Building your own algorithm container

With Amazon SageMaker, you can package your own algorithms that can than be trained and deployed in the SageMaker environment. This notebook will guide you through an example that shows you how to build a Docker container for SageMaker and use it for training and inference.

By packaging an algorithm in a container, you can bring almost any code to the Amazon SageMaker environment, regardless of programming language, environment, framework, or dependencies.

*Note:* SageMaker now includes a pre-built scikit container. We recommend the pre-built container be used for almost all cases requiring a scikit algorithm. However, this example remains relevant as an outline for bringing in other libraries to SageMaker as your own container.

Building your own algorithm container
When should I build my own algorithm container?
Permissions
The example
The presentation
Part 1: Packaging and Uploading your Algorithm for use with Amazon SageMaker
Testing your algorithm on your local machine or on an Amazon SageMaker notebook instance
Part 2: Using your Algorithm in Amazon SageMaker
Set up the environment
Create the session
Upload the data for training
Create an estimator and fit the model
Hosting your model
Run Batch Transform Job
1. Create a Transform Job
2. View Output

or I’m impatient, just let me see the code!

When should I build my own algorithm container?

You may not need to create a container to bring your own code to Amazon SageMaker. When you are using a framework (such as Apache MXNet or TensorFlow) that has direct support in SageMaker, you can simply supply the Python code that implements your algorithm using the SDK entry points for that framework. This set of frameworks is continually expanding, so we recommend that you check the current list if your algorithm is written in a common machine learning environment.

Even if there is direct SDK support for your environment or framework, you may find it more effective to build your own container. If the code that implements your algorithm is quite complex on its own or you need special additions to the framework, building your own container may be the right choice.

If there isn’t direct SDK support for your environment, don’t worry. You’ll see in this walk-through that building your own container is quite straightforward.

Permissions

Running this notebook requires permissions in addition to the normal SageMakerFullAccess permissions. This is because we’ll creating new repositories in Amazon ECR. The easiest way to add these permissions is simply to add the managed policy AmazonEC2ContainerRegistryFullAccess to the role that you used to start your notebook instance. There’s no need to restart your notebook instance when you do this, the new permissions will be available immediately.

The example

Here, we’ll show how to package a simple Python example which showcases the decision tree algorithm from the widely used scikit-learn machine learning package. The example is purposefully fairly trivial since the point is to show the surrounding structure that you’ll want to add to your own code so you can train and host it in Amazon SageMaker.

The ideas shown here will work in any language or environment. You’ll need to choose the right tools for your environment to serve HTTP requests for inference, but good HTTP environments are available in every language these days.

In this example, we use a single image to support training and hosting. This is easy because it means that we only need to manage one image and we can set it up to do everything. Sometimes you’ll want separate images for training and hosting because they have different requirements. Just separate the parts discussed below into separate Dockerfiles and build two images. Choosing whether to have a single image or two images is really a matter of which is more convenient for you to develop and manage.

If you’re only using Amazon SageMaker for training or hosting, but not both, there is no need to build the unused functionality into your container.

The presentation

This presentation is divided into two parts: building the container and using the container.

Part 1: Packaging and Uploading your Algorithm for use with Amazon SageMaker

An overview of Docker

If you’re familiar with Docker already, you can skip ahead to the next section.

For many data scientists, Docker containers are a new concept, but they are not difficult, as you’ll see here.

Docker provides a simple way to package arbitrary code into an image that is totally self-contained. Once you have an image, you can use Docker to run a container based on that image. Running a container is just like running a program on the machine except that the container creates a fully self-contained environment for the program to run. Containers are isolated from each other and from the host environment, so the way you set up your program is the way it runs, no matter where you run it.

Docker is more powerful than environment managers like conda or virtualenv because (a) it is completely language independent and (b) it comprises your whole operating environment, including startup commands, environment variable, etc.

In some ways, a Docker container is like a virtual machine, but it is much lighter weight. For example, a program running in a container can start in less than a second and many containers can run on the same physical machine or virtual machine instance.

Docker uses a simple file called a Dockerfile to specify how the image is assembled. We’ll see an example of that below. You can build your Docker images based on Docker images built by yourself or others, which can simplify things quite a bit.

Docker has become very popular in the programming and devops communities for its flexibility and well-defined specification of the code to be run. It is the underpinning of many services built in the past few years, such as Amazon ECS.

Amazon SageMaker uses Docker to allow users to train and deploy arbitrary algorithms.

In Amazon SageMaker, Docker containers are invoked in a certain way for training and a slightly different way for hosting. The following sections outline how to build containers for the SageMaker environment.

