Using Chainer with the SageMaker Python SDK

With Chainer Estimators, you can train and host Chainer models on Amazon SageMaker.

For information about supported versions of Chainer, see the Chainer README.

For general information about using the SageMaker Python SDK, see Using the SageMaker Python SDK.

Train a Model with Chainer

To train a Chainer model by using the SageMaker Python SDK:

  1. Prepare a training script
  2. Create a sagemaker.chainer.Chainer Estimator
  3. Call the estimator’s fit method

Prepare a Chainer training script

Your Chainer training script must be a Python 2.7 or 3.5 compatible source file.

The training script is similar to a training script you might run outside of SageMaker, but you can access useful properties about the training environment through various environment variables, such as the following:

  • SM_MODEL_DIR: A string representing the path to the directory to write model artifacts to. These artifacts are uploaded to S3 for model hosting.
  • SM_NUM_GPUS: An integer representing the number of GPUs available to the host.
  • SM_OUTPUT_DATA_DIR: A string representing the filesystem path to write output artifacts to. Output artifacts may include checkpoints, graphs, and other files to save, not including model artifacts. These artifacts are compressed and uploaded to S3 to the same S3 prefix as the model artifacts.

Suppose you use two input channels, named ‘train’ and ‘test’, in the call to the Chainer estimator’s fit() method. The following environment variables are set, following the format “SM_CHANNEL_[channel_name]”:

  • SM_CHANNEL_TRAIN: A string representing the path to the directory containing data in the ‘train’ channel
  • SM_CHANNEL_TEST: Same as above, but for the ‘test’ channel.

A typical training script loads data from the input channels, configures training with hyperparameters, trains a model, and saves a model to model_dir so that it can be hosted later. Hyperparameters are passed to your script as arguments and can be retrieved with an argparse.ArgumentParser instance. For example, a training script might start with the following:

import argparse
import os

if __name__ =='__main__':

    parser = argparse.ArgumentParser()

    # hyperparameters sent by the client are passed as command-line arguments to the script.
    parser.add_argument('--epochs', type=int, default=50)
    parser.add_argument('--batch-size', type=int, default=64)
    parser.add_argument('--learning-rate', type=float, default=0.05)

    # Data, model, and output directories
    parser.add_argument('--output-data-dir', type=str, default=os.environ['SM_OUTPUT_DATA_DIR'])
    parser.add_argument('--model-dir', type=str, default=os.environ['SM_MODEL_DIR'])
    parser.add_argument('--train', type=str, default=os.environ['SM_CHANNEL_TRAIN'])
    parser.add_argument('--test', type=str, default=os.environ['SM_CHANNEL_TEST'])

    args, _ = parser.parse_known_args()

    # ... load from args.train and args.test, train a model, write model to args.model_dir.

Because the SageMaker imports your training script, you should put your training code in a main guard (if __name__=='__main__':) if you are using the same script to host your model, so that SageMaker does not inadvertently run your training code at the wrong point in execution.

For more on training environment variables, please visit https://github.com/aws/sagemaker-containers.

Save the Model

In order to save your trained Chainer model for deployment on SageMaker, your training script should save your model to a certain filesystem path called model_dir. This value is accessible through the environment variable SM_MODEL_DIR. The following code demonstrates how to save a trained Chainer model named model as model.npz at the end of training:

import chainer
import argparse
import os

if __name__=='__main__':
    # default to the value in environment variable `SM_MODEL_DIR`. Using args makes the script more portable.
    parser.add_argument('--model-dir', type=str, default=os.environ['SM_MODEL_DIR'])
    args, _ = parser.parse_known_args()

    # ... train `model`, then save it to `model_dir` as file 'model.npz'
    chainer.serializers.save_npz(os.path.join(args.model_dir, 'model.npz'), model)

After your training job is complete, SageMaker will compress and upload the serialized model to S3, and your model data will available in the s3 output_path you specified when you created the Chainer Estimator.

Using third-party libraries

When running your training script on SageMaker, it will have access to some pre-installed third-party libraries including chainer, numpy, and cupy. For more information on the runtime environment, including specific package versions, see SageMaker Chainer Docker containers.

If there are other packages you want to use with your script, you can include a requirements.txt file in the same directory as your training script to install other dependencies at runtime. Both requirements.txt and your training script should be put in the same folder. You must specify this folder in source_dir argument when creating a Chainer estimator. A requirements.txt file is a text file that contains a list of items that are installed by using pip install. You can also specify the version of an item to install. For information about the format of a requirements.txt file, see Requirements Files in the pip documentation.

