dsl: Add PETSc functionality #2570
Conversation
- Temp fix until VecReplaceArray works properly in conjunction with PetscMemoryAllocator
* Compiler: Add basic initguess callback - to be improved
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #2570 +/- ##
==========================================
- Coverage 91.30% 85.39% -5.91%
==========================================
Files 245 261 +16
Lines 48495 50604 +2109
Branches 4261 4326 +65
==========================================
- Hits 44276 43211 -1065
- Misses 3521 6667 +3146
- Partials 698 726 +28
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}
.github/workflows/pytest-petsc.yml
Outdated
| 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
|
|
||
| matrix: | ||
| name: [ | ||
| pytest-docker-py39-gcc-noomp |
There was a problem hiding this comment.
Python 3.9 is EOL soon, so this version should get bumped. It would also be worth adding an Omp run
|
|
||
| - name: Build docker image | ||
| run: | | ||
| docker build -f docker/Dockerfile.devito --build-arg base=zoeleibowitz/petsc_image:latest --tag zoeleibowitz/petsc_devito_image:latest . |
There was a problem hiding this comment.
This image should probably be on the main Devito Dockerhub now
|
|
||
| - 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()]))" |
| ${{ 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 |
There was a problem hiding this comment.
How about naming this folder 'misc' rather than 'random'?
| @@ -17,9 +17,11 @@ on: | |||
| push: | |||
| branches: | |||
| - main | |||
| - master | |||
There was a problem hiding this comment.
These additional "master"s need dropping throughout the CI workflows
|
|
||
|
|
||
| def initialize(iet): | ||
| # should be int because the correct type for argc is a C int |
There was a problem hiding this comment.
Nitpick: comment starts with lowercase
| argv = ArgvSymbol(name='argv') | ||
| Help = Macro('help') | ||
|
|
||
| help_string = c.Line(r'static char help[] = "This is help text.\n";') |
| self.iters = iters | ||
| self.kwargs = kwargs | ||
| self.coupled = isinstance(injectsolve.expr.rhs.fielddata, MultipleFieldData) | ||
| self.args = { |
There was a problem hiding this comment.
Nitpick: whitespace above this line would improve readability
| # the C code cleaner and more modular. This is also a step toward leveraging | ||
| # Devito's `reuse_efuncs` functionality, allowing reuse of efuncs when | ||
| # they are semantically identical. | ||
| objs = frozendict({ |
There was a problem hiding this comment.
Could be worth naming this petsc_objs to avoid potential namespace clashes?
| self._main_matvec_callback = None | ||
| self._main_formfunc_callback = None | ||
| self._user_struct_callback = None | ||
| # TODO: Test pickling. The mutability of these lists |
There was a problem hiding this comment.
Possibly initialise them to one, then generate tuples for each in a lazy manner?
There was a problem hiding this comment.
Possibly remove these, then make the properties into cached properties with the requisite machinery to fill them
…st_log_warning petsc fix pytest log warning
Work in progress PETSc functionality
TODO before merging: