dsl: Add PETSc functionality #2570
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- Temp fix until VecReplaceArray works properly in conjunction with PetscMemoryAllocator
* Compiler: Add basic initguess callback - to be improved
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #2570 +/- ##
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- Coverage 83.01% 76.00% -7.02%
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Files 248 273 +25
Lines 51074 54428 +3354
Branches 4491 4603 +112
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- Hits 42401 41367 -1034
- Misses 7902 12225 +4323
- Partials 771 836 +65
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compiler: Add Devito+PETSc MPI test
Add PETSc logging infrastructure
dsl/compiler: Fix&tidy PETSc mixed solver functionality
…ate logging (#2718) * compiler: Utilise petsctools and start extending solver parameters functionality examples: Add example using argparse in conjunction with PetscInitialize * compiler: Edit argument to PetscInitialize * compiler: Use petsctools to process solver params and start callback to set petsc options * compiler: Progress on petscoptions callbacks * dsl/compiler: Re-factor solver params, add solver_parameters.py file * misc: Add tests * compiler: Start extending the PetscSummary * dsl: Fix hashing for solveexpr * misc: Add tests and clean up * compiler: Add utility function inside petsc routines * misc: Clean up * tests: Add command line tests with random prefixes * compiler: Create dummy op for petscgetargs * misc: Update requirements * misc: Create getargs Op inside function * compiler/dsl: Add get_info functionality to petscsolve * compiler/misc: Drop petscgetargs callback, add functions to logging/get_info, clean up and more tests * workflows: Fix serial wf run
* misc/compiler: Rename/separate files, clean up, add lower_petsc_symbols and change PETScSolve to petscsolve
| # (PetscScalar (*)[rhs_vec->size[1]]) ctx0; | ||
| # This is the case when a1 is a LocalCompositeObject (i.e a1.is_AbstractObject) | ||
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| if o.offset: |
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Is the offset a symbol at this point?
| name: ${{ matrix.name }} | ||
| runs-on: "${{ matrix.os }}" | ||
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| env: | ||
| DOCKER_BUILDKIT: "1" | ||
| DEVITO_ARCH: "${{ matrix.arch }}" | ||
| DEVITO_LANGUAGE: ${{ matrix.language }} | ||
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| strategy: | ||
| # Prevent all build to stop if a single one fails | ||
| fail-fast: false | ||
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| # To be extended | ||
| matrix: | ||
| include: | ||
| - name: pytest-petsc | ||
| os: ubuntu-latest | ||
| arch: "gcc" | ||
| language: "C" | ||
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| steps: | ||
| - name: Checkout devito | ||
| uses: actions/checkout@v4 | ||
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| - name: Log in to DockerHub | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| username: ${{ secrets.DOCKER_USERNAME }} | ||
| password: ${{ secrets.DOCKER_PASSWORD }} | ||
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| - name: Build docker image | ||
| run: | | ||
| docker build -f docker/Dockerfile.petsc --tag devito_petsc_image:test . | ||
| - name: Set run prefix | ||
| run: | | ||
| echo "RUN_CMD=docker run --rm -t -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} --name testrun devito_petsc_image:test" >> $GITHUB_ENV | ||
| id: set-run | ||
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| - name: Set tests | ||
| run : | | ||
| echo "TESTS=tests/test_petsc.py" >> $GITHUB_ENV | ||
| id: set-tests | ||
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| - 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 }} |
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AI about 13 hours ago
In general, the fix is to add an explicit permissions: block that restricts the GITHUB_TOKEN to the minimal scopes needed. For this workflow, the job only needs to read the repository contents (for actions/checkout) and does not push changes, manage issues, or alter other resources. Therefore, we can safely set contents: read and not grant any write permissions.
The cleanest fix without changing functionality is to add a top-level permissions: block (at the root of the workflow) so it applies to all jobs, including pytest. Concretely, in .github/workflows/pytest-petsc.yml, insert:
permissions:
contents: readbetween the concurrency block and the on: block near the top of the file. No other code changes or imports are required. This will ensure that the GITHUB_TOKEN used by actions/checkout, codecov/codecov-action, and any other steps is limited to read-only repository contents, which is sufficient for the existing behavior.
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| group: ${{ github.workflow }}-${{ github.ref }} | ||
| cancel-in-progress: true | ||
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| permissions: | ||
| contents: read | ||
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| on: | ||
| # Trigger the workflow on push or pull request, | ||
| # but only for the master branch |
Work in progress PETSc functionality
TODO: