dsl: Add PETSc functionality

.github/workflows/docker-petsc.yml

@@ -0,0 +1,53 @@
+name: Publish devito-petsc docker image
+
+permissions:
+  contents: read
+
+on:
+  push:
+    branches:
+      - petsc
+
+jobs:
+  build-and-push:
+    name: Build and push devito-petsc image
+    runs-on: ubuntu-latest
+    env:
+      # Use buildkit
+      DOCKER_BUILDKIT: "1"
+
+      PETSC_REPO: https://gitlab.com/ZoeLeibowitz/petsc.git
+      PETSC_BRANCH: zoe/feature-da-section-sf
+
+    steps:
+      - name: Checkout devito
+        uses: actions/checkout@v5
+
+      - name: Set up QEMU
+        uses: docker/setup-qemu-action@v3
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Log in to DockerHub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKER_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
+
+      - name: Build & push petsc image
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          file: docker/Dockerfile.petsc
+          push: true
+          platforms: linux/amd64
+          tags: |
+            devitocodes/devito-petsc:latest
+          build-args: |
+            base=devitocodes/devito:gcc-dev-amd64
+            PETSC_REPO=${{ env.PETSC_REPO }}
+            PETSC_BRANCH=${{ env.PETSC_BRANCH }}
+
+      - name: Remove dangling layers
+        run: docker system prune -f

.github/workflows/examples-mpi.yml

@@ -19,9 +19,11 @@ on:
   push:
     branches:
       - main
+      - petsc
   pull_request:
     branches:
       - main
+      - petsc
 
 jobs:
   build:

.github/workflows/examples.yml

@@ -13,9 +13,11 @@ on:
   push:
     branches:
       - main
+      - petsc
   pull_request:
     branches:
       - main
+      - petsc
 
 jobs:
   tutorials:

.github/workflows/flake8.yml

@@ -13,9 +13,11 @@ on:
    push:
      branches:
        - main
+       - petsc
    pull_request:
      branches:
        - main
+       - petsc
 
 jobs:
   flake8:

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

@@ -13,9 +13,11 @@ on:
   push:
     branches:
       - main
+      - petsc
   pull_request:
     branches:
       - main
+      - petsc
 
 jobs:
   test-mpi-basic:

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

@@ -13,9 +13,11 @@ on:
   push:
     branches:
       - main
+      - petsc
   pull_request:
     branches:
       - main
+      - petsc
 
 jobs:
   pytest:

.github/workflows/pytest-petsc.yml

@@ -0,0 +1,95 @@
+name: CI-petsc
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+on:
+  push:
+    branches:
+      - main
+      - petsc
+  pull_request:
+    branches:
+      - main
+      - petsc
+
+jobs:
+  pytest:
+    name: ${{ matrix.name }}
+    runs-on: "${{ matrix.os }}"
+
+    env:
+      DOCKER_BUILDKIT: "1"
+      DEVITO_ARCH: "${{ matrix.arch }}"
+      DEVITO_LANGUAGE: ${{ matrix.language }}
+
+    strategy:
+      # Prevent all build to stop if a single one fails
+      fail-fast: false
+
+      # To be extended
+      matrix:
+        include:
+        - name: pytest-petsc
+          os: ubuntu-latest
+          arch: "gcc"
+          language: "C"
+
+    steps:
+    - name: Checkout devito
+      uses: actions/checkout@v4
+
+    - name: Log in to DockerHub
+      uses: docker/login-action@v2
+      with:
+        username: ${{ secrets.DOCKER_USERNAME }}
+        password: ${{ secrets.DOCKER_PASSWORD }}
+
+    - name: Build docker image
+      run: |
+          docker build \
+            -f docker/Dockerfile.petsc \
+            --build-arg PETSC_REPO=https://gitlab.com/ZoeLeibowitz/petsc.git \
+            --build-arg PETSC_BRANCH=zoe/feature-da-section-sf \
+            --tag devito_petsc_image:test .
+
+    - name: Set run prefix
+      run: |
+          echo "RUN_CMD=docker run --rm -t -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} --name testrun devito_petsc_image:test"  >> $GITHUB_ENV
+      id: set-run
+
+    - name: Set tests
+      run : |
+          echo "TESTS=tests/test_petsc.py" >> $GITHUB_ENV
+      id: set-tests
+
+    - 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 - serial
+      run: |
+        ${{ env.RUN_CMD }} mpiexec -n 1 pytest -m "not parallel" --cov --cov-config=.coveragerc --cov-report=xml ${{ env.TESTS }}
+
+    - name: Test with pytest - parallel
+      run: |
+        ${{ env.RUN_CMD }} mpiexec -n 1 pytest -m parallel --cov --cov-config=.coveragerc --cov-report=xml ${{ env.TESTS }}
+
+    - name: Test examples
+      run: |
+        ${{ env.RUN_CMD }} mpiexec -n 1 python3 examples/petsc/seismic/01_staggered_acoustic.py
+        ${{ env.RUN_CMD }} mpiexec -n 1 python3 examples/petsc/cfd/01_navierstokes.py
+        ${{ env.RUN_CMD }} mpiexec -n 1 python3 examples/petsc/Poisson/01_poisson.py
+        ${{ env.RUN_CMD }} mpiexec -n 1 python3 examples/petsc/Poisson/02_laplace.py
+        ${{ env.RUN_CMD }} mpiexec -n 1 python3 examples/petsc/Poisson/03_poisson.py
+        ${{ env.RUN_CMD }} mpiexec -n 1 python3 examples/petsc/Poisson/04_poisson.py
+        ${{ env.RUN_CMD }} mpiexec -n 1 python3 examples/petsc/random/01_helmholtz.py
+        ${{ env.RUN_CMD }} mpiexec -n 1 python3 examples/petsc/random/02_biharmonic.py
+
+    - name: Upload coverage to Codecov
+      if: "!contains(matrix.name, 'docker')"
+      uses: codecov/codecov-action@v4
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        name: ${{ matrix.name }}