Create an Estimator

You run Chainer training scripts on SageMaker by creating Chainer Estimators. SageMaker training of your script is invoked when you call fit on a Chainer Estimator. The following code sample shows how you train a custom Chainer script “chainer-train.py”, passing in three hyperparameters (‘epochs’, ‘batch-size’, and ‘learning-rate’), and using two input channel directories (‘train’ and ‘test’).

chainer_estimator = Chainer('chainer-train.py',
                            train_instance_type='ml.p3.2xlarge',
                            train_instance_count=1,
                            framework_version='5.0.0',
                            hyperparameters = {'epochs': 20, 'batch-size': 64, 'learning-rate': 0.1})
chainer_estimator.fit({'train': 's3://my-data-bucket/path/to/my/training/data',
                       'test': 's3://my-data-bucket/path/to/my/test/data'})

Call the fit Method

You start your training script by calling fit on a Chainer Estimator. fit takes both required and optional arguments.

fit Required arguments

  • inputs: This can take one of the following forms: A string s3 URI, for example s3://my-bucket/my-training-data. In this case, the s3 objects rooted at the my-training-data prefix will be available in the default train channel. A dict from string channel names to s3 URIs. In this case, the objects rooted at each s3 prefix will available as files in each channel directory.

For example:

{'train':'s3://my-bucket/my-training-data',
 'eval':'s3://my-bucket/my-evaluation-data'}

fit Optional arguments

  • wait: Defaults to True, whether to block and wait for the training script to complete before returning.
  • logs: Defaults to True, whether to show logs produced by training job in the Python session. Only meaningful when wait is True.

Distributed Training

Chainer allows you to train a model on multiple nodes using ChainerMN, which distributes training with MPI.

In order to run distributed Chainer training on SageMaker, your training script should use a chainermn Communicator object to coordinate training between multiple hosts.

SageMaker runs your script with mpirun if train_instance_count is greater than two. The following are optional arguments modify how MPI runs your distributed training script.

  • use_mpi Boolean that overrides whether to run your training script with MPI.
  • num_processes Integer that determines how many total processes to run with MPI. By default, this is equal to process_slots_per_host times the number of nodes.
  • process_slots_per_host Integer that determines how many processes can be run on each host. By default, this is equal to one process per host on CPU instances, or one process per GPU on GPU instances.
  • additional_mpi_options String of additional options to pass to the mpirun command.

Deploy Chainer models

After an Chainer Estimator has been fit, you can host the newly created model in SageMaker.

After calling fit, you can call deploy on a Chainer Estimator to create a SageMaker Endpoint. The Endpoint runs a SageMaker-provided Chainer model server and hosts the model produced by your training script, which was run when you called fit. This was the model you saved to model_dir.

deploy returns a Predictor object, which you can use to do inference on the Endpoint hosting your Chainer model. Each Predictor provides a predict method which can do inference with numpy arrays or Python lists. Inference arrays or lists are serialized and sent to the Chainer model server by an InvokeEndpoint SageMaker operation.

predict returns the result of inference against your model. By default, the inference result a NumPy array.

# Train my estimator
chainer_estimator = Chainer(entry_point='train_and_deploy.py',
                            train_instance_type='ml.p3.2xlarge',
                            train_instance_count=1,
                            framework_version='5.0.0')
chainer_estimator.fit('s3://my_bucket/my_training_data/')

# Deploy my estimator to a SageMaker Endpoint and get a Predictor
predictor = chainer_estimator.deploy(instance_type='ml.m4.xlarge',
                                     initial_instance_count=1)

# `data` is a NumPy array or a Python list.
# `response` is a NumPy array.
response = predictor.predict(data)

You use the SageMaker Chainer model server to host your Chainer model when you call deploy on an Chainer Estimator. The model server runs inside a SageMaker Endpoint, which your call to deploy creates. You can access the name of the Endpoint by the name property on the returned Predictor.

The SageMaker Chainer Model Server

The Chainer Endpoint you create with deploy runs a SageMaker Chainer model server. The model server loads the model that was saved by your training script and performs inference on the model in response to SageMaker InvokeEndpoint API calls.

You can configure two components of the SageMaker Chainer model server: Model loading and model serving. Model loading is the process of deserializing your saved model back into an Chainer model. Serving is the process of translating InvokeEndpoint requests to inference calls on the loaded model.

You configure the Chainer model server by defining functions in the Python source file you passed to the Chainer constructor.

Load a Model

Before a model can be served, it must be loaded. The SageMaker Chainer model server loads your model by invoking a model_fn function that you must provide in your script. The model_fn should have the following signature:

def model_fn(model_dir)

SageMaker will inject the directory where your model files and sub-directories, saved by save, have been mounted. Your model function should return a model object that can be used for model serving.

SageMaker provides automated serving functions that work with Gluon API net objects and Module API Module objects. If you return either of these types of objects, then you will be able to use the default serving request handling functions.

The following code-snippet shows an example model_fn implementation. This loads returns a Chainer Classifier from a multi-layer perceptron class MLP that extends chainer.Chain. It loads the model parameters from a model.npz file in the SageMaker model directory model_dir.

import chainer
import os

def model_fn(model_dir):
    chainer.config.train = False
    model = chainer.links.Classifier(MLP(1000, 10))
    chainer.serializers.load_npz(os.path.join(model_dir, 'model.npz'), model)
    return model.predictor

Serve a Model

After the SageMaker model server has loaded your model by calling model_fn, SageMaker will serve your model. Model serving is the process of responding to inference requests, received by SageMaker InvokeEndpoint API calls. The SageMaker Chainer model server breaks request handling into three steps:

  • input processing,
  • prediction, and
  • output processing.

In a similar way to model loading, you configure these steps by defining functions in your Python source file.

Each step involves invoking a python function, with information about the request and the return-value from the previous function in the chain. Inside the SageMaker Chainer model server, the process looks like:

# Deserialize the Invoke request body into an object we can perform prediction on
input_object = input_fn(request_body, request_content_type)

# Perform prediction on the deserialized object, with the loaded model
prediction = predict_fn(input_object, model)

# Serialize the prediction result into the desired response content type
output = output_fn(prediction, response_content_type)

The above code-sample shows the three function definitions:

  • input_fn: Takes request data and deserializes the data into an object for prediction.
  • predict_fn: Takes the deserialized request object and performs inference against the loaded model.
  • output_fn: Takes the result of prediction and serializes this according to the response content type.

The SageMaker Chainer model server provides default implementations of these functions. You can provide your own implementations for these functions in your hosting script. If you omit any definition then the SageMaker Chainer model server will use its default implementation for that function.

The RealTimePredictor used by Chainer in the SageMaker Python SDK serializes NumPy arrays to the NPY format by default, with Content-Type application/x-npy. The SageMaker Chainer model server can deserialize NPY-formatted data (along with JSON and CSV data).

If you rely solely on the SageMaker Chainer model server defaults, you get the following functionality:

  • Prediction on models that implement the __call__ method
  • Serialization and deserialization of NumPy arrays.

The default input_fn and output_fn are meant to make it easy to predict on NumPy arrays. If your model expects a NumPy array and returns a NumPy array, then these functions do not have to be overridden when sending NPY-formatted data.

In the following sections we describe the default implementations of input_fn, predict_fn, and output_fn. We describe the input arguments and expected return types of each, so you can define your own implementations.

Process Input

When an InvokeEndpoint operation is made against an Endpoint running a SageMaker Chainer model server, the model server receives two pieces of information:

  • The request Content-Type, for example “application/x-npy”
  • The request data body, a byte array

The SageMaker Chainer model server will invoke an “input_fn” function in your hosting script, passing in this information. If you define an input_fn function definition, it should return an object that can be passed to predict_fn and have the following signature:

def input_fn(request_body, request_content_type)

Where request_body is a byte buffer and request_content_type is a Python string

The SageMaker Chainer model server provides a default implementation of input_fn. This function deserializes JSON, CSV, or NPY encoded data into a NumPy array.

Default NPY deserialization requires request_body to follow the NPY format. For Chainer, the Python SDK defaults to sending prediction requests with this format.

Default json deserialization requires request_body contain a single json list. Sending multiple json objects within the same request_body is not supported. The list must have a dimensionality compatible with the model loaded in model_fn. The list’s shape must be identical to the model’s input shape, for all dimensions after the first (which first dimension is the batch size).

Default csv deserialization requires request_body contain one or more lines of CSV numerical data. The data is loaded into a two-dimensional array, where each line break defines the boundaries of the first dimension.

