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master:

sagify

Sagify

A command-line utility to train and deploy Machine Learning/Deep Learning models on AWS SageMaker in a few simple steps!

For detailed reference to Sagify commands please go to: Read the Docs

Installation

Prerequisites

sagify requires the following:

Python (3.5, 3.6, 3.7, 3.8)
Docker installed and running
Configured awscli

Install sagify

At the command line:

pip install sagify

Getting started

Step 1: Clone Machine Learning demo repository

You're going to clone and train a Machine Learning codebase to train a classifer for the Iris data set.

Clone repository:

git clone https://github.com/Kenza-AI/sagify-demo.git

Optionally, if you want to use Python 2.7 replace the value of REQUIRED_PYTHON and PYTHON_INTERPRETER in test_environment.py and Makefile, respectively, to python2.

Create environment:

make create_environment

Don't forget to activate the virtualenv after the creation of environment by executing workon sagify-demo.

Install dependencies:

make requirements

Step 2: Initialize sagify

sagify init

Type in sagify-demo for SageMaker app name, N in question Are you starting a new project?, src for question Type in the directory where your code lives and make sure to choose your preferred Python version, AWS profile and region. Finally, type requirements.txt in question Type in the path to requirements.txt.

A module called sagify is created under the directory you provided. The structure is:

sagify_base/
    local_test/
        test_dir/
            input/
                config/
                    hyperparameters.json
                data/
                    training/
            model/
            output/
        deploy_local.sh
        train_local.sh
    prediction/
        __init__.py
        nginx.conf
        predict.py
        prediction.py
        predictor.py
        serve
        wsgi.py
    training/
        __init__.py
        train
        training.py
    __init__.py
    build.sh
    Dockerfile
    executor.sh
    push.sh

Step 3: Integrate sagify

As a Data Scientist, you only need to conduct a few actions. Sagify takes care of the rest:

Copy a subset of training data under sagify_base/local_test/test_dir/input/data/training/ to test that training works locally
Implement train(...) function in sagify_base/training/training.py
Implement predict(...) function in sagify_base/prediction/prediction.py
Optionally, specify hyperparameters in sagify_base/local_test/test_dir/input/config/hyperparameters.json

Hence,

Copy iris.data files from data to sagify_base/local_test/test_dir/input/data/training/

Replace the TODOs in the train(...) function in sagify_base/training/training.py file with:

    input_file_path = os.path.join(input_data_path, 'iris.data')
    clf, accuracy = training_logic(input_file_path=input_file_path)

    output_model_file_path = os.path.join(model_save_path, 'model.pkl')
    joblib.dump(clf, output_model_file_path)

    accuracy_report_file_path = os.path.join(model_save_path, 'report.txt')
    with open(accuracy_report_file_path, 'w') as _out:
        _out.write(str(accuracy))

and at the top of the file, add:

import os

from sklearn.externals import joblib

from iris_training import train as training_logic

Replace the body of predict(...) function in sagify_base/prediction/prediction.py with:

model_input = json_input['features']
prediction = ModelService.predict(model_input)

return {
    "prediction": prediction.item()
}

and replace the body of get_model() function in ModelService class in the same file with:

if cls.model is None:
    from sklearn.externals import joblib
    cls.model = joblib.load(os.path.join(_MODEL_PATH, 'model.pkl'))
return cls.model

Step 4: Build Docker image

It's time to build the Docker image that will contain the Machine Learning codebase:

sagify build

If you run docker images | grep sagify-demo in your terminal, you'll see the created Sagify-Demo image.

Step 5: Train model

Time to train the model for the Iris data set in the newly built Docker image:

sagify local train

Model file model.pkl and report file report.txt are now under sagify_base/local_test/test_dir/model/

Step 6: Deploy model

Finally, serve the model as a REST Service:

sagify local deploy

Run the following curl command on your terminal to verify that the REST Service works:

curl -X POST \
http://localhost:8080/invocations \
-H 'Cache-Control: no-cache' \
-H 'Content-Type: application/json' \
-H 'Postman-Token: 41189b9a-40e2-abcf-b981-c31ae692072e' \
-d '{
    "features":[[0.34, 0.45, 0.45, 0.3]]
}'

It will be slow in the first couple of calls as it loads the model in a lazy manner.

