covalent-kubernetes-plugin 0.1.0

Covalent Kubernetes Plugin

 

 

Covalent Kubernetes Plugin

Covalent is a Pythonic workflow tool used to execute tasks on advanced computing hardware. This executor plugin interfaces Covalent with Kubernetes clusters. In order for workflows to be deployable, users must be authenticated to an existing Kubernetes cluster. Users can view their Kubernetes configuration file and validate the connection using the commands

kubectl config view
kubectl get nodes

Users who simply wish to test the plugin on minimal infrastructure should skip to the deployment instructions in the following sections.

Installation

To use this plugin with Covalent, simply install it using pip:

pip install covalent-kubernetes-plugin

Users can optionally enable support for AWS Elastic Kubernetes Service using

pip install covalent-kubernetes-plugin[aws]

You will also need to install Docker to use this plugin.

Configuration

The following shows a reference of a Covalent configuration:

[executors.k8s]
base_image = "python:3.8-slim-bullseye"
k8s_config_file = "/home/user/.kube/config"
k8s_context = "minikube"
registry = "localhost"
registry_credentials_file = ""
data_store = "/tmp"
vcpu = "500m"
memory = "1G"
cache_dir = "/home/user/.cache/covalent"
poll_freq = 10

This describes a configuration for a minimal local deployment with images and data stores also located on the local machine.

Example workflow

Next, interact with the Kubernetes backend via Covalent by declaring an executor class object and attaching it to an electron:

import covalent as ct
from covalent_kubernetes_plugin.k8s import KubernetesExecutor

local_k8s_executor = KubernetesExecutor(
    k8s_context="minikube"
    vcpu="100m",
    memory="500Mi"
)

eks_executor = KubernetesExecutor(
    k8s_context=[e-mail],
    image_repo="covalent-eks-task",
    registry="<account_id>.dkr.ecr.us-east-1.amazonaws.com",
    data_store="s3://<bucket_name>/<file_path>/",
    vcpu="2.0",
    memory="4G"
)

# Run on a local cluster
@ct.electron(executor=local_k8s_executor)
def join_words(a, b):
    return ", ".join([a, b])

# Run on the cloud
@ct.electron(executor=eks_executor)
def excitement(a):
    return f"{a}!"

# Construct a workflow
@ct.lattice
def simple_workflow(a, b):
    phrase = join_words(a, b)
    return excitement(phrase)

# Dispatch the workflow
dispatch_id = ct.dispatch(simple_workflow)("Hello", "World")

For more information about how to get started with Covalent, check out the project homepage and the official documentation.

Local deployment with minikube

First, install kubectl as well as minikube following the instructions here. One or both of these may be available through your system's package manager.

Cluster deployment

Next, create a basic minikube cluster:

minikube start

From here you can view the UI using the command minikube dashboard which should open a page in your browser.

Before deploying the job, you will need to mount the Covalent cache directory so the Covalent server can communicate with the task container:

minikube mount ~/.cache/covalent:/data

If you experience a Connection refused error, ensure that the subnet used by minikube is whitelisted in your firewall. If you use iptables, you can use these commands:

iptables -A INPUT -s 192.168.49.0/24 -j ACCEPT
iptables-save

Task deployment

Next, deploy the test job using the command

kubectl apply -f infra/sample_job.yaml

which should return job.batch/covalent-k8s-test created. You can view the status move from pending to succeeded on the dashboard. After some time, query the status of the job with

kubectl describe jobs/covalent-k8s-test

which returns

Name:             test
Namespace:        default
Selector:         controller-uid=eaa319c3-4440-4411-b178-6289398cdb6a
Labels:           controller-uid=eaa319c3-4440-4411-b178-6289398cdb6a
                  job-name=covalent-k8s-test
Annotations:      <none>
Parallelism:      1
Completions:      1
Completion Mode:  NonIndexed
Start Time:       Thu, 21 Jul 2022 14:25:55 -0400
Completed At:     Thu, 21 Jul 2022 14:26:06 -0400
Duration:         11s
Pods Statuses:    0 Active (0 Ready) / 1 Succeeded / 0 Failed
Pod Template:
  Labels:  controller-uid=eaa319c3-4440-4411-b178-6289398cdb6a
           job-name=test
  Containers:
   test:
    Image:        hello-world:latest
    Port:         <none>
    Host Port:    <none>
    Environment:  <none>
    Mounts:       <none>
  Volumes:        <none>
Events:
  Type    Reason            Age   From            Message
  ----    ------            ----  ----            -------
  Normal  SuccessfulCreate  112s  job-controller  Created pod: test-5fs64
  Normal  Completed         101s  job-controller  Job completed

You are now ready to use the Covalent Kubernetes Plugin with your minikube cluster!

