Merge branch 'devitocodes:master' into master

ZoeLeibowitz · Apr 26, 2024 · 3a7133a · 3a7133a
2 parents d28f3af + 6ac1c2c
commit 3a7133a
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Showing 49 changed files with 1,710 additions and 499 deletions.
diff --git a/.github/workflows/docker-bases.yml b/.github/workflows/docker-bases.yml
@@ -52,7 +52,7 @@ jobs:
         run: docker system prune -a -f
 
       - name: GCC image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.cpu'
@@ -61,6 +61,7 @@ jobs:
           build-args: 'arch=gcc'
           tags: 'devitocodes/bases:cpu-gcc'
 
+
 #######################################################
 ############## Intel OneApi CPU #######################
 #######################################################
@@ -93,7 +94,7 @@ jobs:
         run: docker system prune -a -f
 
       - name: ICX image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.intel'
@@ -103,7 +104,7 @@ jobs:
           tags: 'devitocodes/bases:cpu-icx'
 
       - name: SYCL CPU image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.intel'
@@ -113,7 +114,7 @@ jobs:
           tags: 'devitocodes/bases:cpu-sycl'
 
       - name: SYCL GPU image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.intel'
@@ -154,7 +155,7 @@ jobs:
         run: docker system prune -a -f
 
       - name: NVC image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.nvidia'
@@ -164,7 +165,7 @@ jobs:
           tags: 'devitocodes/bases:nvidia-nvc'
 
       - name: NVCC image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.nvidia'
@@ -174,7 +175,7 @@ jobs:
           tags: 'devitocodes/bases:nvidia-nvcc'
 
       - name: NVC host image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.nvidia'
@@ -215,7 +216,7 @@ jobs:
         run: docker system prune -a -f
 
       - name: AMD image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.amd'
@@ -224,7 +225,7 @@ jobs:
           tags: devitocodes/bases:amd
 
       - name: AMD HIP image
-        uses: docker/build-push-action@v3
+        uses: docker/build-push-action@v5
         with:
           context: .
           file: './docker/Dockerfile.amd'

diff --git a/.github/workflows/docker-devito.yml b/.github/workflows/docker-devito.yml
@@ -106,4 +106,4 @@ jobs:
 
       - name: Run tests
         run: |
-         docker run ${{ matrix.flag }} --rm --name testrun 'devitocodes/devito:${{ matrix.tag }}-dev' pytest ${{ matrix.test }}
+         docker run ${{ matrix.flag }} --rm -t --name testrun 'devitocodes/devito:${{ matrix.tag }}-dev' pytest ${{ matrix.test }}
diff --git a/.github/workflows/pytest-core-mpi.yml b/.github/workflows/pytest-core-mpi.yml
@@ -48,6 +48,12 @@ jobs:
         python3 scripts/clear_devito_cache.py
         python3 -m pytest --cov --cov-config=.coveragerc --cov-report=xml -m parallel tests/
 
+    - name: Test examples with MPI
+      run: |
+        python3 scripts/clear_devito_cache.py
+        DEVITO_MPI=1 mpirun -n 2 python3 -m pytest examples/seismic/acoustic
+        DEVITO_MPI=1 mpirun -n 2 python3 -m pytest examples/seismic/tti
+
     - name: Upload coverage to Codecov
       uses: codecov/codecov-action@v4
       with:
@@ -64,9 +70,12 @@ jobs:
             - name: gcc
               arch: gcc
               os: ubuntu-latest
+              mpiflag: ""
             - name: icx
               arch: icx
               os: ubuntu-latest
+              # Need safe math for icx due to inaccuracy with mpi+sinc interpolation
+              mpiflag: "-e DEVITO_SAFE_MATH=1"
 
       steps:
       - name: Checkout devito
@@ -78,4 +87,9 @@ jobs:
       