Voila! That's a proof that this Machine Learning model is going to be trained and deployed on AWS SageMaker successfully. Now, go to the Usage section in Sagify Docs to see how to train and deploy this Machine Learning model to AWS SageMaker!

Hyperparameter Optimization

Given that you have configured your AWS Account as described in the previous section, you're now ready to perform Bayesian Hyperparameter Optimization on AWS SageMaker! The process is similar to training step.

Step 1: Define Hyperparameter Configuration File

Define the Hyperparameter Configuration File. More specifically, you need to specify in a local JSON file the ranges for the hyperparameters, the name of the objective metric and its type (i.e. Maximize or Minimize). For example:

{
    "ParameterRanges": {
        "CategoricalParameterRanges": [
            {
                "Name": "kernel",
                "Values": ["linear", "rbf"]
            }
        ],
        "ContinuousParameterRanges": [
        {
          "MinValue": 0.001,
          "MaxValue": 10,
          "Name": "gamma"
        }
        ],
        "IntegerParameterRanges": [
            {
                "Name": "C",
                "MinValue": 1,
                "MaxValue": 10
            }
        ]
    },
    "ObjectiveMetric": {
        "Name": "Precision",
        "Type": "Maximize"
    }
}

Step 2: Implement Train function

Replace the TODOs in the train(...) function in sagify_base/training/training.py file with your logic. For example:

    from sklearn import datasets
    iris = datasets.load_iris()

    # Read the hyperparameter config json file
    import json
    with open(hyperparams_path) as _in_file:
        hyperparams_dict = json.load(_in_file)

    from sklearn import svm
    clf = svm.SVC(
        gamma=float(hyperparams_dict['gamma']),  # Values will be read as strings, so make sure to convert them to the right data type
        C=float(hyperparams_dict['C']),
        kernel=hyperparams_dict['kernel']
    )

    from sklearn.model_selection import train_test_split
    X_train, X_test, y_train, y_test = train_test_split(
        iris.data, iris.target, test_size=0.3, random_state=42)

    clf.fit(X_train, y_train)

    from sklearn.metrics import precision_score

    predictions = clf.predict(X_test)

    precision = precision_score(y_test, predictions, average='weighted')

    # Log the objective metric name with its calculated value. In tis example is Precision.
    # The objective name should be exactly the same with the one specified in the hyperparams congig json file.
    # The value must be a numeric (float or int).
    from sagify.api.hyperparameter_tuning import log_metric
    name = "Precision"
    log_metric(name, precision)

    from joblib import dump
    dump(clf, os.path.join(model_save_path, 'model.pkl'))

    print('Training complete.')

Step 3: Build and Push Docker image

sagify build Make sure sagify is in your requirements.txt file.
sagify push

Step 4: Call The CLI Command

And, finally, call the hyperparameter-optimization CLI command. For example:

 sagify cloud hyperparameter-optimization -i s3://my-bucket/training-data/ -o s3://my-bucket/output/ -e ml.m4.xlarge -h local/path/to/hyperparam_ranges.json

Step 5: Monitor Progress

You can monitor the progress via the SageMaker UI console. Here is an example of a finished Hyperparameter Optimization job:

Hyperparameter Optimization Results

Commands

Initialize

Name

Initializes a sagify module

Synopsis

sagify init

Description

This command initializes a sagify module in the directory you provide when asked after you invoke the init command.

Example

sagify init

Configure

Description

Updates an existing configuration value e.g. python version or AWS region.

Synopsis

sagify configure [--aws-region AWS_REGION] [--aws-profile AWS_PROFILE] [--image-name IMAGE_NAME] [--python-version PYTHON_VERSION]

Optional Flags

--aws-region AWS_REGION: AWS region where Docker images are pushed and SageMaker operations (train, deploy) are performed.

--aws-profile AWS_PROFILE: AWS profile to use when interacting with AWS.

