revert python change - google cloud sdk version change instead

to avoid issues with google cloud sdk not allowing python 3.6 we are using an older version of it.
UCDenver-ccp · May 1, 2024 · af5e64d · af5e64d
1 parent fbb6422
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diff --git a/.github/workflows/bert-models-cicd.yaml b/.github/workflows/bert-models-cicd.yaml
@@ -50,41 +50,41 @@ jobs:
 # Note: when trying to run build_push-bert-base with other jobs below, an error is reported on line 90. 
 #       However, when run on its own it works fine.
 
-    # build_push-bert-base:
-    #   name: "build/push bluebert-base container image"
-    #   runs-on: ubuntu-latest
-    #   env:
-    #     IMAGE_NAME: bluebert-base
-    #     DOCKERFILE: base.Dockerfile
-    #   permissions:
-    #     contents: 'read'
-    #     id-token: 'write'
-    #   steps:
-    #   - uses: actions/checkout@v4
-    #     with:
-    #       fetch-depth: 0
-    #   - id: 'auth'
-    #     uses: 'google-github-actions/auth@v2'
-    #     with:
-    #       project_id: ${{ secrets.GCE_PROJECT }}
-    #       service_account: ${{ secrets.SERVICE_ACCOUNT }}
-    #       credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }}
-    #   - name: 'Set up Cloud SDK'
-    #     uses: 'google-github-actions/setup-gcloud@v2'
-    #     with:
-    #       version: '>= 363.0.0'
-    #   - name: Setup Python
-    #     uses: actions/setup-python@v2
-    #     with:
-    #       python-version: 3.7
-    #   - name: Configure Docker Authentication
-    #     run: gcloud --quiet auth configure-docker
-    #   - name: Set MODEL_VERSION env
-    #     run: echo "MODEL_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
-    #   - name: Build Docker Image
-    #     run: docker build --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" -f ${{ env.DOCKERFILE }} .
-    #   - name: Publish Docker Image to Google Container Registry
-    #     run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION"
+    build_push-bert-base:
+      name: "build/push bluebert-base container image"
+      runs-on: ubuntu-latest
+      env:
+        IMAGE_NAME: bluebert-base
+        DOCKERFILE: base.Dockerfile
+      permissions:
+        contents: 'read'
+        id-token: 'write'
+      steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - id: 'auth'
+        uses: 'google-github-actions/auth@v2'
+        with:
+          project_id: ${{ secrets.GCE_PROJECT }}
+          service_account: ${{ secrets.SERVICE_ACCOUNT }}
+          credentials_json: ${{ secrets.SERVICE_ACCOUNT_KEY }}
+      - name: 'Set up Cloud SDK'
+        uses: 'google-github-actions/setup-gcloud@v2'
+        with:
+          version: '>= 363.0.0'
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+      - name: Configure Docker Authentication
+        run: gcloud --quiet auth configure-docker
+      - name: Set MODEL_VERSION env
+        run: echo "MODEL_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+      - name: Build Docker Image
+        run: docker build --tag "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION" -f ${{ env.DOCKERFILE }} .
+      - name: Publish Docker Image to Google Container Registry
+        run: docker push "gcr.io/$PROJECT_ID/$IMAGE_NAME:$MODEL_VERSION"
 
 # # ----------------------------------------------------------------------------------- #
 #   # ----------------------------------------------------------------------------------- #
@@ -2397,124 +2397,124 @@ jobs:
         # # # ----------------------------------------------------------------------------------- #
         # # # ----------------------------------------------------------------------------------- #
 
-        build_push_train-craft_100-train:
-          name: "build/push/train craft_100 model"
-          # needs: "build_push-bert-base"
-          runs-on: ubuntu-latest
-          permissions:
-            contents: "read"
-            id-token: "write"
-          env:
-            TASK_NAME: craft_100
-            DOCKERFILE: train.Dockerfile
-            ENTRYPOINT_FILE: scripts/train.entrypoint.sh
-            BASE_DOCKERFILE: base.Dockerfile
-            DATA_FILE: data/craft_100/data.tsv
-            MODEL_VERSION_KEY: CRAFT_100
-            AI_PLATFORM_JOB_NAME: "craft_100_train_${{ github.run_number }}"
-          steps:
-          - name: Checkout repository
-            uses: actions/checkout@v2
-
-          - name: Authenticate to Google Cloud
-            uses: google-github-actions/auth@v0
-            with:
-              workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
-              service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
-
-          - name: Configure Docker Authentication
-            run: |
-              gcloud --quiet auth configure-docker
+        # build_push_train-craft_100-train:
+        #   name: "build/push/train craft_100 model"
+        #   # needs: "build_push-bert-base"
+        #   runs-on: ubuntu-latest
+        #   permissions:
+        #     contents: "read"
+        #     id-token: "write"
+        #   env:
+        #     TASK_NAME: craft_100
+        #     DOCKERFILE: train.Dockerfile
+        #     ENTRYPOINT_FILE: scripts/train.entrypoint.sh
+        #     BASE_DOCKERFILE: base.Dockerfile
+        #     DATA_FILE: data/craft_100/data.tsv
+        #     MODEL_VERSION_KEY: CRAFT_100
+        #     AI_PLATFORM_JOB_NAME: "craft_100_train_${{ github.run_number }}"
+        #   steps:
+        #   - name: Checkout repository
+        #     uses: actions/checkout@v2
+
+        #   - name: Authenticate to Google Cloud
+        #     uses: google-github-actions/auth@v0
+        #     with:
+        #       workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
+        #       service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
+
+        #   - name: Configure Docker Authentication
+        #     run: |
+        #       gcloud --quiet auth configure-docker
 
