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synthseg - Guide Notebooks Regression - EC2 #266

synthseg - Guide Notebooks Regression - EC2

synthseg - Guide Notebooks Regression - EC2 #266

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 }}