--image-name IMAGE_NAME: Docker image name used when building for use with SageMaker. This shows up as an AWS ECR repository on your AWS account.

--python-version PYTHON_VERSION: Python version used when building SageMaker's Docker images. Curently supported versions: 2.7 , 3.6.

Example

sagify configure --aws-region us-east-2 --aws-profile default --image-name sage-docker-image-name --python-version 3.6

Build

Name

Builds a Docker image

Synopsis

sagify build

Description

This command builds a Docker image from code under the directory sagify is installed in. A REQUIREMENTS_FILE needs to be specified during sagify init or later via sagify configure --requirements-dir for all required dependencies to be installed in the Docker image.

Example

sagify build

Local Train

Name

Executes a Docker image in train mode

Synopsis

sagify local train

Description

This command executes a Docker image in train mode. More specifically, it executes the train(...) function in sagify_base/training/training.py inside an already built Docker image (see Build command section).

Example

sagify local train

Local Deploy

Name

Executes a Docker image in serve mode

Synopsis

sagify local deploy

Description

This command executes a Docker image in serve mode. More specifically, it runs a Flask REST app in Docker image and directs HTTP requests to /invocations endpoint. Then, the /invocations endpoint calls the predict(...) function in sagify_base/prediction/prediction.py (see Build command section on how to build a Docker image).

Example

sagify local deploy

Push

Name

Pushes a Docker image to AWS Elastic Container Service

Synopsis

sagify push [--aws-profile PROFILE_NAME] [--aws-region AWS_REGION] [--iam-role-arn IAM_ROLE] [--external-id EXTERNAL_ID]

Description

This command pushes an already built Docker image to AWS Elastic Container Service. Later on, AWS SageMaker will consume that image from AWS Elastic Container Service for train and serve mode.

Only one of iam-role-arn and _awsprofile can be provided. external-id is ignored when no iam-role-arn is provided.

Optional Flags

--iam-role-arn IAM_ROLE or -i IAM_ROLE: AWS IAM role to use for pushing to ECR

--aws-region AWS_REGION or -r AWS_REGION: The AWS region to push the image to

--aws-profile PROFILE_NAME or -p PROFILE_NAME: AWS profile to use for pushing to ECR

--external-id EXTERNAL_ID or -e EXTERNAL_ID: Optional external id used when using an IAM role

Example

sagify push

Cloud Upload Data

Name

Uploads data to AWS S3

Synopsis

sagify cloud upload-data --input-dir LOCAL_INPUT_DATA_DIR --s3-dir S3_TARGET_DATA_LOCATION

Description

This command uploads content under LOCAL_INPUT_DATA_DIR to S3 under S3_TARGET_DATA_LOCATION

Required Flags

--input-dir LOCAL_INPUT_DATA_DIR or -i LOCAL_INPUT_DATA_DIR: Local input directory

--s3-dir S3_TARGET_DATA_LOCATION or -s S3_TARGET_DATA_LOCATION: S3 target location

Example

sagify cloud upload-data -i ./training_data/ -s s3://my-bucket/training-data/

Cloud Train

Name

Trains your ML/DL model using a Docker image on AWS SageMaker with input from S3

Synopsis

sagify cloud train --input-s3-dir INPUT_DATA_S3_LOCATION --output-s3-dir S3_LOCATION_TO_SAVE_OUTPUT --ec2-type EC2_TYPE [--hyperparams-file HYPERPARAMS_JSON_FILE] [--volume-size EBS_SIZE_IN_GB] [--time-out TIME_OUT_IN_SECS] [--aws-tags TAGS] [--iam-role-arn IAM_ROLE] [--external-id EXTERNAL_ID] [--base-job-name BASE_JOB_NAME] [--job-name JOB_NAME] [--metric-names COMMA_SEPARATED_METRIC_NAMES] [--use-spot-instances FLAG_TO_USE_SPOT_INSTANCES]

Description

This command retrieves a Docker image from AWS Elastic Container Service and executes it on AWS SageMaker in train mode

Required Flags

--input-s3-dir INPUT_DATA_S3_LOCATION or -i INPUT_DATA_S3_LOCATION: S3 location to input data

--output-s3-dir S3_LOCATION_TO_SAVE_OUTPUT or -o S3_LOCATION_TO_SAVE_OUTPUT: S3 location to save output (models, reports, etc). Make sure that the output bucket already exists. Any not existing key prefix will be created by sagify.

