mirror of https://github.com/kubeflow/examples.git
421 lines
22 KiB
Markdown
421 lines
22 KiB
Markdown
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# Kubeflow Pipelines - GitHub Issue Summarization
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<walkthrough-tutorial-duration duration="90"></walkthrough-tutorial-duration>
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## Introduction
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**Note: This tutorial is deprecated. It will be updated soon.**
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[Kubeflow](https://www.kubeflow.org/) is an OSS project to support a machine learning stack on Kubernetes, to make deployments of ML workflows on Kubernetes simple, portable and scalable.
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[**Kubeflow Pipelines**](https://github.com/kubeflow/pipelines) is a component of Kubeflow that makes it easy to compose, deploy and manage end-to-end machine learning workflows. The Kubeflow Pipelines documentation is [here](https://www.kubeflow.org/docs/pipelines/).
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This codelab will walk you through creating your own Kubeflow deployment, and running a KubeFlow Pipelines workflow for model training and serving -- both from the Pipelines UI, and from a Jupyter Notebook.
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### What does a Kubeflow deployment look like?
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A Kubeflow deployment is:
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* __Portable__ - Works on any Kubernetes cluster, whether it lives on Google Cloud Platform (GCP), on premises, or across providers.
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* __Scalable__ - Can utilize fluctuating resources and is only constrained by the number of resources allocated to the Kubernetes cluster.
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* __Composable__ - Enhanced with service workers to work offline or on low-quality networks.
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### What you'll build
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In this lab, you will build a web app that summarizes GitHub issues using Kubeflow Pipelines to train and serve a model. Upon completion, your infrastructure will contain:
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* A Kubernetes Engine cluster with default Kubeflow installation
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* A pipeline that performs distributed training of a Tensor2Tensor model on GPUs
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* A serving container that provides predictions from the trained model
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* A UI that interprets the predictions to provide summarizations for GitHub issues
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* A notebook that creates a pipeline from scratch using the Kubeflow Pipelines SDK
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### What you'll learn
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The pipeline you will build trains a [Tensor2Tensor](https://github.com/tensorflow/tensor2tensor/) model on GitHub issue data, learning to predict issue titles from issue bodies. It then exports the trained model and deploys the exported model using [Tensorflow Serving](https://github.com/tensorflow/serving). The final step in the pipeline launches a web app, which interacts with the TF-Serving instance in order to get model predictions.
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* How to set up a [Kubeflow](https://github.com/kubeflow/kubeflow) cluster using GKE
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* How to build and run ML workflows using Kubeflow Pipelines
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* How to define and run pipelines from within a Kubeflow JupyterHub notebook
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### What you'll need
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* A basic understanding of [Kubernetes](https://kubernetes.io/)
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* An active [GCP project](https://cloud.google.com/resource-manager/docs/creating-managing-projects) for which you have Owner permissions
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* A [GitHub](https://github.com/) account
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* Access to the Google Cloud Shell, available in the [Google Cloud Platform (GCP) Console](https://console.cloud.google.com/home/dashboard)
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This is an advanced codelab focused on Kubeflow. For more background and an introduction to the platform, see the [Introduction to Kubeflow](https://www.kubeflow.org/docs/about/kubeflow/) documentation. Non-relevant concepts and code blocks are glossed over and provided for you to simply copy and paste.
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## Project setup
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Google Cloud Platform (GCP) organizes resources into projects. This allows you to
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collect all the related resources for a single application in one place. For this lab, you'll need a GCP project with billing enabled.
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<walkthrough-project-billing-setup></walkthrough-project-billing-setup>
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## Set up the environment
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> **Note**: For simplicity, these instructions assume you're using the Cloud Shell, but you could also do the lab from your laptop after installing the necessary packages. If you're on your laptop, use of a virtual environment (e.g. Conda or virtualenv) is highly recommended.
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### Cloud Shell
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Visit the [GCP Console](https://console.cloud.google.com/) in the browser and log in with your project credentials.
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Then, click the "Activate Cloud Shell" icon in the top right of the console to start up a [Cloud Shell](https://cloud.google.com/shell/docs/) (if one is not already opened for you). <walkthrough-cloud-shell-icon></walkthrough-cloud-shell-icon>
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/fc32d2fa27e821c4.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/fc32d2fa27e821c4.png" width="30%"/></a> -->
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### Set your GitHub token
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This codelab calls the GitHub API to retrieve publicly available data. To prevent rate-limiting, especially at events where a large number of anonymized requests are sent to the GitHub APIs, set up an access token with no permissions. This is simply to authorize you as an individual rather than anonymous user.
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1. Navigate to [https://github.com/settings/tokens](https://github.com/settings/tokens) and generate a new token with no scopes.
