Initial setup of Payu environment #13
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| name: Build and test conda env | |
| on: pull_request | |
| jobs: | |
| generate_matrix: | |
| uses: ./.github/workflows/get_changed_env.yml | |
| build_base_image: | |
| runs-on: ubuntu-latest | |
| needs: generate_matrix | |
| if: ${{ needs.generate_matrix.outputs.environments != '[]' }} | |
| container: | |
| image: quay.io/singularity/singularity:v3.11.4 | |
| options: --privileged | |
| outputs: | |
| built-container: ${{ steps.changed-container-def.outputs.containerdef_any_changed }} | |
| steps: | |
| - name: Checkout repository | |
| ### Latest at time of writing | |
| uses: actions/checkout@v4 | |
| - name: Check if container definition has changed | |
| id: changed-container-def | |
| uses: tj-actions/changed-files@48d8f15b2aaa3d255ca5af3eba4870f807ce6b3c # v43.0.2 | |
| with: | |
| files_yaml: | | |
| containerdef: | |
| - container/container.def | |
| - name: Build container if definition has changed | |
| if: steps.changed-container-def.outputs.containerdef_any_changed == 'true' | |
| run: | | |
| sudo -E singularity build container/base.sif container/container.def | |
| - name: Upload base container | |
| if: steps.changed-container-def.outputs.containerdef_any_changed == 'true' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: base-container | |
| path: container/base.sif | |
| build-and-test: | |
| runs-on: ubuntu-latest | |
| needs: [ generate_matrix, build_base_image ] | |
| if: ${{ needs.generate_matrix.outputs.environments != '[]' }} | |
| environment: Gadi | |
| strategy: | |
| matrix: | |
| environment: ${{fromJson(needs.generate_matrix.outputs.environments)}} | |
| max-parallel: 1 | |
| fail-fast: false | |
| steps: | |
| - name: Check Gadi Github Environment configuration | |
| run: | | |
| vars_unset=false | |
| if [ -z "${{ vars.ADMIN_DIR }}" ]; then | |
| echo "::error::vars.ADMIN_DIR is unset. ADMIN_DIR is the base directory which will contain the staging and logs sub-directories" | |
| vars_unset=true | |
| fi | |
| if [ -z "${{ vars.CONDA_BASE }}" ]; then | |
| echo "::error::vars.CONDA_BASE is unset. CONDA_BASE is the base deployment directory which will contain apps and module sub-directories" | |
| vars_unset=true | |
| fi | |
| if [ -z "${{ vars.PROJECT }}" ]; then | |
| echo "::error::vars.PROJECT is unset. PROJECT is the project code passed to build+test qsub calls" | |
| vars_unset=true | |
| fi | |
| if [ -z "${{ vars.STORAGE }}" ]; then | |
| echo "::error::vars.STORAGE is unset. STORAGE is the storage flags passed to build+test qsub calls" | |
| vars_unset=true | |
| fi | |
| if [ -z "${{ vars.APPS_USERS_GROUP }}" ]; then | |
| echo "::error::vars.APPS_USERS_GROUP is unset. APPS_USERS_GROUP is used for setting file permissions" | |
| vars_unset=true | |
| fi | |
| if [ -z "${{ vars.APPS_OWNERS_GROUP }}" ]; then | |
| echo "::error::APPS_OWNERS_GROUP is unset. APPS_OWNERS_GROUP is used for setting file permissions" | |
| vars_unset=true | |
| fi | |
| if [ -z "${{ secrets.REPO_PATH }}" ]; then | |
| echo "::error::secrets.REPO_PATH is unset. REPO_PATH is the path where this repository is synced to" | |
| vars_unset=true | |
| fi | |
| if [ "$vars_unset" == "true" ]; then | |
| echo "::error::Required vars in Gadi Github Environment are unset." | |
| exit 1 | |
