Merge branch 'master' into pre-commit-ci-update-config

.github/workflows/guide-notebooks-ec2.yml

@@ -1,63 +1,44 @@
 name: Guide Notebooks Regression - EC2
-run-name: Guide Notebooks Regression - EC2
+run-name: ${{ github.ref_name }} - Guide Notebooks Regression - EC2
 on: [push]
 jobs:
-  start_ec2_runner:
+  start-runner:
+    name: Start self-hosted EC2 runner
     runs-on: ubuntu-latest
-    env:
-      AWS_KEY_ID: ${{ secrets.AWS_KEY_ID }}
-      AWS_KEY_SECRET: ${{ secrets.AWS_KEY_SECRET }}
-      AWS_INSTANCE_TYPE: ${{ vars.AWS_INSTANCE_TYPE }}
-      AWS_IMAGE_ID: ${{ vars.AWS_IMAGE_ID }}
-      AWS_SECURITY_GROUP: ${{ vars.AWS_SECURITY_GROUP }}
     outputs:
-      EC2_INSTANCE_ID: ${{ steps.start_runner.outputs.EC2_INSTANCE_ID }}
+      label: ${{ steps.start-ec2-runner.outputs.label }}
+      ec2-instance-id: ${{ steps.start-ec2-runner.outputs.ec2-instance-id }}
     steps:
-      - name: configure_aws
-        run: |
-          set -xe
-          sudo apt update
-          sudo apt install -y awscli jq
-          mkdir ${HOME}/.aws
-          echo "[default]" > ${HOME}/.aws/credentials
-          echo "aws_access_key_id = ${AWS_KEY_ID}" >> ${HOME}/.aws/credentials
-          echo "aws_secret_access_key = ${AWS_KEY_SECRET}" >> ${HOME}/.aws/credentials
-          echo "region = us-east-1" >> ${HOME}/.aws/credentials
-          cat ${HOME}/.aws/credentials
-      - name: start_runner
-        id: start_runner
-        run: |
-          set -xe
-          output=$(aws ec2 run-instances \
-            --instance-type ${AWS_INSTANCE_TYPE} \
-            --image-id ${AWS_IMAGE_ID} \
-            --security-group-ids ${AWS_SECURITY_GROUP} \
-            --count 1)
-          EC2_INSTANCE_ID=$(echo ${output} | jq -r ".Instances[0].InstanceId")
-          echo "EC2_INSTANCE_ID=${EC2_INSTANCE_ID}" >> "$GITHUB_OUTPUT"
+      - 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:
-    runs-on: [self-hosted, nobrainer-ci-ec2-gpu]
-    needs: start_ec2_runner
+    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: verify-instance
-        env:
-          EC2_INSTANCE_ID: ${{ needs.start_ec2_runner.outputs.EC2_INSTANCE_ID }}
-        run: |
-          set -xe
-          if [[ $(ec2metadata --instance-id) != ${EC2_INSTANCE_ID} ]]; then
-            echo "Running on the wrong instance! Bailing, but try rerunning"
-            exit 1
-          fi
       - name: clone
         uses: actions/checkout@v3
       - name: install
         run: |
           set -xe
           cd ${{ github.workspace }}
-          python -m venv env
-          source env/bin/activate
-          pip install --upgrade pip
+          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 -e .
           nobrainer info
@@ -77,34 +58,31 @@ jobs:
           fi
 
           cd ${{ github.workspace }}
-          source env/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
+          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_ec2_runner:
-    if: always()
+  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
-    needs: [start_ec2_runner, guide_notebooks_regression_ec2]
-    env:
-      AWS_KEY_ID: ${{ secrets.AWS_KEY_ID }}
-      AWS_KEY_SECRET: ${{ secrets.AWS_KEY_SECRET }}
+    if: ${{ always() }} # required to stop the runner even if the error happened in the previous jobs
     steps:
-      - name: configure_aws
-        run: |
-          set -xe
-          sudo apt update
-          sudo apt install -y awscli
-          mkdir ${HOME}/.aws
-          echo "[default]" > ${HOME}/.aws/credentials
-          echo "aws_access_key_id = ${AWS_KEY_ID}" >> ${HOME}/.aws/credentials
-          echo "aws_secret_access_key = ${AWS_KEY_SECRET}" >> ${HOME}/.aws/credentials
-          echo "region = us-east-1" >> ${HOME}/.aws/credentials
-          cat ${HOME}/.aws/credentials
-      - name: stop_runner
-        env:
-          EC2_INSTANCE_ID: ${{ needs.start_ec2_runner.outputs.EC2_INSTANCE_ID }}
-        run: |
-          set -xe
-          aws ec2 terminate-instances --instance-ids ${EC2_INSTANCE_ID}
+      - 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 }}