Update rst files and schema #5851
Workflow file for this run
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| name: GEOS CI | |
| on: | |
| push: | |
| branches: | |
| - develop | |
| pull_request: | |
| workflow_dispatch: | |
| # Cancels in-progress workflows for a PR when updated | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| # Please define `build.args.GEOS_TPL_TAG` in `.devcontainer/devcontainer.json` | |
| jobs: | |
| # Jobs will be cancelled if PR is a draft. | |
| # PR status must be "Open" to run CI. | |
| is_not_draft_pull_request: | |
| # Everywhere in this workflow, we use the most recent ubuntu distribution available in Github Actions | |
| # to ensure maximum support of google cloud's sdk. | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| DOCKER_IMAGE_TAG: ${{ steps.extract_docker_image_tag.outputs.DOCKER_IMAGE_TAG }} | |
| steps: | |
| - name: Check that the PR is not a draft (cancel rest of jobs otherwise) | |
| id: extract_pr_info | |
| run: | | |
| if [[ ${{github.event_name}} == 'pull_request' ]]; then | |
| # We do not rely on the `github.event.pull_request.labels` information since it's cached at the job. | |
| # Changing labels or assignee in the PR would not allow to simply re-run the job with a different outcome. | |
| pr_json=$(curl -H "Accept: application/vnd.github+json" https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.number }}) | |
| # We stop the workflow if the pr is draft | |
| draft_status=$(echo ${pr_json} | jq '.draft') | |
| echo "Draft status of PR is ${draft_status}." | |
| if [[ $draft_status == true ]]; then exit 1 ; fi | |
| fi | |
| # The TPL tag is contained in the codespaces configuration to avoid duplications. | |
| - name: Checkout .devcontainer/devcontainer.json | |
| uses: actions/[email protected] | |
| with: | |
| sparse-checkout: | | |
| .devcontainer/devcontainer.json | |
| sparse-checkout-cone-mode: false | |
| submodules: false | |
| lfs: false | |
| fetch-depth: 1 | |
| - name: Extract docker image tag | |
| id: extract_docker_image_tag | |
| run: | | |
| echo "DOCKER_IMAGE_TAG=$(jq '.build.args.GEOS_TPL_TAG' -r .devcontainer/devcontainer.json)" >> "$GITHUB_OUTPUT" | |
| # PR must be assigned to be merged. | |
| # This job will fail if this is not the case. | |
| if_not_unassigned_pull_request: | |
| needs: [is_not_draft_pull_request] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: If this is a PR, Check that it is assigned | |
| run: | | |
| if [[ ${{github.event_name}} != 'pull_request' ]]; then exit 0 ; fi | |
| pr_json=$(curl -H "Accept: application/vnd.github+json" https://api.github.com/repos/${{ github.repository }}/pulls/${{ github.event.number }}) | |
| NUM_ASSIGNEES=$(echo ${pr_json} | jq '.assignees | length') | |
| echo "There are ${NUM_ASSIGNEES} assignees on this PR." | |
| if [[ $NUM_ASSIGNEES == 0 ]]; then exit 1 ; fi | |
| # Validates that the PR is still pointing to the HEAD of the main branch of the submodules repositories. | |
| # (There are exceptions, read the script about those). | |
| are_submodules_in_sync: | |
| needs: [is_not_draft_pull_request] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| # The integrated test submodule repository contains large data (using git lfs). | |
| # To save time (and money) we do not let Github Actions automatically clone all our (lfs) subrepositories and do it by hand. | |
| - name: Checkout Repository | |
| uses: actions/[email protected] | |
| with: | |
| # Let script update submodules; Github Actions submodule history causes error | |
| submodules: false | |
| lfs: false | |
| fetch-depth: 1 | |
| - name: Check that submodules are up to date | |
| run: "scripts/test_submodule_updated.sh" | |
| check_code_style_and_documentation: | |
| name: ${{ matrix.name }} | |
