Run torsion benchmarks #17
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| # this is adapted from openff-docs/cookbook_preproc.yaml | |
| name: Run torsion benchmarks | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| pr_number: | |
| description: 'Run the benchmarks for PR#: ' | |
| required: true | |
| type: string | |
| path: | |
| description: Path to submission directory | |
| required: true | |
| type: string | |
| env: | |
| description: Path to conda YAML file | |
| required: true | |
| type: string | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ inputs.pr_number || github.ref || github.run_id }} | |
| cancel-in-progress: true | |
| jobs: | |
| start-aws-runner: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| id-token: write | |
| contents: read | |
| outputs: | |
| mapping: ${{ steps.aws-start.outputs.mapping }} | |
| steps: | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::649715411074:role/gh-actions-runner-role | |
| aws-region: us-east-1 | |
| - name: Create cloud runner | |
| id: aws-start | |
| uses: omsf-eco-infra/[email protected] | |
| with: | |
| provider: "aws" | |
| action: "start" | |
| aws_image_id: ami-0d5079d9be06933e5 | |
| aws_instance_type: c6a.8xlarge | |
| aws_region_name: us-east-1 | |
| aws_home_dir: /home/ubuntu | |
| env: | |
| GH_PAT: ${{ secrets.GH_PAT }} | |
| benchmark: | |
| permissions: write-all | |
| runs-on: self-hosted | |
| needs: | |
| - start-aws-runner | |
| steps: | |
| - name: Report dispatch to PR | |
| if: github.event_name == 'workflow_dispatch' && inputs.pr_number != '' | |
| uses: thollander/actions-comment-pull-request@v2 | |
| with: | |
| pr_number: ${{ inputs.pr_number }} | |
| message: > | |
| A workflow has been dispatched to run the benchmarks for this PR. | |
| - Run ID: [${{ github.run_id }}] | |
| - Triggering actor: ${{ github.triggering_actor }} | |
| - Target branch: ${{ github.ref_name }} | |
| [${{ github.run_id }}]: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| - name: Create check | |
| if: github.event_name == 'workflow_dispatch' && inputs.pr_number != '' | |
| id: create-check | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| const created_run = await github.request( | |
| 'POST /repos/{owner}/{repo}/check-runs', | |
| { | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| name: '${{ github.job }}', | |
| head_sha: '${{ github.sha }}', | |
| details_url: '${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}', | |
| status: 'in_progress', | |
| started_at: new Date().toISOString(), | |
| output: { | |
| title: 'Run torsion benchmarks', | |
| summary: 'Results and progress: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}', | |
| text: '' | |
| }, | |
| headers: { | |
| 'X-GitHub-Api-Version': '2022-11-28' | |
| } | |
| } | |
| ) | |
| return created_run.data.id | |
| - name: Install git-lfs | |
| run: | | |
| sudo apt update | |
| sudo apt install -y git-lfs | |
| - uses: actions/checkout@v3 | |
| with: | |
| lfs: true | |
| - name: Install Conda environment | |
| uses: mamba-org/setup-micromamba@v1 | |
| with: | |
| environment-file: ${{ inputs.env }} | |
| - name: Run torsion benchmarks | |
| env: | |
| LICENSE: ${{ secrets.OE_LICENSE }} | |
| shell: bash -l {0} | |
| run: | | |
| set -e | |
| echo "$LICENSE" > /tmp/oe_license.txt | |
| export OE_LICENSE=/tmp/oe_license.txt | |
| python torsions.py ${{ inputs.path }} $(nproc) | |
| rm $OE_LICENSE | |
| - name: Plot results | |
| shell: bash -l {0} | |
| run: | | |
| set -e | |
| input_file=${{ inputs.path }} | |
| input_dir=$(dirname $input_file) | |
| # python plot.py $input_dir -o $input_dir/output | |
| - name: Commit results | |