Some helpful links:

Docker home page
Getting started with Docker
Dockerfile reference
`docker run reference <https://docs.docker.com/engine/reference/run/>`__

How Amazon SageMaker runs your Docker container

Because you can run the same image in training or hosting, Amazon SageMaker runs your container with the argument train or serve. How your container processes this argument depends on the container:

In the example here, we don’t define an ENTRYPOINT in the Dockerfile so Docker will run the command train at training time and serve at serving time. In this example, we define these as executable Python scripts, but they could be any program that we want to start in that environment.
If you specify a program as an ENTRYPOINT in the Dockerfile, that program will be run at startup and its first argument will be train or serve. The program can then look at that argument and decide what to do.
If you are building separate containers for training and hosting (or building only for one or the other), you can define a program as an ENTRYPOINT in the Dockerfile and ignore (or verify) the first argument passed in.

Running your container during training

When Amazon SageMaker runs training, your train script is run just like a regular Python program. A number of files are laid out for your use, under the /opt/ml directory:

/opt/ml
|-- input
|   |-- config
|   |   |-- hyperparameters.json
|   |   `-- resourceConfig.json
|   `-- data
|       `-- <channel_name>
|           `-- <input data>
|-- model
|   `-- <model files>
`-- output
    `-- failure

The input

/opt/ml/input/config contains information to control how your program runs. hyperparameters.json is a JSON-formatted dictionary of hyperparameter names to values. These values will always be strings, so you may need to convert them. resourceConfig.json is a JSON-formatted file that describes the network layout used for distributed training. Since scikit-learn doesn’t support distributed training, we’ll ignore it here.
/opt/ml/input/data/<channel_name>/ (for File mode) contains the input data for that channel. The channels are created based on the call to CreateTrainingJob but it’s generally important that channels match what the algorithm expects. The files for each channel will be copied from S3 to this directory, preserving the tree structure indicated by the S3 key structure.
/opt/ml/input/data/<channel_name>_<epoch_number> (for Pipe mode) is the pipe for a given epoch. Epochs start at zero and go up by one each time you read them. There is no limit to the number of epochs that you can run, but you must close each pipe before reading the next epoch.

The output

/opt/ml/model/ is the directory where you write the model that your algorithm generates. Your model can be in any format that you want. It can be a single file or a whole directory tree. SageMaker will package any files in this directory into a compressed tar archive file. This file will be available at the S3 location returned in the DescribeTrainingJob result.
/opt/ml/output is a directory where the algorithm can write a file failure that describes why the job failed. The contents of this file will be returned in the FailureReason field of the DescribeTrainingJob result. For jobs that succeed, there is no reason to write this file as it will be ignored.

Running your container during hosting

Hosting has a very different model than training because hosting is responding to inference requests that come in via HTTP. In this example, we use our recommended Python serving stack to provide robust and scalable serving of inference requests:

Request serving stack

This stack is implemented in the sample code here and you can mostly just leave it alone.

Amazon SageMaker uses two URLs in the container:

/ping will receive GET requests from the infrastructure. Your program returns 200 if the container is up and accepting requests.
/invocations is the endpoint that receives client inference POST requests. The format of the request and the response is up to the algorithm. If the client supplied ContentType and Accept headers, these will be passed in as well.

The container will have the model files in the same place they were written during training:

/opt/ml
`-- model
    `-- <model files>

The parts of the sample container

In the container directory are all the components you need to package the sample algorithm for Amazon SageMager:

.
|-- Dockerfile
|-- build_and_push.sh
`-- decision_trees
    |-- nginx.conf
    |-- predictor.py
    |-- serve
    |-- train
    `-- wsgi.py

Let’s discuss each of these in turn:

``Dockerfile`` describes how to build your Docker container image. More details below.
``build_and_push.sh`` is a script that uses the Dockerfile to build your container images and then pushes it to ECR. We’ll invoke the commands directly later in this notebook, but you can just copy and run the script for your own algorithms.
``decision_trees`` is the directory which contains the files that will be installed in the container.
``local_test`` is a directory that shows how to test your new container on any computer that can run Docker, including an Amazon SageMaker notebook instance. Using this method, you can quickly iterate using small datasets to eliminate any structural bugs before you use the container with Amazon SageMaker. We’ll walk through local testing later in this notebook.

In this simple application, we only install five files in the container. You may only need that many or, if you have many supporting routines, you may wish to install more. These five show the standard structure of our Python containers, although you are free to choose a different toolset and therefore could have a different layout. If you’re writing in a different programming language, you’ll certainly have a different layout depending on the frameworks and tools you choose.

The files that we’ll put in the container are:

``nginx.conf`` is the configuration file for the nginx front-end. Generally, you should be able to take this file as-is.
``predictor.py`` is the program that actually implements the Flask web server and the decision tree predictions for this app. You’ll want to customize the actual prediction parts to your application. Since this algorithm is simple, we do all the processing here in this file, but you may choose to have separate files for implementing your custom logic.
``serve`` is the program started when the container is started for hosting. It simply launches the gunicorn server which runs multiple instances of the Flask app defined in predictor.py. You should be able to take this file as-is.
``train`` is the program that is invoked when the container is run for training. You will modify this program to implement your training algorithm.
``wsgi.py`` is a small wrapper used to invoke the Flask app. You should be able to take this file as-is.

In summary, the two files you will probably want to change for your application are train and predictor.py.

The Dockerfile

The Dockerfile describes the image that we want to build. You can think of it as describing the complete operating system installation of the system that you want to run. A Docker container running is quite a bit lighter than a full operating system, however, because it takes advantage of Linux on the host machine for the basic operations.

For the Python science stack, we will start from a standard Ubuntu installation and run the normal tools to install the things needed by scikit-learn. Finally, we add the code that implements our specific algorithm to the container and set up the right environment to run under.

Along the way, we clean up extra space. This makes the container smaller and faster to start.

Let’s look at the Dockerfile for the example:

[ ]:

!cat container/Dockerfile

Building and registering the container

The following shell code shows how to build the container image using docker build and push the container image to ECR using docker push. This code is also available as the shell script container/build-and-push.sh, which you can run as build-and-push.sh decision_trees_sample to build the image decision_trees_sample.

This code looks for an ECR repository in the account you’re using and the current default region (if you’re using a SageMaker notebook instance, this will be the region where the notebook instance was created). If the repository doesn’t exist, the script will create it.

[ ]:

%%sh

# The name of our algorithm
algorithm_name=sagemaker-decision-trees

cd container

chmod +x decision_trees/train
chmod +x decision_trees/serve

account=$(aws sts get-caller-identity --query Account --output text)

# Get the region defined in the current configuration (default to us-west-2 if none defined)
region=$(aws configure get region)
region=${region:-us-west-2}

fullname="${account}.dkr.ecr.${region}.amazonaws.com/${algorithm_name}:latest"

# If the repository doesn't exist in ECR, create it.
aws ecr describe-repositories --repository-names "${algorithm_name}" > /dev/null 2>&1

if [ $? -ne 0 ]
then
    aws ecr create-repository --repository-name "${algorithm_name}" > /dev/null
fi

# Get the login command from ECR and execute it directly
aws ecr get-login-password --region ${region}|docker login --username AWS --password-stdin ${fullname}

# Build the docker image locally with the image name and then push it to ECR
# with the full name.

docker build -t ${algorithm_name} .
docker tag ${algorithm_name} ${fullname}

docker push ${fullname}

Testing your algorithm on your local machine or on an Amazon SageMaker notebook instance

While you’re first packaging an algorithm use with Amazon SageMaker, you probably want to test it yourself to make sure it’s working right. In the directory container/local_test, there is a framework for doing this. It includes three shell scripts for running and using the container and a directory structure that mimics the one outlined above.

The scripts are:

train_local.sh: Run this with the name of the image and it will run training on the local tree. For example, you can run $ ./train_local.sh sagemaker-decision-trees. It will generate a model under the /test_dir/model directory. You’ll want to modify the directory test_dir/input/data/... to be set up with the correct channels and data for your algorithm. Also, you’ll want to modify the file input/config/hyperparameters.json to have the hyperparameter settings that you want to test (as strings).
serve_local.sh: Run this with the name of the image once you’ve trained the model and it should serve the model. For example, you can run $ ./serve_local.sh sagemaker-decision-trees. It will run and wait for requests. Simply use the keyboard interrupt to stop it.
predict.sh: Run this with the name of a payload file and (optionally) the HTTP content type you want. The content type will default to text/csv. For example, you can run $ ./predict.sh payload.csv text/csv.

The directories as shipped are set up to test the decision trees sample algorithm presented here.

Part 2: Using your Algorithm in Amazon SageMaker

Once you have your container packaged, you can use it to train models and use the model for hosting or batch transforms. Let’s do that with the algorithm we made above.

Set up the environment

Here we specify a bucket to use and the role that will be used for working with SageMaker.

[ ]:

# S3 prefix
prefix = "DEMO-scikit-byo-iris"

# Define IAM role
import boto3
import re

import os
import numpy as np
import pandas as pd
from sagemaker import get_execution_role

role = get_execution_role()

Create the session

The session remembers our connection parameters to SageMaker. We’ll use it to perform all of our SageMaker operations.

