _build/html/versions
+
+          # create two copies of the documentaiton
+          # 1. the frozen version, represented as vX.X in the version switcher
+          docker build -t micm -f Dockerfile.docs .
+          id=$(docker create micm)
+          docker cp $id:/build/docs/sphinx tmpdocs
+          docker rm -v $id
+          version=$(sed -nr "s/^release = f'v(.+)\{suffix\}'.*$/\1/p" docs/source/conf.py)
+          mv tmpdocs _build/html/versions/${version}
+
+          # 2. stable, represented as vX.X (stable) in the version switcher
+          # edit conf.py to produce a version string that looks like vX.X (stable)
+          docker build -t micm -f Dockerfile.docs --build-arg SUFFIX=" (stable)" .
+          id=$(docker create micm)
+          docker cp $id:/build/docs/sphinx tmpdocs
+          docker rm -v $id
+          mv tmpdocs _build/html/versions/stable
+          mv docs/switcher.json _build/html
+          # Delete everything under _gh-pages/ that is from the
+          # primary branch deployment.  Excludes the other branches
+          # _gh-pages/branch-* paths, and not including
+          # _gh-pages itself.
+          find _gh-pages/ -mindepth 1 ! -path '_gh-pages/branch*' ! -path '_gh-pages/versions*' -delete
+          rsync -a _build/html/versions/stable/* _gh-pages/
+
+      # If a push and not on default branch, then copy the build to
+      # _gh-pages/branch/$brname (transforming '/' into '--')
+      - name: Build and copy documentation (branch)
+        if: |
+          contains(github.event_name, 'push') &&
+          !contains(github.ref, env.DEFAULT_BRANCH)
+        run: |
+          set -x
+          docker build -t micm -f Dockerfile.docs .
+          id=$(docker create micm)
+          docker cp $id:/build/docs/sphinx tmpdocs
+          docker rm -v $id
+          brname="${{github.ref}}"
+          brname="${brname##refs/heads/}"
+          brdir=${brname//\//--}   # replace '/' with '--'
+          rm -rf   _gh-pages/branch/${brdir}
+          rsync -a tmpdocs/ _gh-pages/branch/${brdir}
+
+      # Go through each branch in _gh-pages/branch/, if it's not a
+      # ref, then delete it.
+      - name: Delete old feature branches
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          set -x
+          for brdir in `ls _gh-pages/branch/` ; do
+              brname=${brdir//--/\/}   # replace '--' with '/'
+              if ! git show-ref remotes/origin/$brname ; then
+                  echo "Removing $brdir"
+                  rm -r _gh-pages/branch/$brdir/
+              fi
+          done
+
+      # Add the .nojekyll file
+      - name: nojekyll
+        if: ${{ github.event_name == 'push' }}
+        run: |
+          touch _gh-pages/.nojekyll
+
+      # Deploy
+      # https://github.com/peaceiris/actions-gh-pages
+      - name: Deploy
+        uses: peaceiris/actions-gh-pages@v3
+        if: ${{ github.event_name == 'push' }}
+        with:
+          publish_branch: gh-pages
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: _gh-pages/
+          force_orphan: true

.github/workflows/test.yml

@@ -3,75 +3,104 @@ name: build
 on: [push, pull_request]
 