| needs: [is_not_draft_pull_request] | |
| strategy: | |
| fail-fast : false | |
| matrix: | |
| include: | |
| # Validates the code-style using uncrustify | |
| - name: Check code style | |
| BUILD_AND_TEST_ARGS: --test-code-style | |
| # Validates that the documentation generated using doxygen has no hole. | |
| - name: Check documentation | |
| BUILD_AND_TEST_ARGS: --test-documentation | |
| uses: ./.github/workflows/build_and_test.yml | |
| with: | |
| BUILD_AND_TEST_CLI_ARGS: ${{ matrix.BUILD_AND_TEST_ARGS }} | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }} | |
| DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9 | |
| RUNS_ON: ubuntu-22.04 | |
| USE_SCCACHE: false | |
| # Matrix containing all the CPU build. | |
| # Those are quite fast and can efficiently benefit from the `sccache' tool to make them even faster. | |
| cpu_builds: | |
| name: ${{ matrix.name }} | |
| needs: [is_not_draft_pull_request] | |
| strategy: | |
| # In-progress jobs will not be cancelled if there is a failure | |
| fail-fast : false | |
| matrix: | |
| include: | |
| - name: Ubuntu (20.04, gcc 9.4.0, open-mpi 4.0.3) | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc9 | |
| - name: Ubuntu debug (20.04, gcc 10.5.0, open-mpi 4.0.3) - github codespaces | |
| CMAKE_BUILD_TYPE: Debug | |
| DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc10 | |
| - name: Ubuntu (20.04, gcc 10.5.0, open-mpi 4.0.3) - github codespaces | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/ubuntu20.04-gcc10 | |
| - name: Ubuntu (22.04, gcc 11.4.0, open-mpi 4.1.2) | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11 | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| GCP_BUCKET: geosx/ubuntu22.04-gcc11 | |
| - name: Ubuntu (22.04, gcc 12.3.0, open-mpi 4.1.2) | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc12 | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| - name: Ubuntu (22.04, clang 15.0.7, open-mpi 4.1.2) | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/ubuntu22.04-clang15 | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| - name: Pecan CPU (centos 7.7, gcc 8.2.0, open-mpi 4.0.1, mkl 2019.5) | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/pecan-cpu-gcc8.2.0-openmpi4.0.1-mkl2019.5 | |
| HOST_CONFIG: host-configs/TOTAL/pecan-CPU.cmake | |
| GCP_BUCKET: geosx/Pecan-CPU | |
| - name: Pangea 2 (centos 7.6, gcc 8.3.0, open-mpi 2.1.5, mkl 2019.3) | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/pangea2-gcc8.3.0-openmpi2.1.5-mkl2019.3 | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| GCP_BUCKET: geosx/Pangea2 | |
| - name: Sherlock CPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, openblas 0.3.10) | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-openblas0.3.10-zlib1.2.11 | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| GCP_BUCKET: geosx/Sherlock-CPU | |
| HOST_CONFIG: host-configs/Stanford/sherlock-gcc10-ompi4.1.2-openblas0.3.10.cmake | |
| uses: ./.github/workflows/build_and_test.yml | |
| with: | |
| CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }} | |
| DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }} | |
| DOCKER_REPOSITORY: ${{ matrix.DOCKER_REPOSITORY }} | |
| ENABLE_HYPRE: ${{ matrix.ENABLE_HYPRE }} | |
| ENABLE_TRILINOS: ${{ matrix.ENABLE_TRILINOS }} | |
| GCP_BUCKET: ${{ matrix.GCP_BUCKET }} | |
| HOST_CONFIG: ${{ matrix.HOST_CONFIG }} | |
| RUNS_ON: ubuntu-22.04 | |
| secrets: inherit | |
| # If the 'ci: run integrated tests' PR label is found, the integrated tests will be run immediately after the cpu jobs. | |
| # Note: The integrated tests are optional and are (for the moment) run for convenience only. | |
| run_integrated_tests: | |
| needs: | |
| - is_not_draft_pull_request | |
| - cpu_builds | |
