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Developing and Deploying scikit-learn Models with Kaptain SDK

NOTE: All tutorials in Jupyter Notebook format are available for download. You can either download them to a local computer and upload to the running Jupyter Notebook or run the following command from a Jupyter Notebook Terminal running in your Kaptain installation:

curl -L | tar xz

NOTE: These notebook tutorials have been built for and tested on D2iQ's Kaptain. Without the requisite Kubernetes operators and custom Docker images, these notebooks will likely not work.

Developing and deploying scikit-learn models with Kaptain SDK


This notebook shows how to build and deploy ML models by using different popular machine learning frameworks. This example will be based on scikit-learn library, but because model building will be handled by Kubernetes Job, you can choose to use any other ML library (that can be installed with pip). Currently, the SDK supports XGBoost, Onnx and LightGBM as well as PyTorch and TensorFlow for model deployment. See Kaptain documentation for more info.

To perform distributed training on a cluster’s resources, conduct experiments with multiple parallel trials to obtain the best hyperparameters, and deploying a trained or tuned model typically requires additional steps, such as building a Docker image and providing framework-specific specifications for Kubernetes. This places the burden on each data scientist to learn all the details of all the components.

Instead of doing all the work, using the Kaptain SDK, you can train, tune, and deploy from within a notebook without having to worry about framework specifics, Kubeflow-native SDKs, or even thinking about Kubernetes

What You Will Learn

The Kaptain SDK provides a data science-friendly user experience from within a notebook that hides all the specifics, and focuses on the model as the main abstraction. A model can be trained, tuned, deployed, and tracked.

The example is based on scikit-learn, but it works equally for other data science frameworks. The original scikit-learn example code can be found in the tutorials Recognizing hand-written digits.

The SDK relies on MinIO, an open-source S3-compliant object storage tool, that is already included with your Kaptain installation.

What You Will Need

All you need is this notebook.


NOTE: This notebook requires Kaptain SDK 1.0.0 or later.

  • Install the MinIO Client. Refer to the quickstart guide for instructions.

  • Ensure you are using the correct notebook image, that is, scikit-learn is available:

    set -o errexit
    pip list | grep scikit-learn
    pip list | grep kaptain

How to Create a Docker Credentials File and Kubernetes Secret

For the tutorial, you will need getpass to provide a password interactively without it being immediately visible. It is a standard Python library, so there is no need to install it. A simple import will suffice.

WARNING: Please do not store passwords directly in notebooks. Ideally, credentials are stored safely inside secrets management solutions or provided with service accounts. Please check the section on how to manage secrets in the official Kaptain documentation for more details on how to set up Docker credentials that you can attach to a notebook server. This notebook should be used for demonstration purposes only!

Please type in the container registry username by running the next cell:

import json
import getpass
import pathlib
from base64 import b64encode
docker_user = input()

Enter the password for the Docker container registry when prompted by executing the following code:

docker_password = getpass.getpass()

With these details, base64-encode the username and password and create a Docker configuration file as follows:

# Create a folder to store the Docker configuration file
docker_config_folder = pathlib.Path.joinpath(pathlib.Path.home(), ".docker")

# Write the base64-encoded credentials to the configuration file
docker_credentials = b64encode(f"{docker_user}:{docker_password}".encode()).decode()
config = {"auths": {"": {"auth": docker_credentials}}}
with open(f"{docker_config_folder}/config.json", "w") as outfile:

Define the trainer file

This step writes a file that will be run inside of the training container rather than inside of the notebook kernel. It takes the form of a parameterized training script. The training parameters default inside the training program with the user-defined values being passed in when the container is run. The script is responsible for accessing any datasets that are required for the training run into the container.

