synthseg_fix - Guide Notebooks Regression - EC2 #277
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| name: Guide Notebooks Regression - EC2 | |
| run-name: ${{ github.ref_name }} - Guide Notebooks Regression - EC2 | |
| on: [push] | |
| jobs: | |
| start-runner: | |
| name: Start self-hosted EC2 runner | |
| runs-on: ubuntu-latest | |
| outputs: | |
| label: ${{ steps.start-ec2-runner.outputs.label }} | |
| ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }} | |
| steps: | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v1 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_KEY_SECRET }} | |
| aws-region: ${{ vars.AWS_REGION }} | |
| - name: Start EC2 runner | |
| id: start-ec2-runner | |
| uses: machulav/ec2-github-runner@v2 | |
| with: | |
| mode: start | |
| github-token: ${{ secrets.GH_TOKEN }} | |
| ec2-image-id: ${{ vars.AWS_IMAGE_ID }} | |
| ec2-instance-type: ${{ vars.AWS_INSTANCE_TYPE }} | |
| subnet-id: ${{ vars.AWS_SUBNET }} | |
| security-group-id: ${{ vars.AWS_SECURITY_GROUP }} | |
| guide_notebooks_regression_ec2: | |
| needs: start-runner # required to start the main job when the runner is ready | |
| runs-on: ${{ needs.start-runner.outputs.label }} # run the job on the newly created runner | |
| steps: | |
| - name: clone | |
| uses: actions/checkout@v3 | |
| - name: install | |
| run: | | |
| set -xe | |
| cd ${{ github.workspace }} | |
| source /opt/tensorflow/bin/activate | |
| export LD_LIBRARY_PATH=opt/amazon/efa/lib:/opt/amazon/openmpi/lib:/usr/local/cuda/efa/lib:/usr/local/cuda/lib:/usr/local/cuda:/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/targets/x86_64-linux/lib:/usr/local/lib:/usr/lib | |
| echo $LD_LIBRARY_PATH | |
| pip install matplotlib nilearn | |
| pip install -U tensorflow | |
| pip install -e . | |
| nobrainer info | |
| - name: run | |
| run: | | |
| set -xe | |
| cd ${{ github.workspace }} | |
| git clone https://github.com/neuronets/nobrainer-book.git | |
| cd nobrainer-book | |
| # if there is a matching book branch, switch to it | |
| if [ $(git ls-remote --heads https://github.com/neuronets/nobrainer-book.git ${{ github.ref_name }} | wc -l) -ne 0 ]; then | |
| echo "Checking out branch ${{ github.ref_name }}" | |
| git checkout ${{ github.ref_name }}; | |
| else | |
| echo "No matching branch found, sticking with the default" | |
| fi | |
| cd ${{ github.workspace }} | |
| export LD_LIBRARY_PATH=opt/amazon/efa/lib:/opt/amazon/openmpi/lib:/usr/local/cuda/efa/lib:/usr/local/cuda/lib:/usr/local/cuda:/usr/local/cuda/lib64:/usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/targets/x86_64-linux/lib:/usr/local/lib:/usr/lib | |
| source /opt/tensorflow/bin/activate | |
| for notebook_script in $(ls nobrainer-book/docs/nobrainer-guides/scripts/*.py); do | |
| echo "running ${notebook_script}" | |
| python ${notebook_script} | |
| done | |
| stop-runner: | |
| name: Stop self-hosted EC2 runner | |
| needs: | |
| - start-runner # required to get output from the start-runner job | |
| - guide_notebooks_regression_ec2 # required to wait when the main job is done | |
| runs-on: ubuntu-latest | |
| if: ${{ always() }} # required to stop the runner even if the error happened in the previous jobs | |
| steps: | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v1 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_KEY_SECRET }} | |
| aws-region: ${{ vars.AWS_REGION }} | |
| - name: Stop EC2 runner | |
| uses: machulav/ec2-github-runner@v2 | |
| with: | |
| mode: stop | |
| github-token: ${{ secrets.GH_TOKEN }} | |
| label: ${{ needs.start-runner.outputs.label }} | |
| ec2-instance-id: ${{ needs.start-runner.outputs.ec2-instance-id }} |