| uses: ./.github/workflows/build_and_test.yml | |
| secrets: inherit | |
| with: | |
| BUILD_AND_TEST_CLI_ARGS: --build-exe-only | |
| BUILD_TYPE: integrated_tests | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }} | |
| DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11 | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| GCP_BUCKET: geosx/integratedTests | |
| RUNS_ON: streak2-32core | |
| NPROC: 32 | |
| DOCKER_RUN_ARGS: "--cpus=32 --memory=384g -v /etc/pki/ca-trust/source/anchors/:/usr/local/share/ca-certificates/llnl:ro" | |
| DOCKER_CERTS_DIR: "/usr/local/share/ca-certificates" | |
| DOCKER_CERTS_UPDATE_COMMAND: "update-ca-certificates" | |
| REQUIRED_LABEL: "ci: run integrated tests" | |
| LOCAL_BASELINE_DIR: /data/GEOS/baselines | |
| baseline_log: | |
| needs: [is_not_draft_pull_request] | |
| runs-on: ubuntu-22.04 | |
| steps: | |
| - name: Checkout Repository | |
| uses: actions/[email protected] | |
| with: | |
| submodules: false | |
| lfs: false | |
| fetch-depth: 0 | |
| sparse-checkout: | | |
| scripts | |
| - name: Check that the baseline logs are modified if rebaselines are detected | |
| run: "scripts/check_baseline_log.sh" | |
| code_coverage: | |
| needs: | |
| - is_not_draft_pull_request | |
| uses: ./.github/workflows/build_and_test.yml | |
| secrets: inherit | |
| with: | |
| BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests" | |
| CMAKE_BUILD_TYPE: Debug | |
| CODE_COVERAGE: true | |
| DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }} | |
| DOCKER_REPOSITORY: geosx/ubuntu22.04-gcc11 | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| GCP_BUCKET: geosx/ubuntu22.04-gcc11 | |
| RUNS_ON: Runner_4core_16GB | |
| # If the 'ci: run CUDA builds' PR label is found, the cuda jobs run immediately along side linux jobs. | |
| # Note: CUDA jobs should only be run if PR is ready to merge. | |
| cuda_builds: | |
| name: ${{ matrix.name }} | |
| needs: | |
| - is_not_draft_pull_request | |
| strategy: | |
| # In-progress jobs will not be cancelled if there is a failure | |
| fail-fast : false | |
| matrix: | |
| include: | |
| - name: Ubuntu CUDA debug (20.04, clang 10.0.0 + gcc 9.4.0, open-mpi 4.0.3, cuda-11.8.89) | |
| BUILD_AND_TEST_CLI_ARGS: "--build-exe-only --no-install-schema" | |
| CMAKE_BUILD_TYPE: Debug | |
| DOCKER_REPOSITORY: geosx/ubuntu20.04-clang10.0.0-cuda11.8.89 | |
| ENABLE_HYPRE_DEVICE: CUDA | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| RUNS_ON: streak2 | |
| NPROC: 8 | |
| DOCKER_RUN_ARGS: "--cpus=8 --memory=128g --runtime=nvidia -v /etc/pki/ca-trust/source/anchors/:/usr/local/share/ca-certificates/llnl:ro" | |
| DOCKER_CERTS_DIR: "/usr/local/share/ca-certificates" | |
| DOCKER_CERTS_UPDATE_COMMAND: "update-ca-certificates" | |
| - name: Ubuntu CUDA (20.04, clang 10.0.0 + gcc 9.4.0, open-mpi 4.0.3, cuda-11.8.89) | |
| BUILD_AND_TEST_CLI_ARGS: "--no-install-schema" | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/ubuntu20.04-clang10.0.0-cuda11.8.89 | |
| ENABLE_HYPRE_DEVICE: CUDA | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| RUNS_ON: streak | |
| NPROC: 8 | |
| DOCKER_RUN_ARGS: "--cpus=8 --memory=256g --runtime=nvidia --gpus all -v /etc/pki/ca-trust/source/anchors/:/usr/local/share/ca-certificates/llnl:ro" | |
| DOCKER_CERTS_DIR: "/usr/local/share/ca-certificates" | |
| DOCKER_CERTS_UPDATE_COMMAND: "update-ca-certificates" | |
| - name: Centos (7.7, gcc 8.3.1, open-mpi 1.10.7, cuda 11.8.89) | |
| BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests --no-install-schema" | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/centos7.7-gcc8.3.1-cuda11.8.89 | |
| RUNS_ON: streak2 | |
| NPROC: 8 | |
| DOCKER_RUN_ARGS: "--cpus=8 --memory=128g --runtime=nvidia -v /etc/pki/ca-trust/source/anchors/:/etc/pki/ca-trust/source/anchors/llnl:ro" | |
| DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors" | |
| DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust" | |
| # Below this line, jobs that deploy to Google Cloud. | |
| - name: Pecan GPU (centos 7.7, gcc 8.2.0, open-mpi 4.0.1, mkl 2019.5, cuda 11.5.119) | |
| BUILD_AND_TEST_CLI_ARGS: "--build-exe-only --no-install-schema" | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/pecan-gpu-gcc8.2.0-openmpi4.0.1-mkl2019.5-cuda11.5.119 | |
| HOST_CONFIG: host-configs/TOTAL/pecan-GPU.cmake | |
| RUNS_ON: streak2 | |
| NPROC: 8 | |
| DOCKER_RUN_ARGS: "--cpus=8 --memory=128g --runtime=nvidia -v /etc/pki/ca-trust/source/anchors/:/etc/pki/ca-trust/source/anchors/llnl:ro" | |
| DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors" | |
| DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust" | |
| - name: Sherlock GPU (centos 7.9.2009, gcc 10.1.0, open-mpi 4.1.2, openblas 0.3.10, cuda 11.7.1,) | |
| BUILD_AND_TEST_CLI_ARGS: "--no-run-unit-tests --no-install-schema" | |
| CMAKE_BUILD_TYPE: Release | |
| DOCKER_REPOSITORY: geosx/sherlock-gcc10.1.0-openmpi4.1.2-cuda11.7.1-openblas0.3.10-zlib1.2.11 | |
| ENABLE_HYPRE_DEVICE: CUDA | |
| ENABLE_HYPRE: ON | |
| ENABLE_TRILINOS: OFF | |
| GCP_BUCKET: geosx/Sherlock-GPU | |
| HOST_CONFIG: host-configs/Stanford/sherlock-gcc10-ompi4.1.2-openblas0.3.10-cuda11.7.1-sm70.cmake | |
| RUNS_ON: streak2 | |
| NPROC: 8 | |
| DOCKER_RUN_ARGS: "--cpus=8 --memory=128g --runtime=nvidia -v /etc/pki/ca-trust/source/anchors/:/etc/pki/ca-trust/source/anchors/llnl:ro" | |
| DOCKER_CERTS_DIR: "/etc/pki/ca-trust/source/anchors" | |
| DOCKER_CERTS_UPDATE_COMMAND: "update-ca-trust" | |
| uses: ./.github/workflows/build_and_test.yml | |
| with: | |
| BUILD_AND_TEST_CLI_ARGS: ${{ matrix.BUILD_AND_TEST_CLI_ARGS }} | |
| CMAKE_BUILD_TYPE: ${{ matrix.CMAKE_BUILD_TYPE }} | |
| DOCKER_CERTS_DIR: ${{ matrix.DOCKER_CERTS_DIR }} | |
| DOCKER_CERTS_UPDATE_COMMAND: ${{ matrix.DOCKER_CERTS_UPDATE_COMMAND }} | |
| DOCKER_IMAGE_TAG: ${{ needs.is_not_draft_pull_request.outputs.DOCKER_IMAGE_TAG }} | |
| DOCKER_REPOSITORY: ${{ matrix.DOCKER_REPOSITORY }} | |
| DOCKER_RUN_ARGS: ${{ matrix.DOCKER_RUN_ARGS }} | |
| ENABLE_HYPRE_DEVICE: ${{ matrix.ENABLE_HYPRE_DEVICE }} | |
| ENABLE_HYPRE: ${{ matrix.ENABLE_HYPRE }} | |
| ENABLE_TRILINOS: ${{ matrix.ENABLE_TRILINOS }} | |
| GCP_BUCKET: ${{ matrix.GCP_BUCKET }} | |
| HOST_CONFIG: ${{ matrix.HOST_CONFIG }} | |
| NPROC: ${{ matrix.NPROC }} | |
| RUNS_ON: ${{ matrix.RUNS_ON }} | |
| REQUIRED_LABEL: "ci: run CUDA builds" | |
| secrets: inherit | |
| # Convenience job - passes when all other jobs have passed (must pass the CUDA jobs). | |
| check_that_all_jobs_succeeded: | |
| runs-on: ubuntu-22.04 | |
| needs: | |
| - if_not_unassigned_pull_request | |
| - are_submodules_in_sync | |
| - check_code_style_and_documentation | |
| - cpu_builds | |
| - cuda_builds | |
| - run_integrated_tests | |
| if: ${{ always() }} | |
| steps: | |
| - run: | | |
| echo "if_not_unassigned_pull_request: ${{needs.if_not_unassigned_pull_request.result}}" | |
| echo "are_submodules_in_sync: ${{needs.are_submodules_in_sync.result}}" | |
| echo "check_code_style_and_documentation: ${{needs.check_code_style_and_documentation.result}}" | |
| echo "cpu_builds: ${{needs.cpu_builds.result}}" | |
| echo "cuda_builds: ${{needs.cuda_builds.result}}" | |
| echo "run_integrated_tests: ${{needs.run_integrated_tests.result}} " | |
| ${{ | |
| needs.if_not_unassigned_pull_request.result == 'success' && | |
| needs.are_submodules_in_sync.result == 'success' && | |
| needs.check_code_style_and_documentation.result == 'success' && | |
| needs.cpu_builds.result == 'success' && | |
| needs.cuda_builds.result == 'success' && | |
| needs.run_integrated_tests.result == 'success' | |
| }} |