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2. Save it somewhere safe. If you lose it, you will need to delete and create a new one.
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3. Set the GITHUB_TOKEN environment variable:
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```bash
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export GITHUB_TOKEN=<token>
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```
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### Set your GCP project ID and cluster name
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To find your project ID, visit the GCP Console's Home panel. If the screen is empty, click on Yes at the prompt to create a dashboard.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/fa2a4037585b38d6.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/fa2a4037585b38d6.png" width="40%"/></a> -->
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In the Cloud Shell terminal, run these commands to set the cluster name and project ID. For the zone, pick a zone where `nvidia-tesla-k80`s are available.
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```bash
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export DEPLOYMENT_NAME=kubeflow
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export PROJECT_ID=<your_project_id>
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export ZONE=<your-zone>
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gcloud config set project ${PROJECT_ID}
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gcloud config set compute/zone ${ZONE}
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```
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### Create a storage bucket
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> **Note**: Bucket names must be unique across all of GCP, not just your organization
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Create a Cloud Storage bucket for storing pipeline files. Fill in a new, unique bucket name and issue the "mb" (make bucket) command:
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```bash
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export BUCKET_NAME=kubeflow-${PROJECT_ID}
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gsutil mb gs://${BUCKET_NAME}
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```
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Alternatively, you can create a bucket [via the GCP Console](https://console.cloud.google.com/storage).
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### Install the Kubeflow Pipelines SDK
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Run the following command to install the Kubeflow Pipelines SDK:
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```bash
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pip3 install https://storage.googleapis.com/ml-pipeline/release/0.1.7/kfp.tar.gz --upgrade
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```
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We'll use this SDK a bit later in the lab.
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> **Note**: Python 3.5 or higher is required. If you're running in a Conda Python 3 environment, you'll use `pip` instead of
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`pip3`.
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### Optional: Pin useful dashboards
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In the GCP console, you can pin the __Kubernetes Engine__ and __Storage__ dashboards for easier access. <walkthrough-pin-section-icon></walkthrough-pin-section-icon>
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/2a50622902d75f6a.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/2a50622902d75f6a.png" width="20%"/></a> -->
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## Create a Kubeflow cluster
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### Create a cluster
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Create a managed Kubernetes cluster on Kubernetes Engine by visiting the
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[Kubeflow Click-to-Deploy](https://deploy.kubeflow.cloud/) site in your browser and signing in with your GCP account.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/5dbc46bc61dbd94f.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/5dbc46bc61dbd94f.png" width="60%"/></a> -->
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Fill in the following values in the resulting form:
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* __Project__: Enter your GCP `$PROJECT_ID` in the top field
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* __Deployment name__: Set the default value to __`kubeflow`__. Alternatively, set `$DEPLOYMENT_NAME` to a different value and use it here. Note that this value must be unique within the project.
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* __GKE Zone__: Use the value you have set for `$ZONE`, selecting it from the pulldown.
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* __Kubeflow Version__: v0.4.1
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* Check the __Skip IAP__ box
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/c73a14a93c78ce5.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/c73a14a93c78ce5.png" width="40%"/></a>
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-->
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### Set up kubectl to use your new cluster's credentials
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When the cluster has been instantiated, connect your environment to the Kubernetes Engine cluster by running the following command in your Cloud Shell:
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```bash
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gcloud container clusters get-credentials ${DEPLOYMENT_NAME} \
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--project ${PROJECT_ID} \
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--zone ${ZONE}
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```
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This configures your `kubectl` context so that you can interact with your cluster. To verify the connection, run the following command:
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```bash
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kubectl get nodes -o wide
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```
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You should see two nodes listed, both with a status of "`Ready`", and other information about node age, version, external IP address, OS image, kernel version, and container runtime.
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### Add a GPU node pool to the cluster
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Run the following command to create an accelerator node pool:
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```bash
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gcloud container node-pools create accel \
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--project ${PROJECT_ID} \
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--zone ${ZONE} \
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--cluster ${DEPLOYMENT_NAME} \
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--accelerator type=nvidia-tesla-k80,count=4 \
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--num-nodes 1 \
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--machine-type n1-highmem-8 \
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--disk-size=220GB \
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--scopes cloud-platform \
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--verbosity error
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```
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> **Note**: This can take a few minutes.