.github/workflows/tutorials.yml

@@ -13,9 +13,11 @@ on:
   push:
     branches:
       - main
+      - petsc
   pull_request:
     branches:
       - main
+      - petsc
 
 jobs:
   tutorials:

conftest.py

@@ -15,6 +15,7 @@
 from devito.ir.iet import (FindNodes, FindSymbols, Iteration, ParallelBlock,
                            retrieve_iteration_tree)
 from devito.tools import as_tuple
+from devito.petsc.config import PetscOSError, get_petsc_dir
 
 try:
     from mpi4py import MPI  # noqa
@@ -34,7 +35,7 @@ def skipif(items, whole_module=False):
     accepted = set()
     accepted.update({'device', 'device-C', 'device-openmp', 'device-openacc',
                      'device-aomp', 'cpu64-icc', 'cpu64-icx', 'cpu64-nvc',
-                     'noadvisor', 'cpu64-arm', 'cpu64-icpx', 'chkpnt'})
+                     'noadvisor', 'cpu64-arm', 'cpu64-icpx', 'chkpnt', 'petsc'})
     accepted.update({'nodevice', 'noomp'})
     unknown = sorted(set(items) - accepted)
     if unknown:
@@ -98,6 +99,12 @@ def skipif(items, whole_module=False):
         if i == 'chkpnt' and Revolver is NoopRevolver:
             skipit = "pyrevolve not installed"
             break
+        if i == 'petsc':
+            try:
+                _ = get_petsc_dir()
+            except PetscOSError:
+                skipit = "PETSc is not installed"
+                break
 
     if skipit is False:
         return pytest.mark.skipif(False, reason='')

devito/core/__init__.py

@@ -7,6 +7,7 @@
     Cpu64CXXNoopCOperator, Cpu64CXXNoopOmpOperator,
     Cpu64AdvCXXOperator, Cpu64AdvCXXOmpOperator,
     Cpu64FsgCXXOperator, Cpu64FsgCXXOmpOperator,
+    Cpu64NoopPetscOperator, Cpu64AdvPetscOperator,
     Cpu64CustomCXXOmpOperator, Cpu64CustomCOperator
 )
 from devito.core.intel import (
@@ -45,12 +46,14 @@
 operator_registry.add(Cpu64NoopOmpOperator, Cpu64, 'noop', 'Copenmp')
 operator_registry.add(Cpu64CXXNoopCOperator, Cpu64, 'noop', 'CXX')
 operator_registry.add(Cpu64CXXNoopOmpOperator, Cpu64, 'noop', 'CXXopenmp')
+operator_registry.add(Cpu64NoopPetscOperator, Cpu64, 'noop', 'petsc')
 
 operator_registry.add(Cpu64AdvCOperator, Cpu64, 'advanced', 'C')
 operator_registry.add(Cpu64AdvOmpOperator, Cpu64, 'advanced', 'openmp')
 operator_registry.add(Cpu64AdvOmpOperator, Cpu64, 'advanced', 'Copenmp')
 operator_registry.add(Cpu64AdvCXXOperator, Cpu64, 'advanced', 'CXX')
 operator_registry.add(Cpu64AdvCXXOmpOperator, Cpu64, 'advanced', 'CXXopenmp')
+operator_registry.add(Cpu64AdvPetscOperator, Cpu64, 'advanced', 'petsc')
 
 operator_registry.add(Cpu64FsgCOperator, Cpu64, 'advanced-fsg', 'C')
 operator_registry.add(Cpu64FsgOmpOperator, Cpu64, 'advanced-fsg', 'openmp')

devito/core/cpu.py

@@ -11,13 +11,16 @@
 from devito.passes.iet import (CTarget, CXXTarget, COmpTarget, CXXOmpTarget,
                                avoid_denormals, linearize,
                                mpiize, hoist_prodders, relax_incr_dimensions,
-                               check_stability)
+                               check_stability, PetscTarget)
 from devito.tools import timed_pass
 