The example below shows a custom input_fn for preparing pickled NumPy arrays.

import numpy as np

def input_fn(request_body, request_content_type):
    """An input_fn that loads a pickled numpy array"""
    if request_content_type == "application/python-pickle":
        array = np.load(StringIO(request_body))
        return array
    else:
        # Handle other content-types here or raise an Exception
        # if the content type is not supported.
        pass

Get Predictions

After the inference request has been deserialized by input_fn, the SageMaker Chainer model server invokes predict_fn on the return value of input_fn.

As with input_fn, you can define your own predict_fn or use the SageMaker Chainer model server default.

The predict_fn function has the following signature:

def predict_fn(input_object, model)

Where input_object is the object returned from input_fn and model is the model loaded by model_fn.

The default implementation of predict_fn invokes the loaded model’s __call__ function on input_object, and returns the resulting value. The return-type should be a NumPy array to be compatible with the default output_fn.

The example below shows an overridden predict_fn. This model accepts a Python list and returns a tuple of bounding boxes, labels, and scores from the model in a NumPy array. This predict_fn can rely on the default input_fn and output_fn because input_data is a NumPy array, and the return value of this function is a NumPy array.

import chainer
import numpy as np

def predict_fn(input_data, model):
    with chainer.using_config('train', False), chainer.no_backprop_mode():
        bboxes, labels, scores = model.predict([input_data])
        bbox, label, score = bboxes[0], labels[0], scores[0]
        return np.array([bbox.tolist(), label, score])

If you implement your own prediction function, you should take care to ensure that:

  • The first argument is expected to be the return value from input_fn. If you use the default input_fn, this will be a NumPy array.
  • The second argument is the loaded model.
  • The return value should be of the correct type to be passed as the first argument to output_fn. If you use the default output_fn, this should be a NumPy array.
Process Output

After invoking predict_fn, the model server invokes output_fn, passing in the return-value from predict_fn and the InvokeEndpoint requested response content-type.

The output_fn has the following signature:

def output_fn(prediction, content_type)

Where prediction is the result of invoking predict_fn and content_type is the InvokeEndpoint requested response content-type. The function should return a byte array of data serialized to content_type.

The default implementation expects prediction to be an NumPy and can serialize the result to JSON, CSV, or NPY. It accepts response content types of “application/json”, “text/csv”, and “application/x-npy”.

Working with existing model data and training jobs

Attach to Existing Training Jobs

You can attach an Chainer Estimator to an existing training job using the attach method.

my_training_job_name = "MyAwesomeChainerTrainingJob"
chainer_estimator = Chainer.attach(my_training_job_name)

After attaching, if the training job is in a Complete status, it can be deployed to create a SageMaker Endpoint and return a Predictor. If the training job is in progress, attach will block and display log messages from the training job, until the training job completes.

The attach method accepts the following arguments:

  • training_job_name (str): The name of the training job to attach to.
  • sagemaker_session (sagemaker.Session or None): The Session used to interact with SageMaker

Deploy Endpoints from Model Data

As well as attaching to existing training jobs, you can deploy models directly from model data in S3. The following code sample shows how to do this, using the ChainerModel class.

chainer_model = ChainerModel(model_data="s3://bucket/model.tar.gz", role="SageMakerRole",
    entry_point="transform_script.py")

predictor = chainer_model.deploy(instance_type="ml.c4.xlarge", initial_instance_count=1)

The ChainerModel constructor takes the following arguments:

  • model_data (str): An S3 location of a SageMaker model data .tar.gz file
  • image (str): A Docker image URI
  • role (str): An IAM role name or Arn for SageMaker to access AWS resources on your behalf.
  • predictor_cls (callable[string,sagemaker.Session]): A function to call to create a predictor. If not None, deploy will return the result of invoking this function on the created endpoint name
  • env (dict[string,string]): Environment variables to run with image when hosted in SageMaker.
  • name (str): The model name. If None, a default model name will be selected on each deploy.
  • entry_point (str): Path (absolute or relative) to the Python file which should be executed as the entry point to model hosting.
  • source_dir (str): Optional. Path (absolute or relative) to a directory with any other training source code dependencies including tne entry point file. Structure within this directory will be preserved when training on SageMaker.
  • enable_cloudwatch_metrics (boolean): Optional. If true, training and hosting containers will generate Cloudwatch metrics under the AWS/SageMakerContainer namespace.
  • container_log_level (int): Log level to use within the container. Valid values are defined in the Python logging module.
  • code_location (str): Optional. Name of the S3 bucket where your custom code will be uploaded to. If not specified, will use the SageMaker default bucket created by sagemaker.Session.
  • sagemaker_session (sagemaker.Session): The SageMaker Session object, used for SageMaker interaction”“”

Your model data must be a .tar.gz file in S3. SageMaker Training Job model data is saved to .tar.gz files in S3, however if you have local data you want to deploy, you can prepare the data yourself.