 jobs:
-  build_tests:
-    runs-on: ubuntu-latest
+  docker-build-and-test:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: recursive
-    - name: build Docker image
-      run: docker build -t micm .
-    - name: run tests in container
-      run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
-  # build_tests_with_openmp:
-  #   runs-on: ubuntu-latest
-  #   if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
-  #   steps:
-  #   - uses: actions/checkout@v3
-  #     with:
-  #       submodules: recursive
-  #   - name: build Docker image
-  #     run: docker build -t micm -f Dockerfile.openmp .
-  #   - name: run tests in container
-  #     run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
-  # build_tests_with_mpi:
-  #   runs-on: ubuntu-latest
-  #   if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
-  #   steps:
-  #   - uses: actions/checkout@v3
-  #     with:
-  #       submodules: recursive
-  #   - name: build Docker image
-  #     run: docker build -t micm -f Dockerfile.mpi .
-  #   - name: run tests in container
-  #     run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
-  build_tests_with_memcheck:
+    name: Build and Test - ${{ matrix.dockerfile }}
     runs-on: ubuntu-latest
-    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        dockerfile:
+          - Dockerfile
+          - Dockerfile.coverage
+          - Dockerfile.llvm
+          - Dockerfile.memcheck
+          - Dockerfile.no_json
+          - Dockerfile.nvhpc
+          # - Dockerfile.intel # intel image is too large for GH action
+          # - Dockerfile.openmp
+          # - Dockerfile.mpi
     steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: recursive
-    - name: build Docker image
-      run: docker build -t micm -f Dockerfile.memcheck .
-    - name: run tests in container
-      run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
-  build_tests_for_coverage:
-    runs-on: ubuntu-latest
-    if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
-    steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: recursive
-    - name: build Docker image
-      run: docker build -t micm -f Dockerfile.coverage .
-    - name: run tests in container
-      run: docker run --name test-container -t micm bash -c 'make coverage ARGS="--rerun-failed --output-on-failure -j8"'
-    - name: copy coverage from container
-      run: docker cp test-container:build/coverage.info .
-    - uses: codecov/codecov-action@v3
-      with:
-        token: ${{ secrets.CODECOV_TOKEN }}
-        files: coverage.info
-  build_tests_without_json:
-    runs-on: ubuntu-latest
+      - name: Checkout code
+        uses: actions/checkout@v2
+        with:
+          submodules: recursive
+
+      - name: Build Docker image
+        run: docker build -t micm -f ${{ matrix.dockerfile }} .
+
+      - name: Run tests in container
+        if: matrix.dockerfile != 'Dockerfile.coverage'
+        run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Run coverage tests in container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker run --name test-container -t micm bash -c 'make coverage ARGS="--rerun-failed --output-on-failure -j8"'
+
+      - name: Copy coverage from container
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        run: docker cp test-container:build/coverage.info .
+
+      - name: Upload coverage report
+        if: matrix.dockerfile == 'Dockerfile.coverage'
+        uses: codecov/codecov-action@v3
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: coverage.info
+
+  multiplatform:
     if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name != github.event.pull_request.base.repo.full_name
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os:
+          - macos-latest
+          - ubuntu-latest
+          - windows-latest
+        compiler:
+          - { cpp: g++, c: gcc}
+          - { cpp: clang++, c: clang}
+          - { cpp: cl, c: cl }
+        exclude:
+          - os: windows-latest
+            compiler: { cpp: clang++, c: clang }
+          - os: windows-latest
+            compiler: { cpp: g++, c: gcc }
+          - os: ubuntu-latest
+            compiler: { cpp: cl, c: cl }
+          - os: macos-latest
+            compiler: { cpp: cl, c: cl }
+    env:
+      CC: ${{ matrix.compiler.c }}
+      CXX: ${{ matrix.compiler.cpp }}
     steps:
-    - uses: actions/checkout@v3
-      with:
-        submodules: recursive
-    - name: build Docker image
-      run: docker build -t micm -f Dockerfile.no_json .
-    - name: run tests in container
-      run: docker run --name test-container -t micm bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+      - name: Checkout code
+        uses: actions/checkout@v2
+
+      - name: Install CMake
+        if: matrix.os == 'windows-latest'
+        run: choco install cmake --installargs 'ADD_CMAKE_TO_PATH=System'
+
+      - name: Install CMake
+        if: matrix.os != 'windows-latest'
+        run: |
+          if [[ "${{ matrix.os }}" == "ubuntu-latest" ]]; then
+            sudo apt-get update
+            sudo apt-get install -y cmake
+          elif [[ "${{ matrix.os }}" == "macos-latest" ]]; then
+            brew install cmake
+          fi
+
+      - name: Configure and build
+        run: |
+          mkdir build
+          cd build
+          cmake ..
+          cmake --build .
+
+      - name: Run tests
+        run: |
+          cd build
+          ctest -C Debug --rerun-failed --output-on-failure . --verbose

.gitignore

@@ -4,4 +4,5 @@
 **/CMakeFiles/
 doc/html/
 doc/latex/
-.vscode
+.vscode
+xcode/

CMakeLists.txt

@@ -4,7 +4,7 @@ cmake_minimum_required(VERSION 3.21)
 
 project(
   micm
-  VERSION 3.1.0
+  VERSION 3.2.0
   LANGUAGES CXX
 )
 
@@ -37,8 +37,19 @@ option(ENABLE_OPENMP "Enable OpenMP support" OFF)
 option(ENABLE_COVERAGE "Enable code coverage output" OFF)
 option(ENABLE_MEMCHECK "Enable memory checking in tests" OFF)
 option(ENABLE_JSON "Enable json configureation file reading" ON)
-option(ENABLE_REGRESSION_TESTS "Enable regression tests against the old pre-processed version of micm" ON)
 option(BUILD_DOCS "Build the documentation" OFF)
+option(ENABLE_CUDA "Build with Cuda support" OFF)
+option(ENABLE_OPENACC "Build with OpenACC Support" OFF)
+option(ENABLE_LLVM "Build with LLVM support for JIT-compiling" OFF)
+
+include(CMakeDependentOption)
+# Option to collect custom OpenACC flags
+cmake_dependent_option(ENABLE_GPU_TYPE "Enable custom CUDA flags" OFF
+  "ENABLE_OPENACC OR ENABLE_CUDA" ON)
+
+if(ENABLE_GPU_TYPE)
+  set(GPU_TYPE "" CACHE STRING "The GPU type being targeted")
+endif()
 
 ################################################################################
 # Dependencies