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Install Nvidia drivers on these nodes by applying a *daemonset* :
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```bash
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kubectl apply -f https://raw.githubusercontent.com/GoogleCloudPlatform/container-engine-accelerators/stable/nvidia-driver-installer/cos/daemonset-preloaded.yaml
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```
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### View the Kubeflow central dashboard
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Once the cluster setup is complete, port-forward to view the Kubeflow central dashboard. Click the "Cloud Shell" button in the launcher:
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/73d081ccecbab307.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/73d081ccecbab307.png" width="40%"/></a> -->
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This will open a tab showing your new cluster's services details. Click the __Port Forwarding__ button towards the bottom of the page, then click the __Run in Cloud Shell__ button in the resulting popup window.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/81a2891d64a6e621.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/81a2891d64a6e621.png" width="90%"/></a> -->
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A Cloud Shell window will start up, with the command to port-forward pre-populated at the prompt. Hit ‘return' to actually run the command in the Cloud Shell, then click the __Open in web preview__ button that will appear in the services page.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/fd3923eae05d4eff.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/fd3923eae05d4eff.png" width="50%"/></a> -->
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This will launch the Kubeflow dashboard in a new browser tab.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/19dbaa6018106d2a.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/19dbaa6018106d2a.png" width="90%"/></a> -->
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## Run a pipeline from the Pipelines dashboard
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### Pipeline description
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The pipeline you will run has three steps:
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1. It starts by training a [Tensor2Tensor](https://github.com/tensorflow/tensor2tensor/) model using preprocessed data. (More accurately, this step starts from an existing model checkpoint, then trains for a few more hundred steps-- it would take too long to fully train it). When it finishes, it exports the model in a form suitable for serving by [TensorFlow serving](https://github.com/tensorflow/serving/).
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2. The next step in the pipeline deploys a TensorFlow-serving instance using that model.
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3. The last step launches a web app for interacting with the served model to retrieve predictions.
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### Download and compile the pipeline
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To download the script containing the pipeline definition, execute this command:
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```bash
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curl -O https://raw.githubusercontent.com/kubeflow/examples/master/github_issue_summarization/pipelines/example_pipelines/gh_summ.py
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```
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Compile the pipeline definition file by running it:
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```bash
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python3 gh_summ.py
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```
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You will see the file `gh_summ.py.tar.gz` appear as a result.
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> **Note**: If you get an error, make sure you have installed the Pipelines SDK and are using Python 3. If you're running in a Conda Python 3 environment, you'll use `python` instead of `python3`
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### Upload the compiled pipeline
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From the Kubeflow dashboard, click the __Pipeline Dashboard__ link to navigate to the Kubeflow Pipelines web UI. Click on __Upload pipeline__, and select __Import by URL__. Paste in the following URL, which points to the same pipeline that you just compiled.
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```
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https://github.com/kubeflow/examples/raw/master/github_issue_summarization/pipelines/example_pipelines/gh_summ.py.tar.gz
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```
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Give the pipeline a name (e.g. `gh_summ`).
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/d884e72326017ce5.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/d884e72326017ce5.png" width="90%"/></a> -->
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### Run the pipeline
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Click on the uploaded pipeline in the list —this lets you view the pipeline's static graph— then click on __Start an experiment__ to create a new __Experiment__ using the pipeline.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/e6df677f6234b898.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/e6df677f6234b898.png" width="60%"/></a> -->
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Give the Experiment a name (e.g. the same name as the pipeline, `gh_summ`), then click __Next__ to create it.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/9bb7fc0f06f6c6bf.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/9bb7fc0f06f6c6bf.png" width="60%"/></a> -->
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An Experiment is composed of multiple __Runs__. In Cloud Shell, execute these commands to gather the values to enter into the UI as parameters for the first __Run__:
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```bash
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gcloud config get-value project
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echo ${GITHUB_TOKEN}
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echo "gs://${BUCKET_NAME}/kubecon"
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```
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Give the Run a name (e.g. `gh_summ-1`) and fill in three parameter fields:
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* `project`
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* `github-token`
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* `working-dir`
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/fda08d43b53cfdc8.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/fda08d43b53cfdc8.png" width="60%"/></a> -->
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After filling in the fields, click **Create**.
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> **Note**: The pipeline will take approximately 15 minutes to complete.
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Once the pipeline run is launched, you can click on an individual step in the run to get more information about it, including viewing its *pod* logs.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/ea5e2396ca27e100.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/ea5e2396ca27e100.png" width="90%"/></a> -->
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### View the pipeline definition
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While the pipeline is running, take a [closer look](https://github.com/kubeflow/examples/blob/master/github_issue_summarization/example_pipelines/gh_summ.py) at how it is put together and what it is doing.