Assuming you have a local directory containg your model data named “my_model” you can tar and gzip compress the file and upload to S3 using the following commands:

tar -czf model.tar.gz my_model
aws s3 cp model.tar.gz s3://my-bucket/my-path/model.tar.gz

This uploads the contents of my_model to a gzip compressed tar file to S3 in the bucket “my-bucket”, with the key “my-path/model.tar.gz”.

To run this command, you’ll need the aws cli tool installed. Please refer to our FAQ for more information on installing this.

Examples

Amazon provides several example Jupyter notebooks that demonstrate end-to-end training on Amazon SageMaker using Chainer. Please refer to:

https://github.com/awslabs/amazon-sagemaker-examples/tree/master/sagemaker-python-sdk

These are also available in SageMaker Notebook Instance hosted Jupyter notebooks under the “sample notebooks” folder.

sagemaker.chainer.Chainer Class

The Chainer constructor takes both required and optional arguments.

Required arguments

The following are required arguments to the Chainer constructor. When you create a Chainer object, you must include these in the constructor, either positionally or as keyword arguments.

  • entry_point Path (absolute or relative) to the Python file which should be executed as the entry point to training.
  • role An AWS IAM role (either name or full ARN). The Amazon SageMaker training jobs and APIs that create Amazon SageMaker endpoints use this role to access training data and model artifacts. After the endpoint is created, the inference code might use the IAM role, if accessing AWS resource.
  • train_instance_count Number of Amazon EC2 instances to use for training.
  • train_instance_type Type of EC2 instance to use for training, for example, ‘ml.m4.xlarge’.

Optional arguments

The following are optional arguments. When you create a Chainer object, you can specify these as keyword arguments.

  • source_dir Path (absolute or relative) to a directory with any other training source code dependencies including the entry point file. Structure within this directory will be preserved when training on SageMaker.

  • dependencies (list[str]) A list of paths to directories (absolute or relative) with

    any additional libraries that will be exported to the container (default: []). The library folders will be copied to SageMaker in the same folder where the entrypoint is copied. If the `source_dir` points to S3, code will be uploaded and the S3 location will be used instead. Example:

    The following call >>> Chainer(entry_point=’train.py’, dependencies=[‘my/libs/common’, ‘virtual-env’]) results in the following inside the container:

    >>> $ ls
    
    >>> opt/ml/code
    >>>     ├── train.py
    >>>     ├── common
    >>>     └── virtual-env
    
  • hyperparameters Hyperparameters that will be used for training. Will be made accessible as a dict[str, str] to the training code on SageMaker. For convenience, accepts other types besides str, but str() will be called on keys and values to convert them before training.

  • py_version Python version you want to use for executing your model training code.

  • train_volume_size Size in GB of the EBS volume to use for storing input data during training. Must be large enough to store training data if input_mode=’File’ is used (which is the default).

  • train_max_run Timeout in seconds for training, after which Amazon SageMaker terminates the job regardless of its current status.

  • input_mode The input mode that the algorithm supports. Valid modes: ‘File’ - Amazon SageMaker copies the training dataset from the s3 location to a directory in the Docker container. ‘Pipe’ - Amazon SageMaker streams data directly from s3 to the container via a Unix named pipe.

  • output_path s3 location where you want the training result (model artifacts and optional output files) saved. If not specified, results are stored to a default bucket. If the bucket with the specific name does not exist, the estimator creates the bucket during the fit() method execution.

  • output_kms_key Optional KMS key ID to optionally encrypt training output with.

  • job_name Name to assign for the training job that the fit() method launches. If not specified, the estimator generates a default job name, based on the training image name and current timestamp

  • image_name An alternative docker image to use for training and serving. If specified, the estimator will use this image for training and hosting, instead of selecting the appropriate SageMaker official image based on framework_version and py_version. Refer to: SageMaker Chainer Docker Containers for details on what the Official images support and where to find the source code to build your custom image.

SageMaker Chainer Docker containers

You can visit the SageMaker Chainer containers repository here: https://github.com/aws/sagemaker-chainer-container

For information about SageMaker Chainer Docker containers and their dependencies, see SageMaker Chainer Docker containers.