--ec2-type EC2_TYPE or -e EC2_TYPE: ec2 type. Refer to https://aws.amazon.com/sagemaker/pricing/instance-types/

Optional Flags

--hyperparams-file HYPERPARAMS_JSON_FILE or -h HYPERPARAMS_JSON_FILE: Path to hyperparams JSON file

--volume-size EBS_SIZE_IN_GB or -v EBS_SIZE_IN_GB: Size in GB of the EBS volume (default: 30)

--time-out TIME_OUT_IN_SECS or -s TIME_OUT_IN_SECS: Time-out in seconds (default: 24 60 60)

--aws-tags TAGS or -a TAGS: Tags for labeling a training job of the form tag1=value1;tag2=value2. For more, see https://docs.aws.amazon.com/sagemaker/latest/dg/API_Tag.html.

--iam-role-arn IAM_ROLE or -r IAM_ROLE: AWS IAM role to use for training with SageMaker

--external-id EXTERNAL_ID or -x EXTERNAL_ID: Optional external id used when using an IAM role

--base-job-name BASE_JOB_NAME or -n BASE_JOB_NAME: Optional prefix for the SageMaker training job

--job-name JOB_NAME: Optional name for the SageMaker training job. NOTE: if a --base-job-name is passed along with this option, it will be ignored.

--use-spot-instances FLAG_TO_USE_SPOT_INSTANCES: Optional flag that specifies whether to use SageMaker Managed Spot instances for training. It should be used only for training jobs that take less than 1 hour. More information: https://docs.aws.amazon.com/sagemaker/latest/dg/model-managed-spot-training.html (default: False).

--metric-names COMMA_SEPARATED_METRIC_NAMES: Optional comma-separated metric names for tracking performance of training jobs. Example: Precision,Recall,AUC. Then, make sure you log these metric values using the log_metric function in the train function:

```
...
from sagify.api.hyperparameter_tuning import log_metric
log_metric("Precision:, precision)
log_metric("Accuracy", accuracy)
...
```

When the training jobs finishes, they will be stored in the CloudWatch algorithm metrics logs of the SageMaker training job:

Algorithm Metrics

Example

sagify cloud train -i s3://my-bucket/training-data/ -o s3://my-bucket/output/ -e ml.m4.xlarge -h local/path/to/hyperparams.json -v 60 -t 86400 --metric-names Accuracy,Precision

Cloud Hyperparameter Optimization

Name

Executes a Docker image in hyperparameter-optimization mode on AWS SageMaker

Synopsis

sagify cloud hyperparameter-optimization --input-s3-dir INPUT_DATA_S3_LOCATION --output-s3-dir S3_LOCATION_TO_SAVE_MULTIPLE_TRAINED_MODELS --ec2-type EC2_TYPE [--hyperparams-config-file HYPERPARAM_RANGES_JSON_FILE] [--max-jobs MAX_NUMBER_OF_TRAINING_JOBS] [--max-parallel-jobs MAX_NUMBER_OF_PARALLEL_TRAINING_JOBS] [--volume-size EBS_SIZE_IN_GB] [--time-out TIME_OUT_IN_SECS] [--aws-tags TAGS] [--iam-role-arn IAM_ROLE] [--external-id EXTERNAL_ID] [--base-job-name BASE_JOB_NAME] [--job-name JOB_NAME] [--wait WAIT_UNTIL_HYPERPARAM_JOB_IS_FINISHED] [--use-spot-instances FLAG_TO_USE_SPOT_INSTANCES]

Description

This command retrieves a Docker image from AWS Elastic Container Service and executes it on AWS SageMaker in hyperparameter-optimization mode