| fi | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Download base container | |
| if: needs.build_base_image.outputs.built-container == 'true' | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: base-container | |
| path: container | |
| - name: Setup SSH | |
| uses: access-nri/actions/.github/actions/setup-ssh@main | |
| id: ssh | |
| with: | |
| hosts: | | |
| ${{ secrets.HOST }} | |
| ${{ secrets.HOST_DATA }} | |
| private-key: ${{ secrets.SSH_KEY }} | |
| - name: Create parent repository directories | |
| run: | | |
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | |
| mkdir -p ${{ secrets.REPO_PATH }} | |
| EOT | |
| - name: Sync repository to Gadi | |
| run: | | |
| rsync -e 'ssh -i ${{ steps.ssh.outputs.private-key-path }}' \ | |
| -avz --delete --exclude=/.git/ --exclude=/.github/ \ | |
| ./ \ | |
| ${{ secrets.USER }}@${{ secrets.HOST_DATA }}:${{ secrets.REPO_PATH }} | |
| - name: Create Admin dirs on Gadi | |
| run: | | |
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | |
| set -e | |
| export ADMIN_DIR="${{ vars.ADMIN_DIR }}" | |
| export CONDA_BASE="${{ vars.CONDA_BASE }}" | |
| export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}" | |
| export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}" | |
| export REPO_PATH="${{ secrets.REPO_PATH }}" | |
| source "${REPO_PATH}"/scripts/install_config.sh | |
| source "${REPO_PATH}"/scripts/functions.sh | |
| mkdir -p "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}" | |
| set_admin_perms "${ADMIN_DIR}" "${JOB_LOG_DIR}" "${BUILD_STAGE_DIR}" | |
| EOT | |
| - name: Build conda environment | |
| run: | | |
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | |
| set -e | |
| export SCRIPT_DIR="${{ secrets.REPO_PATH }}/scripts" | |
| export CONDA_ENVIRONMENT="${{ matrix.environment }}" | |
| export ADMIN_DIR="${{ vars.ADMIN_DIR }}" | |
| export CONDA_BASE="${{ vars.CONDA_BASE }}" | |
| export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}" | |
| export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}" | |
| PROJECT=${{ vars.PROJECT }} | |
| STORAGE=${{ vars.STORAGE }} | |
| source "${SCRIPT_DIR}"/install_config.sh | |
| cd "${JOB_LOG_DIR}" | |
| qsub -N build_"${CONDA_ENVIRONMENT}" -lncpus=1,mem=20GB,walltime=2:00:00,jobfs=50GB,storage="${STORAGE}" \ | |
| -v SCRIPT_DIR,CONDA_ENVIRONMENT,ADMIN_DIR,CONDA_BASE,APPS_USERS_GROUP,APPS_OWNERS_GROUP \ | |
| -P "${PROJECT}" -q copyq -Wblock=true -Wumask=037 \ | |
| "${SCRIPT_DIR}"/build.sh | |
| EOT | |
| - name: Test conda environment | |
| run: | | |
| ssh ${{ secrets.USER }}@${{ secrets.HOST }} -i ${{ steps.ssh.outputs.private-key-path }} /bin/bash <<'EOT' | |
| set -e | |
| export SCRIPT_DIR="${{secrets.REPO_PATH}}/scripts" | |
| export CONDA_ENVIRONMENT="${{ matrix.environment }}" | |
| export ADMIN_DIR="${{ vars.ADMIN_DIR }}" | |
| export CONDA_BASE="${{ vars.CONDA_BASE }}" | |
| export APPS_USERS_GROUP="${{ vars.APPS_USERS_GROUP }}" | |
| export APPS_OWNERS_GROUP="${{ vars.APPS_OWNERS_GROUP }}" | |
| PROJECT=${{ vars.PROJECT }} | |
| STORAGE=${{ vars.STORAGE }} | |
| source "${SCRIPT_DIR}"/install_config.sh | |
| cd "${JOB_LOG_DIR}" | |
| qsub -N test_"${CONDA_ENVIRONMENT}" -lncpus=4,mem=20GB,walltime=0:20:00,jobfs=50GB,storage="${STORAGE}" \ | |
| -v SCRIPT_DIR,CONDA_ENVIRONMENT,ADMIN_DIR,CONDA_BASE,APPS_USERS_GROUP,APPS_OWNERS_GROUP \ | |
| -P "${PROJECT}" -Wblock=true -Wumask=037 \ | |
| "${SCRIPT_DIR}"/test.sh | |
| EOT |