dsl: Add PETSc functionality #2570
Open
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
- 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 +/- ##
==========================================
- Coverage 83.03% 75.98% -7.05%
==========================================
Files 248 273 +25
Lines 50499 53844 +3345
Branches 4440 4551 +111
==========================================
- Hits 41930 40913 -1017
- Misses 7807 12106 +4299
- Partials 762 825 +63
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
|
![github-advanced-security[bot]](https://avatars.githubusercontent.com/in/57789?s=60&v=4){kind=small}
Comment on lines
21
to
90
| name: ${{ matrix.name }}-${{ matrix.set }} | ||
| 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 | ||
|
|
||
| matrix: | ||
| name: [ | ||
| pytest-docker-py39-gcc-noomp | ||
| ] | ||
| include: | ||
| - name: pytest-docker-py39-gcc-noomp | ||
| python-version: '3.9' | ||
| os: ubuntu-latest | ||
| arch: "gcc" | ||
| language: "C" | ||
| sympy: "1.12" | ||
|
|
||
| steps: | ||
| - name: Checkout devito | ||
| uses: actions/checkout@v4 | ||
|
|
||
| - name: Log in to DockerHub | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| username: ${{ secrets.DOCKER_USERNAME }} | ||
| password: ${{ secrets.DOCKER_PASSWORD }} | ||
|
|
||
| - name: Build docker image | ||
| run: | | ||
| docker build -f docker/Dockerfile.devito --build-arg base=zoeleibowitz/petsc_image:latest --tag zoeleibowitz/petsc_devito_image:latest . | ||
| - name: Set run prefix | ||
| run: | | ||
| echo "RUN_CMD=docker run --rm -t -e CODECOV_TOKEN=${{ secrets.CODECOV_TOKEN }} --name testrun zoeleibowitz/petsc_devito_image:latest" >> $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 | ||
| run: | | ||
| ${{ env.RUN_CMD }} mpiexec -n 1 pytest --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/random/01_helmholtz.py | ||
| - name: Upload coverage to Codecov | ||
| if: "!contains(matrix.name, 'docker')" | ||
| uses: codecov/codecov-action@v4 | ||
| with: | ||
| token: ${{ secrets.CODECOV_TOKEN }} | ||
| name: ${{ matrix.name }} |
Check warning
Code scanning / CodeQL
Workflow does not contain permissions Medium
Show autofix suggestion
Hide autofix suggestion
Copilot Autofix
AI about 2 months ago
To fix the problem, add an explicit permissions block to the workflow, setting it to the minimum required. Since the workflow (as presented) only checks out code, tests, and uploads results to Codecov (which does not require repository write access), contents: read is sufficient. Place the permissions setting at the workflow root, just after the name: statement (top-level, before on: and jobs:), so it applies to all present and future jobs unless specifically overridden. No other code or permissions changes are needed.
Suggested changeset
1
.github/workflows/pytest-petsc.yml
| @@ -1,4 +1,6 @@ | ||
| name: CI-petsc | ||
| permissions: | ||
| contents: read | ||
|
|
||
| concurrency: | ||
| group: ${{ github.workflow }}-${{ github.ref }} |
Copilot is powered by AI and may make mistakes. Always verify output.
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
EdCaunt
reviewed
Oct 27, 2025
| # (PetscScalar (*)[rhs_vec->size[1]]) ctx0; | ||
| # This is the case when a1 is a LocalCompositeObject (i.e a1.is_AbstractObject) | ||
|
|
||
| if o.offset: |
There was a problem hiding this comment.
Is the offset a symbol at this point?
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Work in progress PETSc functionality
TODO: