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Training and saving models with CML on a self-hosted AWS EC2 runner (part 1)

We can use CML to automatically retrain models whenever data, model code, or parameters change. In this guide we show how to create a pipeline that provisions an AWS EC2 instance to retrain a model and save the output on a regular basis. This way we can prevent drift by ensuring that our model always uses the latest input data.

  • Rob de Wit
  • April 26, 20228 min read
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When you first develop a machine learning model, you will probably do so on your local machine. You can easily change algorithms, parameters, and input data right in your text editor, notebook, or terminal. Imagine you have a long-running model for which you want to detect possible drift, however. In that case it would be beneficial to automatically retrain your model on a regular basis.

In this guide, we will show how you can use CML (Continuous Machine Learning) to do just that. CML is an open-source library for implementing continuous integration and delivery (CI/CD) in machine learning projects. This way we can define a pipeline to train a model and keep track of various versions. Although we could do so directly in our CI/CD pipeline (e.g. GitHub Actions Workflows), the runners used for this generally don’t have a lot of processing power. Therefore it makes more sense to provision a dedicated runner that is tailored to our computing needs.

At the end of this guide we will have set up a CML workflow that does the following on a daily basis:

  1. Provision an Amazon Web Services (AWS) EC2 instance
  2. Train the model
  3. Save the model and its metrics to a GitHub repository
  4. Create a pull request with the new outputs
  5. Terminate the AWS EC2 instance

In a follow-up post we will expand upon this by using DVC to designate a remote storage for our resulting models. But let's focus on CML first!

All files needed for this guide can be found in this repository.

This guide can be followed on its own, but also as an extension to this example in the docs.

We wil be using GitHub for our CI/CD and AWS for our computing resources. With slight modifications, however, you can use GitLab CI/CD, Google Cloud or Microsoft Azure.

Prerequisites

Before we begin, make sure you have the following things set up:

  1. You have created an AWS account (free tier suffices)
  2. You have created a PERSONAL_ACCESS_TOKEN on GitHub with the repo scope
  3. You have created an AWS_ACCESS_KEY_ID and AWS_SECRET_ACCESS_KEY on AWS
  4. You have added the PERSONAL_ACCES_TOKEN, AWS_ACCESS_KEY_ID, and AWS_SECRET_ACCESS_KEY as GitHub secrets

It also helps to clone the template repository for this tutorial.

Training a model and saving it

To kick off, we will adapt train.py from the CML getting started guide. Here we create a simple RandomForestClassifier() based on some generated data. We then use the model to make some predictions and plot those predictions in a confusion matrix.

While running the script the model is kept in memory, meaning it is discarded as soon as the script finishes. In order to save the model for later, we need to dump it as a binary file. We do so with joblib.dump(). Later we can read the model using joblib.load() when we need to.

You can also use pickle.dump() if you prefer.

The outputs of train.py are:

  • metrics.txt: a file containing metrics on model performance (in this case accuracy)
  • confusion_matrix.png: a plot showing the classification results of our model
  • random_forest.joblib: the binary output of the trained model

All of these files are saved to the model directory.

import json
import os

import joblib
import matplotlib.pyplot as plt
import numpy as np
from sklearn.ensemble import RandomForestClassifier
from sklearn.metrics import plot_confusion_matrix

# Read in data
X_train = np.genfromtxt("data/train_features.csv")
y_train = np.genfromtxt("data/train_labels.csv")
X_test = np.genfromtxt("data/test_features.csv")
y_test = np.genfromtxt("data/test_labels.csv")

# Fit a model
depth = 5
clf = RandomForestClassifier(max_depth=depth)
clf.fit(X_train, y_train)

# Calculate accuracy
acc = clf.score(X_test, y_test)
print(acc)

# Create model folder if it does not yet exist
if not os.path.exists("model"):
    os.makedirs("model")

# Write metrics to file
with open("model/metrics.txt", "w+") as outfile:
    outfile.write("Accuracy: " + str(acc) + "\n")

# Plot confusion matrix
disp = plot_confusion_matrix(clf, X_test, y_test, normalize="true", cmap=plt.cm.Blues)
plt.savefig("model/confusion_matrix.png")

# Save the model
joblib.dump(clf, "model/random_forest.joblib")

Train the model on a daily basis

Now that we have a script to train our model and save it as a file, let’s set up our CI/CD to provision a runner and run the script. We define our workflow in cml.yaml and save it in the .github/workflows directory. This way GitHub will automatically run the workflow whenever it is triggered. In this case the triggers are on (manual) request as well as daily (automatic) schedule.

