Merge pull request GeoSymCodes#8 from GeoSymCodes/updateMaster

Update main branch in relation to original devito

.github/workflows/examples-mpi.yml

@@ -24,7 +24,17 @@ on:
 jobs:
   build:
     name: Examples with mpi
-    runs-on: ["self-hosted", "mpi", "examples"]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        mpi: ['openmpi', 'intelmpi']
+
+        include:
+        - mpi: openmpi
+          mpiarg: "-n 2 --oversubscribe"
+
+        - mpi: intelmpi
+          mpiarg: "-n 4"
 
     env:
       DEVITO_MPI: "1"
@@ -38,18 +48,19 @@ jobs:
     - name: Checkout devito
       uses: actions/checkout@v3
 
-    - name: Set environment
-      run: |
-        source $ENVHOME/devito-cpu-mpi/bin/activate
-        echo "PATH=$PATH" >> $GITHUB_ENV
-        echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" >> $GITHUB_ENV
+    - name: Setup MPI
+      uses: mpi4py/setup-mpi@v1
+      with:
+        mpi: ${{ matrix.mpi }}
 
     - name: Install dependencies
       run: |
         pip install --upgrade pip
         pip install -e .[extras,mpi,tests]
+        python3 scripts/clear_devito_cache.py
 
     - name: Test mpi notebooks
+      continue-on-error: true
       run : |
         ./scripts/create_ipyparallel_mpi_profile.sh
         ipcluster start --profile=mpi --engines=mpi -n 4 --daemonize
@@ -60,11 +71,11 @@ jobs:
 
     - name: Test seismic examples
       run: |
-        mpirun -n 4 pytest examples/seismic/tti/tti_example.py
-        mpirun -n 4 pytest examples/seismic/elastic/elastic_example.py
-        mpirun -n 4 pytest examples/seismic/viscoacoustic/viscoacoustic_example.py
-        mpirun -n 4 pytest examples/seismic/viscoelastic/viscoelastic_example.py
+        mpirun ${{ matrix.mpiarg }} pytest examples/seismic/tti/tti_example.py
+        mpirun ${{ matrix.mpiarg }} pytest examples/seismic/elastic/elastic_example.py
+        mpirun ${{ matrix.mpiarg }} pytest examples/seismic/viscoacoustic/viscoacoustic_example.py
+        mpirun ${{ matrix.mpiarg }} pytest examples/seismic/viscoelastic/viscoelastic_example.py
 
     - name: Test fwi examples with mpi
       run: |
-        mpirun -n 4 python examples/seismic/inversion/fwi.py
+        mpirun ${{ matrix.mpiarg }} python examples/seismic/inversion/fwi.py

.github/workflows/examples.yml

@@ -46,11 +46,11 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install -e .[tests]
-        pip install matplotlib pyrevolve
+        pip install -e .[tests,extras]
 
     - name: Tests in examples
-      run: py.test --cov --cov-config=.coveragerc --cov-report=xml examples/
+      run: |
+        py.test --cov --cov-config=.coveragerc --cov-report=xml examples/
 
     - name: Seismic acoustic examples
       run: |
@@ -87,7 +87,6 @@ jobs:
         python examples/cfd/example_diffusion.py
 
     - name: Upload coverage to Codecov
-      if: matrix.name != 'pytest-docker-py37-gcc-omp'
       uses: codecov/codecov-action@v3
       with:
         token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/flake8.yml

@@ -21,10 +21,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v3
-    - name: Set up Python 3.7
+    - name: Set up Python 3.9
       uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.9
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/pytest-core-mpi.yml

@@ -15,7 +15,7 @@ on:
       - main
 
 jobs:
-  build:
+  test-mpi-basic:
     name: pytest-mpi
     runs-on: ubuntu-20.04
     strategy:
@@ -25,6 +25,7 @@ jobs:
     env:
       DEVITO_LANGUAGE: "openmp"
       DEVITO_ARCH: "gcc-9"
+      OMP_NUM_THREADS: "1"
       CC: "gcc-9"
       CXX: "g++-9"
 
@@ -52,3 +53,29 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         name: pytest-mpi
+
+  test-mpi-docker:
+      name: pytest-mpi
+      runs-on: ${{ matrix.os }}
+      strategy:
+        matrix:
+          name: [gcc, icx]
+          include:
+            - name: gcc
+              arch: gcc
+              os: ubuntu-latest
+            - name: icx
+              arch: icx
+              os: ubuntu-latest
+
+      steps:
+      - name: Checkout devito
+        uses: actions/checkout@v3
+
+      - name: Build docker image
+        run: |
+          docker build . --file docker/Dockerfile.devito --tag devito_img --build-arg base=devitocodes/bases:cpu-${{ matrix.arch }}
+      
+      - name: Test with pytest
+        run: |
+          docker run --rm -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} -e OMP_NUM_THREADS=1 --name testrun devito_img pytest tests/test_mpi.py

.github/workflows/pytest-core-nompi.yml

@@ -30,18 +30,18 @@ jobs:
 
       matrix:
         name: [
-           pytest-ubuntu-py39-gcc11-noomp,
+           pytest-ubuntu-py311-gcc11-noomp,
            pytest-ubuntu-py38-gcc12-omp,
-           pytest-ubuntu-py39-gcc7-omp,
+           pytest-ubuntu-py37-gcc7-omp,
            pytest-ubuntu-py310-gcc10-noomp,
            pytest-ubuntu-py38-gcc8-omp,
            pytest-ubuntu-py39-gcc9-omp,
            pytest-osx-py37-clang-omp,
         ]
         set: [base, adjoint]
         include:
-        - name: pytest-ubuntu-py39-gcc11-noomp
-          python-version: '3.9'
+        - name: pytest-ubuntu-py311-gcc11-noomp
+          python-version: '3.11'
           os: ubuntu-22.04
           arch: "gcc-11"
           language: "C"
@@ -54,8 +54,8 @@ jobs:
           language: "openmp"
           sympy: "1.10"
 