Required Flags

--input-s3-dir INPUT_DATA_S3_LOCATION or -i INPUT_DATA_S3_LOCATION: S3 location to input data

--ec2-type EC2_TYPE or -e EC2_TYPE: ec2 type. Refer to https://aws.amazon.com/sagemaker/pricing/instance-types/

--hyperparams-config-file HYPERPARAM_RANGES_JSON_FILE or -h HYPERPARAM_RANGES_JSON_FILE: Local path to hyperparameters configuration file. Example:

{
    "ParameterRanges": {
        "CategoricalParameterRanges": [
            {
                "Name": "kernel",
                "Values": ["linear", "rbf"]
            }
        ],
        "ContinuousParameterRanges": [
        {
          "MinValue": 0.001,
          "MaxValue": 10,
          "Name": "gamma"
        }
        ],
        "IntegerParameterRanges": [
            {
                "Name": "C",
                "MinValue": 1,
                "MaxValue": 10
            }
        ]
    },
    "ObjectiveMetric": {
        "Name": "Precision",
        "Type": "Maximize"
    }
}

Optional Flags

--max-jobs MAX_NUMBER_OF_TRAINING_JOBS or -m MAX_NUMBER_OF_TRAINING_JOBS: Maximum total number of training jobs to start for the hyperparameter tuning job (default: 3)

--max-parallel-jobs MAX_NUMBER_OF_PARALLEL_TRAINING_JOBS or -p MAX_NUMBER_OF_PARALLEL_TRAINING_JOBS: Maximum number of parallel training jobs to start (default: 1)

--volume-size EBS_SIZE_IN_GB or -v EBS_SIZE_IN_GB: Size in GB of the EBS volume (default: 30)

--time-out TIME_OUT_IN_SECS or -s TIME_OUT_IN_SECS: Time-out in seconds (default: 24 60 60)

--aws-tags TAGS or -a TAGS: Tags for labeling a training job of the form tag1=value1;tag2=value2. For more, see https://docs.aws.amazon.com/sagemaker/latest/dg/API_Tag.html.

--iam-role-arn IAM_ROLE or -r IAM_ROLE: AWS IAM role to use for training with SageMaker

--external-id EXTERNAL_ID or -x EXTERNAL_ID: Optional external id used when using an IAM role

--base-job-name BASE_JOB_NAME or -n BASE_JOB_NAME: Optional prefix for the SageMaker training job

--job-name JOB_NAME: Optional name for the SageMaker training job. NOTE: if a --base-job-name is passed along with this option, it will be ignored.

--wait WAIT_UNTIL_HYPERPARAM_JOB_IS_FINISHED or -w WAIT_UNTIL_HYPERPARAM_JOB_IS_FINISHED: Optional flag to wait until Hyperparameter Tuning is finished. (default: don't wait)

Example

sagify cloud hyperparameter-optimization -i s3://my-bucket/training-data/ -o s3://my-bucket/output/ -e ml.m4.xlarge -h local/path/to/hyperparam_ranges.json -v 60 -t 86400

Cloud Deploy

Name

Executes a Docker image in serve mode on AWS SageMaker

Synopsis

sagify cloud deploy --s3-model-location S3_LOCATION_TO_MODEL_TAR_GZ --num-instance NUMBER_OF_EC2_INSTANCES --ec2-type EC2_TYPE [--aws-tags TAGS] [--iam-role-arn IAM_ROLE] [--external-id EXTERNAL_ID] [--endpoint-name ENDPOINT_NAME]

Description

This command retrieves a Docker image from AWS Elastic Container Service and executes it on AWS SageMaker in serve mode. You can update an endpoint (model or number of instances) by specifying the endpoint-name.

Required Flags

--s3-model-location S3_LOCATION_TO_MODEL_TAR_GZ or -m S3_LOCATION_TO_MODEL_TAR_GZ: S3 location to to model tar.gz

--num-instances NUMBER_OF_EC2_INSTANCES or n NUMBER_OF_EC2_INSTANCES: Number of ec2 instances

--ec2-type EC2_TYPE or e EC2_TYPE: ec2 type. Refer to https://aws.amazon.com/sagemaker/pricing/instance-types/

Optional Flags

--aws-tags TAGS or -a TAGS: Tags for labeling a training job of the form tag1=value1;tag2=value2. For more, see https://docs.aws.amazon.com/sagemaker/latest/dg/API_Tag.html.