       - name: Test with pytest
         run: |
-          docker run --rm -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} -e OMP_NUM_THREADS=1 --name testrun devito_img pytest tests/test_mpi.py
+          docker run --rm -t -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} -e OMP_NUM_THREADS=1 --name testrun devito_img pytest tests/test_mpi.py
+
+      - name: Test examples with MPI
+        run: |
+          docker run --rm -t ${{ matrix.mpiflag }} -e DEVITO_MPI=1 -e OMP_NUM_THREADS=1 --name examplerun devito_img mpiexec -n 2 pytest examples/seismic/acoustic
+          docker run --rm -t -e DEVITO_MPI=1 -e OMP_NUM_THREADS=1 --name examplerun devito_img mpiexec -n 2 pytest examples/seismic/tti
diff --git a/.github/workflows/pytest-core-nompi.yml b/.github/workflows/pytest-core-nompi.yml
@@ -36,7 +36,7 @@ jobs:
            pytest-ubuntu-py310-gcc10-noomp,
            pytest-ubuntu-py312-gcc13-omp,
            pytest-ubuntu-py39-gcc9-omp,
-           pytest-osx-py37-clang-omp,
+           pytest-osx-py312-clang-omp,
            pytest-docker-py39-gcc-omp,
            pytest-docker-py39-icx-omp
         ]
@@ -84,8 +84,8 @@ jobs:
           language: "openmp"
           sympy: "1.9"
 
-        - name: pytest-osx-py37-clang-omp
-          python-version: '3.7'
+        - name: pytest-osx-py312-clang-omp
+          python-version: '3.12'
           os: macos-latest
           arch: "clang"
           language: "C"
@@ -112,7 +112,7 @@ jobs:
           test-set: 'adjoint'
 
         exclude:
-        - name: pytest-osx-py37-clang-omp
+        - name: pytest-osx-py312-clang-omp
           set: adjoint
 
     steps:
@@ -133,7 +133,7 @@ jobs:
     - name: Set run prefix
       run: |
           if [[ "${{ matrix.name }}" =~ "docker" ]]; then
-              echo "RUN_CMD=docker run --rm -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} --name testrun devito_img"  >> $GITHUB_ENV
+              echo "RUN_CMD=docker run --rm -t -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} --name testrun devito_img"  >> $GITHUB_ENV
           else
               echo "RUN_CMD=" >> $GITHUB_ENV
           fi

diff --git a/.github/workflows/pytest-gpu.yml b/.github/workflows/pytest-gpu.yml
@@ -57,7 +57,7 @@ jobs:
           base: "devitocodes/bases:nvidia-nvc"
           tags: ["self-hosted", "nvidiagpu"]
           test_drive_cmd: "nvidia-smi"
-          flags: '--gpus all --rm --name testrun-nvc'
+          flags: '--gpus all --rm -t --name testrun-nvc'
 
         - name: pytest-gpu-omp-amd
           test_files: "tests/test_adjoint.py tests/test_gpu_common.py tests/test_gpu_openmp.py"
@@ -66,7 +66,7 @@ jobs:
           test_drive_cmd: "rocm-smi"
           # Attach the AMD GPU devices `/dev` and add user to video and render (109 on wampa) group
           # Options from https://rocmdocs.amd.com/en/latest/ROCm_Virtualization_Containers/ROCm-Virtualization-&-Containers.html
-          flags: "--network=host --device=/dev/kfd --device=/dev/dri --ipc=host --group-add video --group-add $(getent group render | cut -d: -f3) --cap-add=SYS_PTRACE --security-opt seccomp=unconfined --rm --name testrun-amd"
+          flags: "--network=host --device=/dev/kfd --device=/dev/dri --ipc=host --group-add video --group-add $(getent group render | cut -d: -f3) --cap-add=SYS_PTRACE --security-opt seccomp=unconfined --rm -t --name testrun-amd"
 
     steps:
     - name: Checkout devito

diff --git a/.github/workflows/tutorials.yml b/.github/workflows/tutorials.yml
@@ -22,15 +22,14 @@ jobs:
     env:
       DEVITO_ARCH: "${{ matrix.compiler }}"
       DEVITO_LANGUAGE: ${{ matrix.language }}
-      PYTHON_VERSION: "3.9"
 
     strategy:
       # Prevent all build to stop if a single one fails
       fail-fast: false
       matrix:
         name: [
           tutos-ubuntu-gcc-py39,
-          tutos-osx-clang-py39,
+          tutos-osx-clang-py311,
           tutos-docker-gcc-py39
           ]
 