-        - name: pytest-ubuntu-py39-gcc7-omp
-          python-version: '3.9'
+        - name: pytest-ubuntu-py37-gcc7-omp
+          python-version: '3.7'
           os: ubuntu-20.04
           arch: "gcc-7"
           language: "openmp"
@@ -78,7 +78,7 @@ jobs:
         - name: pytest-ubuntu-py39-gcc9-omp
           python-version: '3.9'
           os: ubuntu-20.04
-          arch: "gcc-9"
+          arch: "custom"
           language: "openmp"
           sympy: "1.9"
 
@@ -117,14 +117,14 @@ jobs:
     - name: Set run prefix
       run: |
           if [[ "${{ matrix.name }}" =~ "docker" ]]; then
-              echo "RUN_CMD=docker run --rm -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} -e DEVITO_ARCH=${{ matrix.arch }} --name testrun devito_img"  >> $GITHUB_ENV
+              echo "RUN_CMD=docker run --rm -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} --name testrun devito_img"  >> $GITHUB_ENV
           else
               echo "RUN_CMD=" >> $GITHUB_ENV
           fi
       id: set-run
 
     - name: Install ${{ matrix.arch }} compiler
-      if: "runner.os == 'linux' && !contains(matrix.name, 'docker')"
+      if: "runner.os == 'linux' && !contains(matrix.name, 'docker') && matrix.arch !='custom' "
       run : |
         sudo apt-get install -y ${{ matrix.arch }}
 
@@ -144,9 +144,12 @@ jobs:
         pip install -e .[tests]
         pip install sympy==${{matrix.sympy}}
 
+    - name: Check configuration
+      run: |
+        ${{ env.RUN_CMD }} python3 -c "from devito import configuration; print(''.join(['%s: %s \n' % (k, v) for (k, v) in configuration.items()]))"
+
     - name: Test with pytest
       run: |
-        ${{ env.RUN_CMD }} ${{ matrix.arch }} --version
         ${{ env.RUN_CMD }} pytest -k "${{ matrix.test-set }}" -m "not parallel" --cov --cov-config=.coveragerc --cov-report=xml ${{ env.TESTS }}
 
     - name: Upload coverage to Codecov

.github/workflows/triggers.yml

@@ -0,0 +1,27 @@
+name: Master triggers
+
+on:
+  push:
+    branches:
+      - master         # Push events on master branch
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Trigger doc build
+      uses: peter-evans/repository-dispatch@v2
+      with:
+        token: ${{ secrets.DEPLOY_DOC_PAT }}
+        repository: devitocodes/devitoproject.org
+        event-type: deploy-docs
+
+    - name: Trigger pro submodule update
+      uses: peter-evans/repository-dispatch@v2
+      with:
+        token: ${{ secrets.PRO_SUBMODULE }}
+        repository: devitocodespro/devitopro
+        event-type: update-submodule

.github/workflows/tutorials.yml

@@ -22,64 +22,63 @@ jobs:
     env:
       DEVITO_ARCH: "${{ matrix.compiler }}"
       DEVITO_LANGUAGE: ${{ matrix.language }}
-      PYTHON_VERSION: "3.7"
+      PYTHON_VERSION: "3.9"
 
     strategy:
       # Prevent all build to stop if a single one fails
       fail-fast: false
       matrix:
         name: [
-          tutos-ubuntu-gcc-py37,
-          tutos-osx-gcc-py37,
-          tutos-osx-clang-py37,
+          tutos-ubuntu-gcc-py39,
+          tutos-osx-clang-py39,
           ]
 
         include:
-          - name: tutos-ubuntu-gcc-py37
+          - name: tutos-ubuntu-gcc-py39
             os: ubuntu-latest
             compiler: gcc
             language: "openmp"
 
-          - name: tutos-osx-gcc-py37
+          - name: tutos-osx-clang-py39
             os: macos-latest
-            compiler: gcc-11
-            language: "openmp"
+            compiler: clang
+            language: "C"
 
     steps:
     - name: Checkout devito
       uses: actions/checkout@v3
 
-    - name: Set up Python 3.7
-      if: matrix.name != 'tutos-docker-gcc-py37'
+    - name: Set up Python 3.9
+      if: "!contains(matrix.name, 'docker')"
       uses: actions/setup-python@v4
       with:
-        python-version: 3.7
+        python-version: 3.9
 
     - uses: maxim-lobanov/setup-xcode@v1
       if: runner.os == 'macOS'
       with:
         xcode-version: latest-stable
 
     - name: Build docker image
-      if: matrix.name == 'tutos-docker-gcc-py37'
+      if: "contains(matrix.name, 'docker')"
       run: |
           docker build . --file docker/Dockerfile.devito --tag devito_img
 
     - name: Set run prefix
       run: |
-          if [ "${{ matrix.name }}" == 'tutos-docker-gcc-py37' ]; then
+          if [ "${{ matrix.name }}" == 'tutos-docker-gcc-py39' ]; then
               echo "RUN_CMD=docker run --rm --name testrun devito_img" >> $GITHUB_ENV
           else
               echo "RUN_CMD=" >> $GITHUB_ENV
           fi
       id: set-run
 
     - name: Install dependencies
-      if: matrix.name != 'tutos-docker-gcc-py37'
+      if: matrix.name != 'tutos-docker-gcc-py39'
       run: |
         python -m pip install --upgrade pip
-        pip install -e .[tests]
-        pip install matplotlib blosc
+        pip install -e .[tests,extras]
+        pip install blosc
 
     - name: Seismic notebooks
       run: |