--iam-role-arn IAM_ROLE or -r IAM_ROLE: AWS IAM role to use for deploying with SageMaker

--external-id EXTERNAL_ID or -x EXTERNAL_ID: Optional external id used when using an IAM role

--endpoint-name ENDPOINT_NAME: Optional name for the SageMaker endpoint

Example

sagify cloud deploy -m s3://my-bucket/output/model.tar.gz -n 3 -e ml.m4.xlarge

Cloud Batch Transform

Name

Executes a Docker image in batch transform mode on AWS SageMaker, i.e. runs batch predictions on user defined S3 data

Synopsis

sagify cloud batch-transform --s3-model-location S3_LOCATION_TO_MODEL_TAR_GZ --s3-input-location S3_INPUT_LOCATION --s3-output-location S3_OUTPUT_LOCATION --num-instance NUMBER_OF_EC2_INSTANCES --ec2-type EC2_TYPE [--aws-tags TAGS] [--iam-role-arn IAM_ROLE] [--external-id EXTERNAL_ID] [--wait WAIT_UNTIL_BATCH_TRANSFORM_JOB_IS_FINISHED] [--job-name JOB_NAME]

Description

This command retrieves a Docker image from AWS Elastic Container Service and executes it on AWS SageMaker in batch transform mode, i.e. runs batch predictions on user defined S3 data. SageMaker will spin up REST container(s) and call it/them with input data(features) from a user defined S3 path.

Things to do:

You should implement the predict function that expects a JSON containing the required feature values. It's the same predict function used for deploying the model as a REST service. Example of a JSON:
```
{
"features": [5.1,3.5,1.4,0.2]
}
```
The input S3 path should contain a file or multiple files where each line is a JSON, the same JSON format as the one expected in the predict function. Example of a file:
```
{"features": [5.1,3.5,1.4,0.2]}
{"features": [4.9,3.0,1.4,0.2]}
{"features": [4.7,3.2,1.3,0.2]}
{"features": [4.6,3.1,1.5,0.2]}
```

Required Flags

--s3-model-location S3_LOCATION_TO_MODEL_TAR_GZ or -m S3_LOCATION_TO_MODEL_TAR_GZ: S3 location to to model tar.gz

--s3-input-location S3_INPUT_LOCATION or -i S3_INPUT_LOCATION: s3 input data location

--s3-output-location S3_OUTPUT_LOCATION or -o S3_OUTPUT_LOCATION: s3 location to save predictions

--num-instances NUMBER_OF_EC2_INSTANCES or n NUMBER_OF_EC2_INSTANCES: Number of ec2 instances

--ec2-type EC2_TYPE or e EC2_TYPE: ec2 type. Refer to https://aws.amazon.com/sagemaker/pricing/instance-types/

Optional Flags

--aws-tags TAGS or -a TAGS: Tags for labeling a training job of the form tag1=value1;tag2=value2. For more, see https://docs.aws.amazon.com/sagemaker/latest/dg/API_Tag.html.

--iam-role-arn IAM_ROLE or -r IAM_ROLE: AWS IAM role to use for deploying with SageMaker

--external-id EXTERNAL_ID or -x EXTERNAL_ID: Optional external id used when using an IAM role

--wait WAIT_UNTIL_BATCH_TRANSFORM_JOB_IS_FINISHED or -w WAIT_UNTIL_BATCH_TRANSFORM_JOB_IS_FINISHED: Optional flag to wait until Batch Transform is finished. (default: don't wait)

--job-name JOB_NAME: Optional name for the SageMaker batch transform job

Example

sagify cloud batch-transform -m s3://my-bucket/output/model.tar.gz -i s3://my-bucket/input_features -o s3://my-bucket/predictions -n 3 -e ml.m4.xlarge