-          - name: Set MODEL_VERSION env
-            run: |
-              echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+        #   - name: Set MODEL_VERSION env
+        #     run: |
+        #       echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
 
-          - name: Set BASE_VERSION env
-            run: |
-              echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+        #   - name: Set BASE_VERSION env
+        #     run: |
+        #       echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
 
-          - name: Build Docker Image
-            run: |
-              docker build --build-arg "PROJECT_ID=$PROJECT_ID" \
-                           --build-arg "TASK_NAME=$TASK_NAME" \
-                           --build-arg "BASE_VERSION=$BASE_VERSION" \
-                           --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
-                           --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
-                           -f ${{ env.DOCKERFILE }} .
+        #   - name: Build Docker Image
+        #     run: |
+        #       docker build --build-arg "PROJECT_ID=$PROJECT_ID" \
+        #                    --build-arg "TASK_NAME=$TASK_NAME" \
+        #                    --build-arg "BASE_VERSION=$BASE_VERSION" \
+        #                    --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
+        #                    --tag "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
+        #                    -f ${{ env.DOCKERFILE }} .
 
-          - name: Publish Docker Image to Google Container Registry
-            run: |
-              docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION"
+        #   - name: Publish Docker Image to Google Container Registry
+        #     run: |
+        #       docker push "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION"
 
-          - name: Submit a training job to AI Plaform to train and cache the model
-            run: |
-              gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \
-              --scale-tier basic_gpu --region "$GCE_REGION" \
-              --master-image-uri "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
-              -- \
-              NO_ARG \
-              "gs://$MODEL_STORAGE_BUCKET"
+        #   - name: Submit a training job to AI Plaform to train and cache the model
+        #     run: |
+        #       gcloud ai-platform jobs submit training ${{ env.AI_PLATFORM_JOB_NAME }} \
+        #       --scale-tier basic_gpu --region "$GCE_REGION" \
+        #       --master-image-uri "gcr.io/$PROJECT_ID/$TASK_NAME-train:$MODEL_VERSION" \
+        #       -- \
+        #       NO_ARG \
+        #       "gs://$MODEL_STORAGE_BUCKET"
 
-          - name: Monitor the training job
-            run: |
-              sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
-            timeout-minutes: 180
+        #   - name: Monitor the training job
+        #     run: |
+        #       sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
+        #     timeout-minutes: 180
 
-        # # # ----------------------------------------------------------------------------------- #
-        # # #          BUILD/PUSH CRAFT_RELATIONS INFLUENCE CLASSIFICATION CONTAINER IMAGE       #
-        # # # ----------------------------------------------------------------------------------- #
+        # # # # ----------------------------------------------------------------------------------- #
+        # # # #          BUILD/PUSH CRAFT_RELATIONS INFLUENCE CLASSIFICATION CONTAINER IMAGE       #
+        # # # # ----------------------------------------------------------------------------------- #
 
-        build_push-craft_100-predict:
-          name: "build/push craft_100 predict container"
-          needs: "build_push_train-craft_100-train"
-          runs-on: ubuntu-latest
-          permissions:
-            contents: "read"
-            id-token: "write"
-          env:
-            TASK_NAME: craft_100
-            DOCKERFILE: predict.Dockerfile
-            TRAIN_DOCKERFILE: train.Dockerfile
-            TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh
-            ENTRYPOINT_FILE: scripts/predict.entrypoint.sh
-            BASE_DOCKERFILE: base.Dockerfile
-            MODEL_VERSION_KEY: CRAFT_100
-            CLASSIFICATION_LABELS: "label1 label2 false"
-            DATA_FILE: data/craft_100/data.tsv
-          steps:
-          - name: Checkout repository
-            uses: actions/checkout@v2
-
-          - name: Authenticate to Google Cloud
-            uses: google-github-actions/auth@v0
-            with:
-              workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
-              service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
+        # build_push-craft_100-predict:
+        #   name: "build/push craft_100 predict container"
+        #   needs: "build_push_train-craft_100-train"
+        #   runs-on: ubuntu-latest
+        #   permissions:
+        #     contents: "read"
+        #     id-token: "write"
+        #   env:
+        #     TASK_NAME: craft_100
+        #     DOCKERFILE: predict.Dockerfile
+        #     TRAIN_DOCKERFILE: train.Dockerfile
+        #     TRAIN_ENTRYPOINT_FILE: scripts/train.entrypoint.sh
+        #     ENTRYPOINT_FILE: scripts/predict.entrypoint.sh
+        #     BASE_DOCKERFILE: base.Dockerfile
+        #     MODEL_VERSION_KEY: CRAFT_100
+        #     CLASSIFICATION_LABELS: "label1 label2 false"
+        #     DATA_FILE: data/craft_100/data.tsv
+        #   steps:
+        #   - name: Checkout repository
+        #     uses: actions/checkout@v2
+
+        #   - name: Authenticate to Google Cloud
+        #     uses: google-github-actions/auth@v0
+        #     with:
+        #       workload_identity_provider: ${{ secrets.WORKLOAD_IDENTITY_PROVIDER_LOCATION }}
+        #       service_account: "${{ secrets.SERVICE_ACCOUNT }}@${{ secrets.GCE_PROJECT }}.iam.gserviceaccount.com"
 