[ ]:

import sagemaker as sage
from time import gmtime, strftime

sess = sage.Session()

Upload the data for training

When training large models with huge amounts of data, you’ll typically use big data tools, like Amazon Athena, AWS Glue, or Amazon EMR, to create your data in S3. For the purposes of this example, we’re using some the classic Iris dataset, which we have included.

We can use use the tools provided by the SageMaker Python SDK to upload the data to a default bucket.

[ ]:

WORK_DIRECTORY = "data"

data_location = sess.upload_data(WORK_DIRECTORY, key_prefix=prefix)

Create an estimator and fit the model

In order to use SageMaker to fit our algorithm, we’ll create an Estimator that defines how to use the container to train. This includes the configuration we need to invoke SageMaker training:

The container name. This is constructed as in the shell commands above.
The role. As defined above.
The instance count which is the number of machines to use for training.
The instance type which is the type of machine to use for training.
The output path determines where the model artifact will be written.
The session is the SageMaker session object that we defined above.

Then we use fit() on the estimator to train against the data that we uploaded above.

[ ]:

account = sess.boto_session.client("sts").get_caller_identity()["Account"]
region = sess.boto_session.region_name
image = "{}.dkr.ecr.{}.amazonaws.com/sagemaker-decision-trees:latest".format(account, region)

tree = sage.estimator.Estimator(
    image,
    role,
    1,
    "ml.c4.2xlarge",
    output_path="s3://{}/output".format(sess.default_bucket()),
    sagemaker_session=sess,
)

tree.fit(data_location)

Hosting your model

You can use a trained model to get real time predictions using HTTP endpoint. Follow these steps to walk you through the process.

Deploy the model

Deploying the model to SageMaker hosting just requires a deploy call on the fitted model. This call takes an instance count, instance type, and optionally serializer and deserializer functions. These are used when the resulting predictor is created on the endpoint.

[ ]:

from sagemaker.predictor import csv_serializer

predictor = tree.deploy(1, "ml.m4.xlarge", serializer=csv_serializer)

Choose some data and use it for a prediction

In order to do some predictions, we’ll extract some of the data we used for training and do predictions against it. This is, of course, bad statistical practice, but a good way to see how the mechanism works.

[ ]:

shape = pd.read_csv("data/iris.csv", header=None)
shape.sample(3)

[ ]:

# drop the label column in the training set
shape.drop(shape.columns[[0]], axis=1, inplace=True)
shape.sample(3)

[ ]:

import itertools

a = [50 * i for i in range(3)]
b = [40 + i for i in range(10)]
indices = [i + j for i, j in itertools.product(a, b)]

test_data = shape.iloc[indices[:-1]]

Prediction is as easy as calling predict with the predictor we got back from deploy and the data we want to do predictions with. The serializers take care of doing the data conversions for us.

[ ]:

print(predictor.predict(test_data.values).decode("utf-8"))

Optional cleanup

When you’re done with the endpoint, you’ll want to clean it up.

[ ]:

sess.delete_endpoint(predictor.endpoint)

Run Batch Transform Job

You can use a trained model to get inference on large data sets by using Amazon SageMaker Batch Transform. A batch transform job takes your input data S3 location and outputs the predictions to the specified S3 output folder. Similar to hosting, you can extract inferences for training data to test batch transform.

Create a Transform Job

We’ll create an Transformer that defines how to use the container to get inference results on a data set. This includes the configuration we need to invoke SageMaker batch transform:

The instance count which is the number of machines to use to extract inferences
The instance type which is the type of machine to use to extract inferences
The output path determines where the inference results will be written

[ ]:

transform_output_folder = "batch-transform-output"
output_path = "s3://{}/{}".format(sess.default_bucket(), transform_output_folder)

transformer = tree.transformer(
    instance_count=1,
    instance_type="ml.m4.xlarge",
    output_path=output_path,
    assemble_with="Line",
    accept="text/csv",
)

We use tranform() on the transfomer to get inference results against the data that we uploaded. You can use these options when invoking the transformer.

The data_location which is the location of input data
The content_type which is the content type set when making HTTP request to container to get prediction
The split_type which is the delimiter used for splitting input data
The input_filter which indicates the first column (ID) of the input will be dropped before making HTTP request to container

[ ]:

transformer.transform(
    data_location, content_type="text/csv", split_type="Line", input_filter="$[1:]"
)
transformer.wait()

For more information on the configuration options, see CreateTransformJob API

View Output

Lets read results of above transform job from s3 files and print output

[ ]:

s3_client = sess.boto_session.client("s3")
s3_client.download_file(
    sess.default_bucket(), "{}/iris.csv.out".format(transform_output_folder), "/tmp/iris.csv.out"
)
with open("/tmp/iris.csv.out") as f:
    results = f.readlines()
print("Transform results: \n{}".format("".join(results)))