Calibration #359
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| name: Calibration | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| commit: | |
| description: '40-character commit hash' | |
| required: true | |
| default: "" | |
| type: string | |
| schedule: | |
| - cron: 31 2 * * * | |
| env: | |
| REPO_PATH: /mnt/tlo/TLOmodel | |
| OUTPUT_ROOT: /mnt/tlodev2stg/tlo-dev-fs-2/task-runner/output | |
| RUNS_NUMBER: 10 | |
| PYTHON_VER: 3.11 | |
| RUN_NAME: 021_long_run_all_diseases_run | |
| PROCESS_NAME: 022_long_run_all_diseases_process | |
| jobs: | |
| # Do a single clone from the remote repository, to reduce bandwidth usage. | |
| # The repo is cloned to a directory outside of the runner workspace, because | |
| # we want it to survive the current job, but this also means we can't use the | |
| # `actions/checkout` workflow. | |
| setup: | |
| name: Setup | |
| runs-on: [tlo-dev-vm-1] | |
| strategy: | |
| fail-fast: false | |
| outputs: | |
| # Environment variables can be passed to following steps within the same job by adding | |
| # them to `GITHUB_ENV`, but to pass data to other jobs we have to necessarily use | |
| # `GITHUB_OUTPUT`. | |
| environment_path: ${{ steps.vars.outputs.environment_path }} | |
| worktree_path: ${{ steps.vars.outputs.worktree_path }} | |
| output_dir: ${{ steps.out-dir.outputs.output_dir }} | |
| skip_tasks: ${{ steps.tasks.outputs.skip_tasks }} | |
| tasks: ${{ steps.tasks.outputs.tasks }} | |
| steps: | |
| - name: Generate environment variables | |
| id: vars | |
| run: | | |
| if [[ ${{ github.event_name }} == 'workflow_dispatch' ]] && [[ -n "${{ inputs.commit }}" ]]; then | |
| SHA=${{ inputs.commit }} | |
| else | |
| SHA=${{ github.sha }} | |
| fi | |
| ENV="/mnt/tlo/env-${SHA}" | |
| if [[ -d "${ENV}" ]]; then | |
| echo "Virtual environment directory ${ENV} already exists, leaving..." | |
| exit 1 | |
| fi | |
| WORKTREE_PATH="/mnt/tlo/${SHA}" | |
| if [[ -d "${WORKTREE_PATH}" ]]; then | |
| echo "Worktree directory ${WORKTREE_PATH} already exists, leaving..." | |
| exit 1 | |
| fi | |
| echo "SHA=${SHA}" | |
| echo "SHA=${SHA}" >> "${GITHUB_ENV}" | |
| echo "ENV=${ENV}" | |
| echo "ENV=${ENV}" >> "${GITHUB_ENV}" | |
| echo "environment_path=${ENV}" >> "${GITHUB_OUTPUT}" | |
| echo "WORKTREE_PATH=${WORKTREE_PATH}" | |
| echo "WORKTREE_PATH=${WORKTREE_PATH}" >> "${GITHUB_ENV}" | |
| echo "worktree_path=${WORKTREE_PATH}" >> "${GITHUB_OUTPUT}" | |
| - name: Clone remote TLO repository and fetch desired commit | |
| run: | | |
| # If the repository doesn't exist on disk, clone it. | |
| if [[ ! -d "${REPO_PATH}" ]]; then | |
| git clone --depth=1 --branch="${{ github.ref_name }}" "https://github.com/${{ github.repository }}.git" "${REPO_PATH}" | |
| fi | |
| # In any case, fetch the requested commit. | |
| git -C "${REPO_PATH}" fetch --depth=1 origin "${SHA}" | |
| - name: Create worktree | |
| run: | | |
| git -C "${REPO_PATH}" worktree add "${WORKTREE_PATH}" ${SHA} | |
| - name: Create virtual environment | |
| run: | | |
| python${PYTHON_VER} -m venv "${ENV}" | |
| source "${ENV}/bin/activate" | |
| pip install -r requirements/dev.txt | |
| pip install -e . | |
| working-directory: "${{ env.WORKTREE_PATH }}" | |
| - name: Generate output directory | |
| id: out-dir | |
| run: | | |
| commit_dir=$(git show -s --date=format:'%Y-%m-%d_%H%M%S' --format=%cd_%h "${SHA}") | |
| output_dir="${OUTPUT_ROOT}/${commit_dir}" | |
| echo "output_dir=${output_dir}" | |
| echo "output_dir=${output_dir}" >> "${GITHUB_ENV}" | |
| echo "output_dir=${output_dir}" >> "${GITHUB_OUTPUT}" | |
| working-directory: "${{ env.WORKTREE_PATH }}" | |
| - name: Generate list of tasks | |
| id: tasks | |
| run: | | |
| SKIP_TASKS="false" | |
| if [[ -d "${output_dir}" ]]; then | |
| echo "Output directory ${output_dir} already exists, setting RUNS_NUMBER to 1 and skipping further task runs" | |
| RUNS_NUMBER=1 | |