-          - name: Configure Docker Authentication
-            run: |
-              gcloud --quiet auth configure-docker
+        #   - name: Configure Docker Authentication
+        #     run: |
+        #       gcloud --quiet auth configure-docker
 
-          - name: Set MODEL_VERSION env
-            run: |
-              echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+        #   - name: Set MODEL_VERSION env
+        #     run: |
+        #       echo "MODEL_VERSION=$(grep ${{ env.MODEL_VERSION_KEY }} MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
 
-          - name: Set BASE_VERSION env
-            run: |
-              echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
+        #   - name: Set BASE_VERSION env
+        #     run: |
+        #       echo "BASE_VERSION=$(grep 'BASE' MODEL_VERSIONS | cut -f 2 -d '=')" >> $GITHUB_ENV
 
-          - name: Build Docker Image
-            run: |
-              docker build --build-arg "PROJECT_ID=$PROJECT_ID" \
-                           --build-arg "TASK_NAME=$TASK_NAME" \
-                           --build-arg "BASE_VERSION=$BASE_VERSION" \
-                           --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
-                           --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \
-                           --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \
-                           --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \
-                           -f ${{ env.DOCKERFILE }} .
+        #   - name: Build Docker Image
+        #     run: |
+        #       docker build --build-arg "PROJECT_ID=$PROJECT_ID" \
+        #                    --build-arg "TASK_NAME=$TASK_NAME" \
+        #                    --build-arg "BASE_VERSION=$BASE_VERSION" \
+        #                    --build-arg "TUNED_MODEL_VERSION=$MODEL_VERSION" \
+        #                    --build-arg "MODEL_STORAGE_BUCKET=$MODEL_STORAGE_BUCKET" \
+        #                    --build-arg "CLASSIFICATION_LABELS=${{ env.CLASSIFICATION_LABELS }}" \
+        #                    --tag "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" \
+        #                    -f ${{ env.DOCKERFILE }} .
 
-          - name: Publish Docker Image to Google Container Registry
-            run: |
-              docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" 
+        #   - name: Publish Docker Image to Google Container Registry
+        #     run: |
+        #       docker push "gcr.io/$PROJECT_ID/$TASK_NAME-predict:$MODEL_VERSION" 
diff --git a/MODEL_VERSIONS b/MODEL_VERSIONS
@@ -1,4 +1,4 @@
-BASE=0.7
+BASE=0.8
 BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE=0.1
 BL_CHEMICAL_TO_GENE=0.1
 BL_DISEASE_TO_PHENOTYPIC_FEATURE=0.1

diff --git a/base.Dockerfile b/base.Dockerfile
@@ -1,4 +1,4 @@
-FROM tensorflow/tensorflow:1.15.4-gpu
+FROM tensorflow/tensorflow:1.15.5-gpu-py3
 
 RUN \
     # Update nvidia GPG key - from: https://github.com/NVIDIA/nvidia-docker/issues/1631
@@ -15,13 +15,8 @@ RUN apt-get update && apt-get install -y \
   less \
   vim \
   wget \
-  python3.8 \
   && rm -rf /var/lib/apt/lists/*
 
-RUN rm /usr/bin/python3 && \
-    ln -s python3.8 /usr/bin/python3 && \
-    python3 -V
-
 # set up directories that will be used by this container (and its children) 
 RUN mkdir -p /home/dev/models/baseline && \
     mkdir -p /home/dev/output && \
@@ -32,10 +27,10 @@ WORKDIR /home/dev
 # Installs google cloud sdk, this allows use of gsutil
 # from: https://cloud.google.com/ai-platform/training/docs/custom-containers-training
 RUN wget -nv \
-    https://dl.google.com/dl/cloudsdk/release/google-cloud-sdk.tar.gz && \
+    https://dl.google.com/dl/cloudsdk/channels/rapid/downloads/google-cloud-cli-422.0.0-linux-x86_64.tar.gz && \
     mkdir /root/tools && \
-    tar xvzf google-cloud-sdk.tar.gz -C /root/tools && \
-    rm google-cloud-sdk.tar.gz && \
+    tar xvzf google-cloud-cli-422.0.0-linux-x86_64.tar.gz -C /root/tools && \
+    rm google-cloud-cli-422.0.0-linux-x86_64.tar.gz && \
     /root/tools/google-cloud-sdk/install.sh --usage-reporting=false \
         --path-update=false --bash-completion=false \
         --disable-installation-options && \