To use the Kaptain SDK, you need to add code to do three things to the original model code:

  1. In the block at the end of main() to save the trained model to the cluster’s built-in object storage, MinIO.

  2. Also in the block at the end of main(), to record the metrics of interest.

  3. Parameters that will change need to be retrieved from the CLI

import os
import argparse
import time

from sklearn import datasets, svm, metrics
from sklearn.model_selection import train_test_split
from sklearn.linear_model import LogisticRegression

from joblib import dump

from kaptain.platform.model_export_util import ModelExportUtil
from kaptain.platform.metadata_util import MetadataUtil

def main():
    parser = argparse.ArgumentParser()

    # Arguments that will be passed to your training code

        help="Kernel coefficient"

        help="Regularization parameter"

    args, _ = parser.parse_known_args()

    # Load the MNIST digit dataset
    digits = datasets.load_digits()

    # flatten the images
    n_samples = len(digits.images)
    data = digits.images.reshape((n_samples, -1))

    # Create a classifier: a support vector classifier
    clf = svm.SVC(C=args.c, gamma=args.gamma)

    # Split data into 50% train and 50% test subsets
    X_train, X_test, y_train, y_test = train_test_split(
        data,, test_size=0.5, shuffle=False

    # Learn the digits on the train subset, y_train)

    # Predict the value of the digit on the test subset
    predicted = clf.predict(X_test)

        f"Classification report for classifier {clf}:\n"
        f"{metrics.classification_report(y_test, predicted)}\n"

    cm = metrics.confusion_matrix(y_test, predicted)
    print(f"Confusion matrix:\n{cm}")

    score = clf.score(X_test, y_test)
    print(f"\nModel accuracy: {score}")

    model_upload_path = os.getenv("TRAINED_MODEL_UPLOAD_PATH")
    if model_upload_path:
        model_file_name = "model.joblib"

        print(f"Exporting model to {model_upload_path}/{model_file_name} ...")

        dump(clf, model_file_name)
        print("Export completed.")

        # Record model accuracy metrics
        MetadataUtil.record_metrics({"accuracy": score})
        # Because the job executes too quickly, we need to wait to allow metric collector container fetch the metrics

if __name__ == "__main__":


Describe the model

The central abstraction of the Kaptain SDK is a Model class that encapsulates all the configuration and high-level APIs required for the model training, tuning, and serving. Prior to creating an instance of the Model class, let’s consider an example where we need to specify additional dependecies required for model training, tuning and serving, and also provide minimal required configuration for the model server.

Model dependencies can be provided via pip requirements.txt. For example:

%%writefile requirements.txt

Below is an example of the minimally required serving configuration for a scikit-learn model. To learn more about advanced configuration options, consult the Kaptain SDK documentation.

serving_config = {
    "requirements_file": "requirements.txt",  # the model dependenies file. You can provide a different file for serving-specific dependencies

Finally, a Model instance requires providing a base Docker image (base_image) to use for model training, a target Docker repository and image name (image_name) to publish trainer code to (packed in a Docker image too), and a list of additional files that are required for the model code or the trainer code (extra_files).

base_image = "mesosphere/kubeflow:2.2.0-base"
image_name = "mesosphere/kubeflow:mnist-sklearn-sdk"

# name of the file with additional python packages to install into the model image (e.g. "requirements.txt")
requirements = "requirements.txt"
import os

from kaptain import envs
from kaptain.model.models import Model
from kaptain.model.frameworks import ModelFramework

envs.VERBOSE = True
envs.DEBUG = True

model = Model(
    description="MSNIT Model",

The id is a unique identifier of the model. The identifier shown indicates it is an MNIST model in development.

The fields member and description are for humans: to inform your colleagues and yourself of what the model is about. version is the models’ own version, so it is easy to identify models by their iteration. The framework and framework_version are for the time being human-friendly metadata.

Since a Docker image is built in the background when you train or tune a Model instance, a base_image has to be provided. The name of the final image image_name must be provided with or without image tag. If the tag is omitted, a concatenation of model id, framework, and framework_version is used.

The main_file specifies the name of file that contains the model code, that is, for the purposes of this tutorial.

To specify additional Python packages required for training or serving, provide the path to your requirements file via the requirements parameter of the Model class. Details on the format of the requirements file can be found in the pip official documentation.