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### View TensorBoard
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The first step in the pipeline performs training and generates a model. Once this step is complete, view __Artifacts__ and click the blue Start TensorBoard button, then once it's ready, click __Open Tensorboard__.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/d55eb03c4d04f64d.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/d55eb03c4d04f64d.png" width="90%"/></a> -->
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### View the web app and make some predictions
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The last step in the pipeline deploys a web app, which provides a UI for querying the trained model - served via [TF Serving](https://github.com/tensorflow/serving/) - to make predictions. After the pipeline completes, connect to the web app by visiting the Kubeflow central dashboard page, and appending __`/webapp/`__ at the end of the URL. (The trailing slash is required).
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You should see something like this:
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/e3722fd7cfbf0508.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/e3722fd7cfbf0508.png" width="80%"/></a> -->
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Click the __Populate Random Issue__ button to retrieve a block of text. Click on __Generate TItle__ to call the trained model and display a prediction.
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> **Note**: It can take a few seconds to display a summary— for this lab we're not using GPUs for the TensorFlow Serving instance.
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<!-- ### If you have trouble setting up a GPU node pool or running the training pipeline
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If you have any trouble running the training pipeline, or if you had any issues setting up a GPU node pool, try this shorter pipeline. It uses an already-exported TensorFlow model, skips the training step, and takes only a minute or so to run. Download the Python pipeline definition here:
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[https://raw.githubusercontent.com/amygdala/code-snippets/master/ml/kubeflow-pipelines/samples/kubeflow-tf/gh_summ_serve.py](https://raw.githubusercontent.com/amygdala/code-snippets/master/ml/kubeflow-pipelines/samples/kubeflow-tf/gh_summ_serve.py)
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or the compiled version of the pipeline here:
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[https://github.com/amygdala/code-snippets/blob/master/ml/kubeflow-pipelines/samples/kubeflow-tf/gh_summ_serve.py.tar.gz?raw=true](https://github.com/amygdala/code-snippets/blob/master/ml/kubeflow-pipelines/samples/kubeflow-tf/gh_summ_serve.py.tar.gz?raw=true) -->
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## Run a pipeline from a Jupyter notebook
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### Create a JupyterHub instance
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You can also interactively define and run Kubeflow Pipelines from a Jupyter notebook. To create a notebook, navigate to the __JupyterHub__ link on the central Kubeflow dashboard.
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The first time you visit JupyterHub, you'll first be asked to log in. You can use any username/password you like
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(remember what it was).
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Then you will be prompted to spawn an instance. Select the TensorFlow 1.12 CPU image from the pulldown menu as shown below. Then click the __Spawn__ button, which generates a new *pod* in your cluster.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/e39288bb48582572.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/e39288bb48582572.png" width="60%"/></a> -->
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> **Note**: JupyterHub will take 3-5 minutes to become available. You can view the status of the container on the Kubernetes Engine -> Workloads section of the GCP Console.
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### Download a notebook
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Once JupyterHub becomes available, open a terminal.
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<!-- <a href="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/7a9738d871be5765.png" target="_blank"><img src="https://storage.googleapis.com/amy-jo/images/kf_pipelines_codelab_imgs/7a9738d871be5765.png" width="60%"/></a> -->
|
||
|
||
In the Terminal window, run:
|
||
|
||
```bash
|
||
cd work
|
||
curl -O https://raw.githubusercontent.com/kubeflow/examples/master/github_issue_summarization/pipelines/example_pipelines/pipelines-kubecon.ipynb
|
||
```
|
||
|
||
Return to the JupyterHub home screen, navigate to the `work` folder, and open the notebook you just downloaded.
|
||
|
||
### Execute the notebook
|
||
|
||
In the Setup section, find the second command cell (it starts with `import kfp`). Fill in your own values for the environment variables `WORKING_DIR`, `PROJECT_NAME`, and `GITHUB_TOKEN`, then execute the notebook one step at a time.
|
||
|
||
Follow the instructions in the notebook for the remainder of the lab.
|
||
|
||
|
||
## Clean up
|
||
|
||
### Destroy the cluster
|
||
|
||
|
||
> **Note**: Cluster deletion can take a few minutes to complete
|
||
|
||
|
||
To remove all resources created by the Click-to-Deploy launcher, navigate to
|
||
[Deployment Manager](http://console.cloud.google.com/dm/deployments) in the GCP Console and
|
||
delete the `$DEPLOYMENT_NAME` deployment.
|
||
|
||
### Remove the GitHub token
|
||
|
||
If you have no further use for it, navigate to
|
||
[https://github.com/settings/tokens](https://github.com/settings/tokens) and remove the generated token.
|
||
|
||
|
||
## Conclusion
|
||
|
||
<walkthrough-conclusion-trophy></walkthrough-conclusion-trophy>
|
||
|
||
Congratulations -- you've created ML workflows using Kubeflow Pipelines!
|
||
|