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rebuild base
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@bill-baumgartner
bill-baumgartner committed Jan 26, 2024
1 parent ea85b44 commit 2b33d8d
Showing 1 changed file with 119 additions and 119 deletions.
238 changes: 119 additions & 119 deletions .github/workflows/bert-models-cicd.yaml
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Expand Up @@ -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"

# # ----------------------------------------------------------------------------------- #
# # ----------------------------------------------------------------------------------- #
Expand Down Expand Up @@ -528,95 +528,95 @@ jobs:



# # # ----------------------------------------------------------------------------------- #
# # # ----------------------------------------------------------------------------------- #
# # # ----------------------------------------------------------------------------------- #
# # # TRAIN BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_GPT MODEL #
# # # ----------------------------------------------------------------------------------- #
# # # ----------------------------------------------------------------------------------- #
# # # ----------------------------------------------------------------------------------- #
# # # # ----------------------------------------------------------------------------------- #
# # # # ----------------------------------------------------------------------------------- #
# # # # ----------------------------------------------------------------------------------- #
# # # # TRAIN BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_GPT MODEL #
# # # # ----------------------------------------------------------------------------------- #
# # # # ----------------------------------------------------------------------------------- #
# # # # ----------------------------------------------------------------------------------- #

build_push_train-bl_chemical_to_disease_or_phenotypic_feature_gpt-train:
name: "build/push/train bl_chemical_to_disease_or_phenotypic_feature_gpt model"
# needs: "build_push-bert-base"
runs-on: ubuntu-latest
env:
TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature_gpt
DOCKERFILE: train.Dockerfile
ENTRYPOINT_FILE: scripts/train.entrypoint.sh
BASE_DOCKERFILE: base.Dockerfile
DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature_gpt/data.tsv
MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_GPT
AI_PLATFORM_JOB_NAME: "bl_chemical_to_disease_or_phenotypic_feature_gpt_train_${{ github.run_number }}"
steps:
# - uses: actions/checkout@v3
# with:
# fetch-depth: 0
# - name: Setup Python
# uses: actions/setup-python@v2
# with:
# python-version: 3.7
# - name: Set up Cloud SDK
# uses: google-github-actions/setup-gcloud@main
# with:
# project_id: ${{ secrets.GCE_PROJECT }}
# service_account_key: ${{ secrets.GCE_SA_KEY }}
# version: '290.0.1'
- 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: ${{ secrets.SERVICE_ACCOUNT_KEY }}
- name: 'Set up Cloud SDK'
uses: 'google-github-actions/setup-gcloud@v2'
with:
version: '>= 363.0.0'
- name: Setup Python
uses: actions/setup-python@v2
with:
python-version: 3.7
- name: Configure Docker Authentication
run: |
gcloud --quiet auth configure-docker
# build_push_train-bl_chemical_to_disease_or_phenotypic_feature_gpt-train:
# name: "build/push/train bl_chemical_to_disease_or_phenotypic_feature_gpt model"
# # needs: "build_push-bert-base"
# runs-on: ubuntu-latest
# env:
# TASK_NAME: bl_chemical_to_disease_or_phenotypic_feature_gpt
# DOCKERFILE: train.Dockerfile
# ENTRYPOINT_FILE: scripts/train.entrypoint.sh
# BASE_DOCKERFILE: base.Dockerfile
# DATA_FILE: data/bl_chemical_to_disease_or_phenotypic_feature_gpt/data.tsv
# MODEL_VERSION_KEY: BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_GPT
# AI_PLATFORM_JOB_NAME: "bl_chemical_to_disease_or_phenotypic_feature_gpt_train_${{ github.run_number }}"
# steps:
# # - uses: actions/checkout@v3
# # with:
# # fetch-depth: 0
# # - name: Setup Python
# # uses: actions/setup-python@v2
# # with:
# # python-version: 3.7
# # - name: Set up Cloud SDK
# # uses: google-github-actions/setup-gcloud@main
# # with:
# # project_id: ${{ secrets.GCE_PROJECT }}
# # service_account_key: ${{ secrets.GCE_SA_KEY }}
# # version: '290.0.1'
# - 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 ${{ 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: 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 ${{ env.AI_PLATFORM_JOB_NAME }}"
timeout-minutes: 500
# - name: Publish Docker Image to Google Container Registry
# run: |
# docker push "gcr.io/$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: Monitor the training job
# run: |
# sh -c ".github/workflows/monitor-ai-platform-job.sh ${{ env.AI_PLATFORM_JOB_NAME }}"
# timeout-minutes: 500

# # -------------------------------------------------------------------------------------- #
# # BUILD/PUSH BL_CHEMICAL_TO_DISEASE_OR_PHENOTYPIC_FEATURE_GPT CLASSIFICATION CONTAINER IMAGE #
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