@@ -39,26 +38,29 @@ jobs:
             os: ubuntu-latest
             compiler: gcc
             language: "openmp"
+            pyver: "3.9"
 
-          - name: tutos-osx-clang-py39
+          - name: tutos-osx-clang-py311
             os: macos-latest
             compiler: clang
             language: "C"
+            pyver: "3.11"
 
           - name: tutos-docker-gcc-py39
             os: ubuntu-latest
             compiler: gcc
             language: "openmp"
+            pyver: "3.9"
 
     steps:
     - name: Checkout devito
       uses: actions/checkout@v4
 
-    - name: Set up Python 3.9
+    - name: Set up Python ${{ matrix.pyver }}
       if: "!contains(matrix.name, 'docker')"
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: ${{ matrix.pyver }}
 
     - uses: maxim-lobanov/setup-xcode@v1
       if: runner.os == 'macOS'
@@ -73,7 +75,7 @@ jobs:
     - name: Set run prefix
       run: |
           if [ "${{ matrix.name }}" == 'tutos-docker-gcc-py39' ]; then
-              echo "RUN_CMD=docker run --rm --name testrun devito_img" >> $GITHUB_ENV
+              echo "RUN_CMD=docker run --rm -t --name testrun devito_img" >> $GITHUB_ENV
           else
               echo "RUN_CMD=" >> $GITHUB_ENV
           fi

diff --git a/FAQ.md b/FAQ.md
@@ -596,9 +596,9 @@ By default, Devito compiles the generated code using flags that maximize the run
 
 [top](#Frequently-Asked-Questions)
 
-## Can I control the MPI domain decomposition
+## Can I control the MPI domain decomposition?
 
-Until Devito v3.5 included, domain decomposition occurs along the fastest axis. As of later versions, domain decomposition occurs along the slowest axis, for performance reasons.  And yes, it is possible to control the domain decomposition in user code, but this is not neatly documented. Take a look at `test_custom_topology` in [this file](https://github.com/devitocodes/devito/blob/master/tests/test_mpi.py). In essence, `Grid` accepts the optional argument `topology`, which allows the user to pass a custom topology as an n-tuple, where `n` is the number of distributed dimensions. For example, for a two-dimensional grid, the topology `(4, 1)` will decompose the slowest axis into four partitions, one partition per MPI rank, while the fastest axis will be replicated over all MPI ranks.
+Until Devito v3.5 included, domain decomposition occurs along the fastest axis. As of later versions, domain decomposition occurs along the slowest axis, for performance reasons.  And yes, it is possible to control the domain decomposition in user code, but this is not neatly documented. Take a look at `class CustomTopology` in [distributed.py](https://github.com/devitocodes/devito/blob/master/devito/mpi/distributed.py) and `test_custom_topology` in [this file](https://github.com/devitocodes/devito/blob/master/tests/test_mpi.py). In essence, `Grid` accepts the optional argument `topology`, which allows the user to pass a custom topology as an n-tuple, where `n` is the number of distributed dimensions. For example, for a two-dimensional grid, the topology `(4, 1)` will decompose the slowest axis into four partitions, one partition per MPI rank, while the fastest axis will be replicated over all MPI ranks.
 
 
 [top](#Frequently-Asked-Questions)

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,3 +1,7 @@
 include versioneer.py
 include devito/_version.py
-include requirements.txt requirements-optional.txt
+include requirements.txt
+include requirements-optional.txt
+include requirements-testing.txt
+include requirements-mpi.txt
+include requirements-nvidia.txt