| shell: bash -l {0} | |
| run: | | |
| git config --global user.name github-actions | |
| git config --global user.email [email protected] | |
| git config --global init.defaultBranch main | |
| # Commit the benchmark results and push | |
| input_file=${{ inputs.path }} # path to the input YAML file | |
| input_dir=$(dirname $input_file) # parent directory of input YAML file | |
| git add $input_dir/output/rmsd.csv | |
| git add $input_dir/output/een.csv | |
| git add $input_dir/output/minimized.json | |
| git add $input_dir/output/metrics.json | |
| git commit -m "Add benchmark results" | |
| git push | |
| echo input_dir="${input_dir}" >> $GITHUB_ENV | |
| - name: Upload to zenodo | |
| env: | |
| ZENODO_TOKEN: ${{ secrets.ZENODO_TOKEN }} | |
| ZENODO_URL: "https://zenodo.org" | |
| shell: bash -l {0} | |
| run: | | |
| # TODO: make and bundle plot(s) | |
| bzip2 torsions-dev.sqlite | |
| micromamba env export > env.yaml | |
| input_files=$(python get_files.py ${{ inputs.path }}) | |
| python zenodo_upload.py --title "YDS Upload ${{ inputs.pr_number }}" \ | |
| torsions-dev.sqlite.bz2 $input_dir/output/rmsd.csv \ | |
| torsions-dev.sqlite.bz2 $input_dir/output/een.csv \ | |
| env.yaml torsions.py $input_files | |
| - name: Report status to PR | |
| id: reportStatusToPr | |
| if: always() && github.event_name == 'workflow_dispatch' && inputs.pr_number != '' | |
| uses: thollander/actions-comment-pull-request@v2 | |
| with: | |
| pr_number: ${{ inputs.pr_number }} | |
| message: > | |
| A workflow dispatched to run torsion benchmarks for this PR has just finished. | |
| - Run ID: [${{ github.run_id }}] | |
| - Triggering actor: ${{ github.triggering_actor }} | |
| - Target branch: ${{ github.ref_name }} | |
| - Job status: **${{ job.status }}** | |
| [${{ github.run_id }}]: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| - name: Report status to PR on templating failure | |
| if: always() && steps.reportStatusToPr.outcome == 'failure' | |
| uses: thollander/actions-comment-pull-request@v2 | |
| with: | |
| pr_number: ${{ inputs.pr_number }} | |
| message: > | |
| A workflow dispatched to run torsion benchmarks for this PR has just failed. | |
| - Run ID: [${{ github.run_id }}] | |
| - Triggering actor: ${{ github.triggering_actor }} | |
| - Target branch: ${{ github.ref_name }} | |
| - Job status: **${{ job.status }}** | |
| [${{ github.run_id }}]: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| - name: Update check | |
| if: always() && github.event_name == 'workflow_dispatch' && inputs.pr_number != '' | |
| uses: actions/github-script@v6 | |
| with: | |
| script: | | |
| await github.request( | |
| 'PATCH /repos/{owner}/{repo}/check-runs/{check_run_id}', | |
| { | |
| owner: context.repo.owner, | |
| repo: context.repo.repo, | |
| check_run_id: ${{ steps.create-check.outputs.result }}, | |
| status: 'completed', | |
| conclusion: '${{ job.status }}', | |
| completed_at: new Date().toISOString(), | |
| headers: { | |
| 'X-GitHub-Api-Version': '2022-11-28' | |
| } | |
| } | |
| ) | |
| stop-aws-runner: | |
| runs-on: ubuntu-latest | |
| permissions: | |
| id-token: write | |
| contents: read | |
| needs: | |
| - start-aws-runner | |
| - benchmark | |
| if: ${{ always() }} | |
| steps: | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::649715411074:role/gh-actions-runner-role | |
| aws-region: us-east-1 | |
| - name: Stop instances | |
| uses: omsf-eco-infra/[email protected] | |
| with: | |
| provider: "aws" | |
| action: "stop" | |
| instance_mapping: ${{ needs.start-aws-runner.outputs.mapping }} | |
| aws_region_name: us-east-1 | |
| env: | |
| GH_PAT: ${{ secrets.GH_PAT }} |