More details are available with ?Model.

Train/tune the model

Training the model is as easy as the following function call:

memory = "1G"
cpu = "0.5"
model.train(cpu=cpu, memory=memory, hyperparameters={})
2022-07-13 10:53:21,794 kaptain-log[INFO]: Building Docker image.
2022-07-13 10:53:21,794 kaptain-log[INFO]: Creating secret docker-796a4baf6ede29c6 in namespace user1.
2022-07-13 10:53:21,805 kaptain-log[INFO]: Creating secret context-796a4baf6ede29c6 in namespace user1.
2022-07-13 10:53:21,812 kaptain-log[INFO]: Creating job kaniko-796a4baf6ede29c6 in namespace user1.
2022-07-13 10:53:27,083 kaptain-log[INFO]: Waiting for Image Build to start...
2022-07-13 10:53:32,251 kaptain-log[INFO]: Image Build started in pod: kaniko-796a4baf6ede29c6--1-crzlx.
2022-07-13 10:53:34,534 kaptain-log[INFO]: [kaniko-796a4baf6ede29c6--1-crzlx/kaniko] logs:
 [36mINFO [0m[0000] Retrieving image manifest mesosphere/kubeflow:2.2.0-base 
 [36mINFO [0m[0000] Retrieving image mesosphere/kubeflow:2.2.0-base 
 [36mINFO [0m[0001] Retrieving image manifest mesosphere/kubeflow:2.2.0-base 
 [36mINFO [0m[0001] Retrieving image mesosphere/kubeflow:2.2.0-base 
 [36mINFO [0m[0002] Built cross stage deps: map[]                
2022-07-13 10:54:14,026 kaptain-log[INFO]: [kaniko-796a4baf6ede29c6--1-crzlx/kaniko] logs:
 [36mINFO [0m[0002] Retrieving image manifest mesosphere/kubeflow:2.2.0-base 
 [36mINFO [0m[0002] Retrieving image mesosphere/kubeflow:2.2.0-base 
 [36mINFO [0m[0003] Retrieving image manifest mesosphere/kubeflow:2.2.0-base 
 [36mINFO [0m[0003] Retrieving image mesosphere/kubeflow:2.2.0-base 
 [36mINFO [0m[0004] Executing 0 build triggers                   
 [36mINFO [0m[0004] Unpacking rootfs as cmd COPY . /kaptain requires it. 
 [36mINFO [0m[0041] Taking snapshot of full filesystem...        
2022-07-13 10:55:00,361 kaptain-log[INFO]: [kaniko-796a4baf6ede29c6--1-crzlx/kaniko] logs:
 [36mINFO [0m[0088] LABEL checksum=cbefed5a490ca265be68f9486ad37086 
2022-07-13 10:55:42,354 kaptain-log[INFO]: [kaniko-796a4baf6ede29c6--1-crzlx/kaniko] logs:
 [36mINFO [0m[0088] Applying label checksum=cbefed5a490ca265be68f9486ad37086 
 [36mINFO [0m[0088] WORKDIR /kaptain                             
 [36mINFO [0m[0088] cmd: workdir                                 
 [36mINFO [0m[0088] Changed working directory to /kaptain        
 [36mINFO [0m[0088] Creating directory /kaptain                  
 [36mINFO [0m[0088] COPY . /kaptain                              
 [36mINFO [0m[0088] RUN if [ -e requirements.txt ]; then pip install --no-cache -r requirements.txt; fi 
 [36mINFO [0m[0088] cmd: /bin/bash                               
 [36mINFO [0m[0088] args: [-cu if [ -e requirements.txt ]; then pip install --no-cache -r requirements.txt; fi] 
 [36mINFO [0m[0088] Running: [/bin/bash -cu if [ -e requirements.txt ]; then pip install --no-cache -r requirements.txt; fi] 
Requirement already satisfied: scikit-learn>0.24.2 in /opt/conda/lib/python3.8/site-packages (from -r requirements.txt (line 1)) (1.1.1)
Requirement already satisfied: joblib>=1.0.0 in /opt/conda/lib/python3.8/site-packages (from scikit-learn>0.24.2->-r requirements.txt (line 1)) (1.1.0)
Requirement already satisfied: threadpoolctl>=2.0.0 in /opt/conda/lib/python3.8/site-packages (from scikit-learn>0.24.2->-r requirements.txt (line 1)) (3.1.0)
Requirement already satisfied: numpy>=1.17.3 in /opt/conda/lib/python3.8/site-packages (from scikit-learn>0.24.2->-r requirements.txt (line 1)) (1.21.6)
Requirement already satisfied: scipy>=1.3.2 in /opt/conda/lib/python3.8/site-packages (from scikit-learn>0.24.2->-r requirements.txt (line 1)) (1.8.1)