+from devito.petsc.iet.passes import lower_petsc_symbols
+
 __all__ = ['Cpu64NoopCOperator', 'Cpu64NoopOmpOperator', 'Cpu64AdvCOperator',
            'Cpu64AdvOmpOperator', 'Cpu64FsgCOperator', 'Cpu64FsgOmpOperator',
            'Cpu64CustomOperator', 'Cpu64CustomCXXOperator', 'Cpu64AdvCXXOperator',
-           'Cpu64AdvCXXOmpOperator', 'Cpu64FsgCXXOperator', 'Cpu64FsgCXXOmpOperator']
+           'Cpu64AdvCXXOmpOperator', 'Cpu64FsgCXXOperator', 'Cpu64FsgCXXOmpOperator',
+           'Cpu64NoopPetscOperator']
 
 
 class Cpu64OperatorMixin:
@@ -144,6 +147,9 @@ def _specialize_iet(cls, graph, **kwargs):
         # Symbol definitions
         cls._Target.DataManager(**kwargs).process(graph)
 
+        # Lower PETSc symbols
+        lower_petsc_symbols(graph, **kwargs)
+
         return graph
 
 
@@ -222,6 +228,9 @@ def _specialize_iet(cls, graph, **kwargs):
         # Symbol definitions
         cls._Target.DataManager(**kwargs).process(graph)
 
+        # Lower PETSc symbols
+        lower_petsc_symbols(graph, **kwargs)
+
         # Linearize n-dimensional Indexeds
         linearize(graph, **kwargs)
 
@@ -361,6 +370,15 @@ class Cpu64CXXNoopOmpOperator(Cpu64NoopOperator):
     LINEARIZE = True
 
 
+class Cpu64NoopPetscOperator(Cpu64NoopOperator):
+    _Target = PetscTarget
+
+    @classmethod
+    def _rcompile_wrapper(cls, **kwargs0):
+        kwargs0['language'] = 'petsc'
+        return super()._rcompile_wrapper(**kwargs0)
+
+
 class Cpu64AdvCOperator(Cpu64AdvOperator):
     _Target = CTarget
 
@@ -370,6 +388,15 @@ class Cpu64AdvCXXOperator(Cpu64AdvOperator):
     LINEARIZE = True
 
 
+class Cpu64AdvPetscOperator(Cpu64AdvOperator):
+    _Target = PetscTarget
+
+    @classmethod
+    def _rcompile_wrapper(cls, **kwargs0):
+        kwargs0['language'] = 'petsc'
+        return super()._rcompile_wrapper(**kwargs0)
+
+
 class Cpu64AdvOmpOperator(Cpu64AdvOperator):
     _Target = COmpTarget
 

devito/data/decomposition.py

@@ -450,6 +450,39 @@ def index_loc_to_glb(self, *args):
         else:
             raise TypeError("Expected 1 arguments, found %d" % len(args))
 
+    def index_glb_to_loc_unsafe(self, glb_idx, rel=True):
+        """
+        Convert a global index to a local index even if not owned.
+        WARNING: Must not be used to index data as there are no guard
+        rails against returning out of bound indices.
+        """
+        if not self.loc_empty:
+            loc_abs_min = self.loc_abs_min - self.glb_min
+            loc_abs_max = self.loc_abs_max - self.glb_min
+            glb_max = self.glb_max - self.glb_min
+        else:
+            loc_abs_min = self.loc_abs_min
+            loc_abs_max = self.loc_abs_max
+            glb_max = self.glb_max
+
+        glb_min = 0
+
+        base = loc_abs_min if rel else 0
+
+        # index_glb_to_loc(index)
+        # -> Base case, empty local subdomain
+        if self.loc_empty:
+            return None
+        # -> Handle negative index
+        if glb_idx < 0:
+            glb_idx = glb_max + glb_idx + 1
+        # -> Do the actual conversion
+        if loc_abs_min <= glb_idx <= loc_abs_max or glb_min <= glb_idx <= glb_max:
+            return glb_idx - base
+        else:
+            # This should raise an exception when used to access a numpy.array
+            return glb_idx
+
     def reshape(self, *args):
         """
         Create a new Decomposition with extended or reduced boundary subdomains.