| # Set variable to make task job run, but exit immediately, so that | |
| # the build doesn't fail. | |
| SKIP_TASKS="true" | |
| fi | |
| echo "SKIP_TASKS=${SKIP_TASKS}" | |
| echo "SKIP_TASKS=${SKIP_TASKS}" >> "${GITHUB_ENV}" | |
| echo "skip_tasks=${SKIP_TASKS}" >> "${GITHUB_OUTPUT}" | |
| RUNS="[" | |
| for run in $(seq 0 $((${RUNS_NUMBER} - 1))); do | |
| RUNS="${RUNS}\"${run}\"," | |
| done | |
| RUNS="${RUNS}]" | |
| echo "tasks=${RUNS}" | |
| echo "tasks=${RUNS}" >> "${GITHUB_OUTPUT}" | |
| - name: Write info.txt file | |
| if: ${{ env.SKIP_TASKS == 'false' }} | |
| run: | | |
| mkdir -p "${output_dir}" | |
| info_txt="${output_dir}/info.txt" | |
| git -C "${WORKTREE_PATH}" log --pretty=format:"%H%x09%ad%x09%s" --date=iso-strict -n 1 > "${info_txt}" | |
| echo -e "\n${GITHUB_SERVER_URL}/${GITHUB_REPOSITORY}/actions/runs/${GITHUB_RUN_ID}" >> "${info_txt}" | |
| echo "Content of ${info_txt}:" | |
| cat "${info_txt}" | |
| # Run the tasks. | |
| tasks: | |
| needs: setup | |
| name: Run task ${{ matrix.index }} | |
| runs-on: [tlo-dev-vm-1, tasks] # Use only runners dedicated to running the tasks. | |
| timeout-minutes: 5760 # = 4 * 24 * 60 minutes = 4 days | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| index: ${{ fromJSON(needs.setup.outputs.tasks) }} | |
| steps: | |
| - name: Run the task | |
| run: | | |
| if [[ "${{ needs.setup.outputs.skip_tasks }}" == true ]]; then | |
| echo "Nothing to be done, exiting..." | |
| exit 0 | |
| fi | |
| source "${{ needs.setup.outputs.environment_path }}/bin/activate" | |
| draw=0 | |
| task_output_dir="${{ needs.setup.outputs.output_dir }}/${RUN_NAME}/${draw}/${{ matrix.index }}" | |
| mkdir -p "${task_output_dir}" | |
| tlo scenario-run --output-dir "${task_output_dir}" --draw "${draw}" ${{ matrix.index }} "${{ needs.setup.outputs.worktree_path }}/src/scripts/calibration_analyses/scenarios/long_run_all_diseases.py" | |
| working-directory: "${{ needs.setup.outputs.worktree_path }}" | |
| # Do the postprocessing | |
| postprocess: | |
| name: Post processing | |
| needs: [setup, tasks] | |
| runs-on: [tlo-dev-vm-1, postprocess] # Use only the runners dedicated to postprocessing | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - name: Run post-processing | |
| run: | | |
| if [[ "${{ needs.setup.outputs.skip_tasks }}" == true ]]; then | |
| echo "Nothing to be done, exiting..." | |
| exit 0 | |
| fi | |
| source "${{ needs.setup.outputs.environment_path }}/bin/activate" | |
| task_output_dir="${{ needs.setup.outputs.output_dir }}/${PROCESS_NAME}" | |
| mkdir -p "${task_output_dir}" | |
| python3 "${{ needs.setup.outputs.worktree_path }}/src/scripts/calibration_analyses/analysis_scripts/process.py" "${task_output_dir}" "${RUN_NAME}" "${{ needs.setup.outputs.worktree_path }}/resources" | |
| python3 "${{ needs.setup.outputs.worktree_path }}/src/scripts/task_runner/generate_html.py" "${OUTPUT_ROOT}" > "${OUTPUT_ROOT}/index.html" | |
| working-directory: "${{ needs.setup.outputs.worktree_path }}" | |
| - name: Compress log files | |
| run: | | |
| find "${{ needs.setup.outputs.output_dir }}" -name '*.log' -exec gzip --best --force --verbose '{}' \; | |
| # Cleanup stage, to remove temporary directories and such | |
| cleanup: | |
| name: Cleanup job | |
| timeout-minutes: 10 | |
| needs: [setup, tasks, postprocess] | |
| # `always()` to run even if tasks and postprocess are skipped, but make sure | |
| # `setup` was successful, to avoid cleaning up existing worktrees and | |
| # environments used by other builds. | |
| if: ${{ always() && needs.setup.result == 'success' }} | |
| runs-on: [tlo-dev-vm-1] | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - name: Cleanup worktree | |
| run: | | |
| git -C "${REPO_PATH}" worktree remove -f "${{ needs.setup.outputs.worktree_path }}" || true | |
| - name: Cleanup virtual environment | |
| run: | | |
| rm -rvf "${{ needs.setup.outputs.environment_path }}" |