WARNING: Running pip as the 'root' user can result in broken permissions and conflicting behaviour with the system package manager. It is recommended to use a virtual environment instead:
 [36mINFO [0m[0090] ENTRYPOINT ["python", "-u", ""]   
 [36mINFO [0m[0090] Taking snapshot of full filesystem...        
2022-07-13 10:55:42,562 kaptain-log[INFO]: Image build completed successfully. Image pushed: mesosphere/kubeflow:mnist-sklearn-sdk
2022-07-13 10:55:42,562 kaptain-log[INFO]: Deleting job kaniko-796a4baf6ede29c6 in namespace user1.
2022-07-13 10:55:42,571 kaptain-log[INFO]: Deleting secret docker-796a4baf6ede29c6 in namespace user1.
2022-07-13 10:55:42,575 kaptain-log[INFO]: Deleting secret context-796a4baf6ede29c6 in namespace user1.
2022-07-13 10:55:42,584 kaptain-log[INFO]: Creating secret train-55ad1342dff5eede in namespace user1.
2022-07-13 10:55:42,595 kaptain-log[INFO]: Creating secret train-registry-85c8e1f285264a44 in namespace user1.
2022-07-13 10:55:42,603 kaptain-log[INFO]: Submitting a new training job "mnist-job-6f2f5c2a".
2022-07-13 10:55:42,604 kaptain-log[INFO]: Creating job mnist-job-6f2f5c2a in namespace user1.
2022-07-13 10:55:42,616 kaptain-log[INFO]: Waiting for the training job to complete...
2022-07-13 10:55:47,853 kaptain-log[INFO]: Waiting for Master Node Training Model to start...
2022-07-13 10:56:43,720 kaptain-log[INFO]: Master Node Training Model started in pod: mnist-job-6f2f5c2a--1-lq5fj.
2022-07-13 10:56:45,764 kaptain-log[INFO]: [mnist-job-6f2f5c2a--1-lq5fj/sklearn] logs:
Classification report for classifier SVC(gamma=0.001):
              precision    recall  f1-score   support
           0       1.00      0.99      0.99        88
           1       0.99      0.97      0.98        91
           2       0.99      0.99      0.99        86
           3       0.98      0.87      0.92        91
           4       0.99      0.96      0.97        92
           5       0.95      0.97      0.96        91
           6       0.99      0.99      0.99        91
           7       0.96      0.99      0.97        89
           8       0.94      1.00      0.97        88
           9       0.93      0.98      0.95        92
    accuracy                           0.97       899
   macro avg       0.97      0.97      0.97       899
weighted avg       0.97      0.97      0.97       899
Confusion matrix:
[[87  0  0  0  1  0  0  0  0  0]
 [ 0 88  1  0  0  0  0  0  1  1]
 [ 0  0 85  1  0  0  0  0  0  0]
 [ 0  0  0 79  0  3  0  4  5  0]
 [ 0  0  0  0 88  0  0  0  0  4]
 [ 0  0  0  0  0 88  1  0  0  2]
 [ 0  1  0  0  0  0 90  0  0  0]
 [ 0  0  0  0  0  1  0 88  0  0]
 [ 0  0  0  0  0  0  0  0 88  0]
 [ 0  0  0  1  0  1  0  0  0 90]]
Model accuracy: 0.9688542825361512
2022-07-13 10:56:56,807 kaptain-log[WARNING]: Reason: FailedMount, message: MountVolume.SetUp failed for volume "kube-api-access-cdn48" : object "user1"/"kube-root-ca.crt" not registered
2022-07-13 10:56:56,921 kaptain-log[INFO]: [mnist-job-6f2f5c2a--1-lq5fj/sklearn] logs:
Exporting model to s3://kaptain/models/dev/mnist/trained/5ec8779b6b5345ed8aea0b5d82c3b5f7/model.joblib ...
Export completed.
2022-07-13 10:56:57,330 kaptain-log[WARNING]: Reason: FailedMount, message: MountVolume.SetUp failed for volume "kube-api-access-cdn48" : object "user1"/"kube-root-ca.crt" not registered
2022-07-13 10:56:57,949 kaptain-log[INFO]: Deleting secret train-55ad1342dff5eede in namespace user1.
2022-07-13 10:56:57,953 kaptain-log[INFO]: Deleting secret train-registry-85c8e1f285264a44 in namespace user1.
2022-07-13 10:56:57,959 kaptain-log[INFO]: Model training is completed.

