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