The name of the workflow doesn’t matter, as long as it’s a .yaml and located in the .github/workflows directory. You can have multiple workflows in there as well. You can learn more in the documentation here.

name: CML
on: # Here we use two triggers: manually and daily at 08:00
  workflow_dispatch:
  schedule:
    - cron: '0 8 * * *'
jobs:
  deploy-runner:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - uses: iterative/setup-cml@v1
      - name: Deploy runner on EC2
        env:
          REPO_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
        run: |
          cml runner \
              --cloud=aws \
              --cloud-region=eu-west \
              --cloud-type=t2.micro \
              --labels=cml-runner \
              --single
  train-model:
    needs: deploy-runner
    runs-on: [self-hosted, cml-runner]
    timeout-minutes: 120 # 2h
    steps:
      - uses: actions/checkout@v2
      - uses: actions/setup-python@v2
        with:
          python-version: '3.x'
      - uses: actions/setup-node@v3
        with:
          node-version: '16'
      - uses: iterative/setup-cml@v1
      - name: Train model
        env:
          REPO_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
        run: |
          cml ci
          pip install -r requirements.txt
          python get_data.py
          python train.py

In this example we are using a t2.micro AWS EC2 instance. At the time of writing this is included in the AWS free tier. Make sure that you qualify for this free usage to prevent unexpected spending. When you specify a bulkier cloud-type, your expenses will rise.

The workflow we defined first provisions a runner on AWS, and then uses that runner to train the model. After completing the training job, CML automatically terminates the runner to prevent you from incurring further costs. Once the runner is terminated, however, the model is lost along with it. Let's see how we can save our model in the next step!

Export the model to our Git repository

CML allows us to export the model from our runner to our Git repository. Let's extend the training stage of our workflow by pushing random_forest.joblib to a new experiment branch and creating a pull request.

cml pr is the command that specifies which files should be included in the pull request. The commands after that are used to generate a report in the pull request that displays the confusion matrix and calculated metrics.

train-model:
  needs: deploy-runner
  runs-on: [self-hosted, cml-runner]
  timeout-minutes: 120 # 2h
  steps:
    - uses: actions/checkout@v2
    - uses: actions/setup-python@v2
      with:
        python-version: '3.x'
    - uses: actions/setup-node@v3
      with:
        node-version: '16'
    - uses: iterative/setup-cml@v1
    - name: Train model
      env:
        REPO_TOKEN: ${{ secrets.PERSONAL_ACCESS_TOKEN }}
      run: |
        cml ci
        pip install -r requirements.txt
        python get_data.py
        python train.py

        # Create pull request
        cml pr model/random_forest.joblib

        # Create CML report
        cat model/metrics.txt > report.md
        cml publish model/confusion_matrix.png --md >> report.md
        cml send-comment --pr --update report.md

Et voilà! We are now running a daily model training on an AWS EC2 instance and saving the resulting model to our GitHub repository.

There is still some room for improvement, though. This approach works well when our resulting model is small (less than 100MB), but we wouldn't want to store large models in our Git repository. In a follow-up post we will describe how we can use DVC, another Iterative open-source tool, for storage when we're dealing with larger files.

Conclusions

There are many cases in which it's a good idea to retrain models periodically. For example, you could be using the latest data available to you in order to prevent model drift. CML allows you to automate this process.

In this guide, we explored how to set up CML for a daily training job using a self-hosted runner. We automatically provisioned this runner on AWS, exported the resulting files to our Git repository, and terminated the runner to prevent racking up our AWS bill.

In a follow-up post we will explore how to use DVC when the resulting model is too large to store directly in our Git repository.

Another great extension of our CI/CD would be a deploy step to bring the latest version of our model into production. This step might be conditional on the performance of the model; we could decide to only start using it in production if it performs better than previous iterations. All of this warrants a guide of its own, however, so look out for that in the future! 😉