The default gpus argument is 0, but it is shown here as an explicit option. Use ?Model.train to see all supported arguments.

NOTE: When resource quotas are set for a namespace, users have to specify cpu and memory explicitly in the SDK. Otherwise, tasks such as training and tuning will fail with Error creating: pods ... is forbidden: failed quota: kf-resource-quota: must specify cpu,memory. These fields are optional when resource quotas are not set. In case the issue appears for other types of workloads, it is recommended to configure defaults for the user namespace using the Limit Range.

The low accuracy of the model is to make the demonstration of distributed training quicker, as in the next section the model’s hyperparameters are optimized anyway.

Run an experiment

trials = 12
parallel_trials = 2
from import Double, Discrete

hyperparams = {"--gamma": Double(0.0001, 0.001), "--c": Double(0.01, 1.00)}

2022-07-13 10:57:25,048 kaptain-log[INFO]: Skipping image build for the model - the image 'mesosphere/kubeflow:mnist-sklearn-sdk' with the same contents has already been published to the registry.
2022-07-13 10:57:25,055 kaptain-log[INFO]: Creating secret tune-a2163517dfee427b in namespace user1.
2022-07-13 10:57:25,067 kaptain-log[INFO]: Creating secret tune-registry-c093d8a74d90db33 in namespace user1.
2022-07-13 10:57:25,073 kaptain-log[INFO]: Creating experiment mnist-tune-dd9115bc in namespace user1
2022-07-13 10:57:25,309 kaptain-log[INFO]: Experiment mnist-tune-dd9115bc has been created.
Progress: 100%|█████████████████████████|12/12 [time: 03:30, accuracy: 0.9622, trials running: 0, pending: 0, failed: 0, killed: 0]
2022-07-13 11:00:55,730 kaptain-log[INFO]: Model tuning completed, final status: Succeeded
2022-07-13 11:00:55,737 kaptain-log[INFO]: Experiment results:
parameters: {'--gamma': '0.0003626001536284', '--c': '0.9760872894343234'}, best_trial_name: mnist-tune-dd9115bc-z6m2nlww
2022-07-13 11:00:55,738 kaptain-log[INFO]: Copying saved model with the best metrics from the trial to the target location.
2022-07-13 11:00:55,937 kaptain-log[INFO]: Removing intermediate trial models from the storage.

