Add FEniCS Nextflow benchmark and update environment configurations #196
Workflow file for this run
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
| name: CI | |
| on: | |
| push: | |
| branches-ignore: | |
| pull_request: | |
| branches: [ main ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # Runs the workflow once per day at 3:15am | |
| schedule: | |
| - cron: '3 16 * * *' | |
| env: | |
| CACHE_NUMBER: 1 # increase to reset cache manually | |
| jobs: | |
| tests: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: checkout repo content | |
| uses: actions/checkout@v2 | |
| - name: Setup Mambaforge | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| miniforge-version: latest | |
| activate-environment: model-validation | |
| use-mamba: true | |
| - name: Update environment | |
| run: mamba env update -n model-validation -f environment_benchmarks.yml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: run-fenics-benchmarks | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/FEniCS/ | |
| snakemake --use-conda --force --cores 'all' | |
| - name: run-fenics-nextflow-benchmark | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/FEniCS_nextflow/ | |
| nextflow run main.nf | |
| - name: run-Kratos-benchmarks | |
| shell: bash -l {0} | |
| run: | | |
| cd $GITHUB_WORKSPACE/benchmarks/linear-elastic-plate-with-hole/Kratos/ | |
| snakemake --use-conda --force --cores 'all' | |
| #- name: run-optimization-workflow | |
| # shell: bash -l {0} | |
| # run: | | |
| # cd $GITHUB_WORKSPACE/usecases/optimization_paper/optimization_workflow/ | |
| # snakemake -c 1 | |
| #- name: run-optimization-paper | |
| # shell: bash -l {0} | |
| # run: | | |
| # cd $GITHUB_WORKSPACE/usecases/optimization_paper/ | |
| # doit | |
| - name: Archive fenics data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: fenics-output | |
| path: | | |
| benchmarks/linear-elastic-plate-with-hole/FEniCS/data | |
| - name: Archive kratos data | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: kratos-output | |
| path: | | |
| benchmarks/linear-elastic-plate-with-hole/Kratos/data | |