Verify the Model is Exported to MinIO

First, you will need to install the MinIO Client. Refer to the quickstart guide for instructions.

set -o errexit

minio_accesskey=$(kubectl get secret minio-creds-secret -o jsonpath="{.data.accesskey}" | base64 --decode)
minio_secretkey=$(kubectl get secret minio-creds-secret -o jsonpath="{.data.secretkey}" | base64 --decode)

mc --no-color alias set minio http://kaptain-minio.kubeflow ${minio_accesskey} ${minio_secretkey}
mc --no-color ls -r minio/kaptain/models
Added `minio` successfully.
[2022-07-13 10:56:45 UTC] 337KiB dev/mnist/trained/5ec8779b6b5345ed8aea0b5d82c3b5f7/model.joblib
[2022-07-13 10:35:06 UTC] 337KiB dev/mnist/trained/607131bcb901423eaef2c8649ddb90ef/model.joblib
[2022-07-13 11:00:55 UTC] 314KiB dev/mnist/tuned/e49a5080578c4fff91e62478c0c792c3/model.joblib

Log and Hyperparameters Metrics to MLflow

Hyperparameters and metrics can easily be logged to the MLFlow instance which was bundled with Kaptain. You can log metrics from tuning by executing the following:

import mlflow

# Log a batch of metrics
with mlflow.start_run(
        run_name =,
        description = model.description,
        tags = {"version": model.version}):
        {f"{name}.{key}": value for name, values in model.metrics.items() for key, value in values.items()})

Deploy the Model

Model is ready to be deployed. A trained model can be deployed as an auto-scalable inference service with a single call. When providing additional serving dependencies, make sure to specify sufficient resources (mostly memory) in order for the server to install them without issues.

model.deploy(cpu="0.5", memory="500M", replace=True)
2022-07-13 11:01:23,209 kaptain-log[INFO]: Building deployment artifacts and uploading to s3://kaptain/models/dev/mnist/deploy/e347c6f4ec91424c94b47f503663d685
2022-07-13 11:01:23,277 kaptain-log[INFO]: Deploying model from s3://kaptain/models/dev/mnist/deploy/e347c6f4ec91424c94b47f503663d685
2022-07-13 11:01:23,279 kaptain-log[INFO]: Reading secrets dev-mnist-secret in namespace user1.
2022-07-13 11:01:23,292 kaptain-log[INFO]: Patching secret dev-mnist-secret in namespace user1.
2022-07-13 11:01:23,298 kaptain-log[INFO]: Reading service account dev-mnist-service-account in namespace user1.
2022-07-13 11:01:23,304 kaptain-log[INFO]: Patching service account dev-mnist-service-account in namespace user1.

NAME                 READY                           PREV                    LATEST URL                                                              
dev-mnist            False                              0                       100                               
dev-mnist            False                              0                       100                               
dev-mnist            False                              0                       100                               
dev-mnist            False                              0                       100                               
dev-mnist            True                               0                       100                               

2022-07-13 11:01:43,180 kaptain-log[INFO]: Model dev/mnist deployed successfully. Cluster URL: http://dev-mnist.user1.svc.cluster.local

Test the Model Endpoint

import codecs, json
import matplotlib.pyplot as plt

from sklearn.datasets import load_digits

image_index = 7

digits = load_digits()

plt.matshow(digits.images[image_index], cmap="binary")

n_samples = len(digits.images)
data = digits.images.reshape(n_samples, -1).tolist()

serving_req = {"instances": [data[image_index]]}

with open("input.json", "w") as json_file:
    json.dump(serving_req, json_file)

set -o errexit

namespace=$(cat /var/run/secrets/


curl --location \
     --silent \
     --fail \
     --retry 10 \
     --retry-delay 10 \
     --header "Content-Type: application/json" \
     $url \
     -d@input.json | python -m json.tool
    "predictions": [

We can see that the class with label “7” has the largest probability; the neural network correctly predicts the image to be a number 7.

This tutorial includes code from the MinIO Project (“MinIO”), which is © 2014-2022 MinIO, Inc. MinIO is made available subject to the terms and conditions of the Apache Software Foundation, Apache License V2.0. The complete source code for the version of MinIO packaged with Kaptain 2.2.0 is available at this URL:

For a full list of attributed 3rd party software, see

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