Reference configuration

The steps above generated the following authentication and configuration settings:

> kubectl config view --minify
apiVersion: v1
clusters:
- cluster:
    certificate-authority: /home/user/.minikube/ca.crt
    extensions:
    - extension:
        last-update: Sun, 24 Jul 2022 16:09:01 EDT
        provider: minikube.sigs.k8s.io
        version: v1.26.0
      name: cluster_info
    server: https://192.168.59.100:8443
  name: minikube
contexts:
- context:
    cluster: minikube
    extensions:
    - extension:
        last-update: Sun, 24 Jul 2022 16:09:01 EDT
        provider: minikube.sigs.k8s.io
        version: v1.26.0
      name: context_info
    namespace: default
    user: minikube
  name: minikube
current-context: minikube
kind: Config
preferences: {}
users:
- name: minikube
  user:
    client-certificate: /home/user/.minikube/profiles/minikube/client.crt
    client-key: /home/user/.minikube/profiles/minikube/client.key

Cleanup

When you are done using your cluster, delete it:

minikube delete

AWS Elastic Kubernetes Service deployment with Terraform

This section assumes you have already downloaded and configured the AWS CLI tool with an IAM user who has permissions to create an EKS cluster. To get started, download and install Terraform.

Cluster deployment

You can edit the input variables by copying the file infra/defaults.tfvars to infra/.tfvars and editing the contents.

Next, run the following:

make deploy

It may take 15 to 20 minutes to deploy this infrastructure. Note that AWS charges $0.10 per hour for EKS clusters and EC2 instances vary in price. Running this command will cost money on AWS.

To view the Kubernetes dashboard, update your KUBECONFIG environment variable as instructed in the deployment output, run kubectl proxy and then navigate to the dashboard. It may take some time for resources to initially appear.

Adding users

Initially only the user who created the cluster will be able to access it. To view the auth config map, run

kubectl -n kube-system get configmap aws-auth -o yaml

We can add another IAM user newuser as a cluster administrator using

kubectl -n kube-system edit configmap aws-auth

and inserting the following entry:

data:
  mapUsers: |
    - userarn: arn:aws:iam::<account_id>:user/newuser
      username: newuser
      groups:
      - system:masters

The IAM user should not need any additional permissions.

Task deployment

Make sure the context is properly set, check with

kubectl config get-contexts

If it is set to anything other than the EKS cluster, execute

kubectl config use-context <my-cluster-name>

You can now deploy a job using the same method as you did with minikube.

To view the status of jobs, run

kubectl describe jobs --selector=job-name=test

Reference configuration

The steps above generated the following authentication and configuration settings:

> kubectl get configmap -n kube-system aws-auth -o yaml
apiVersion: v1
data:
  mapRoles: |
    - groups:
      - system:bootstrappers
      - system:nodes
      rolearn: arn:aws:iam::<account_id>:role/covalent-eks-cluster-nodegroup-NodeInstanceRole-1VH95YLZKOX47
      username: system:node:{{EC2PrivateDNSName}}
    - groups:
      - system:bootstrappers
      - system:nodes
      rolearn: arn:aws:iam::<account_id>:role/covalent-eks-cluster-nodegroup-NodeInstanceRole-1NDG6XAZXQKJM
      username: system:node:{{EC2PrivateDNSName}}
  mapUsers: |
    - userarn: "arn:aws:iam::<account_id>:user/newuser"
      username: newuser
      groups:
      - system:masters
kind: ConfigMap

> kubectl config view --minify
apiVersion: v1
clusters:
- cluster:
    certificate-authority-data: DATA+OMITTED
    server: https://0A418BB2CE053D6E26E86072C9B2BAFF.yl4.us-east-1.eks.amazonaws.com
  name: arn:aws:eks:us-east-1:836486484887:cluster/covalent-eks-cluster
contexts:
- context:
    cluster: arn:aws:eks:us-east-1:836486484887:cluster/covalent-eks-cluster
    user: arn:aws:eks:us-east-1:836486484887:cluster/covalent-eks-cluster
  name: arn:aws:eks:us-east-1:836486484887:cluster/covalent-eks-cluster
current-context: arn:aws:eks:us-east-1:836486484887:cluster/covalent-eks-cluster
kind: Config
preferences: {}
users:
- name: arn:aws:eks:us-east-1:836486484887:cluster/covalent-eks-cluster
  user:
    exec:
      apiVersion: client.authentication.k8s.io/v1alpha1
      args:
      - --region
      - us-east-1
      - eks
      - get-token
      - --cluster-name
      - covalent-eks-cluster
      command: aws
      env: null
      interactiveMode: IfAvailable
      provideClusterInfo: false

Cleanup

When you are done, delete the cluster:

make clean

Release Notes

Release notes are available in the Changelog.

Citation

Please use the following citation in any publications:

W. J. Cunningham, S. K. Radha, F. Hasan, J. Kanem, S. W. Neagle, and S. Sanand. Covalent. Zenodo, 2022. https://doi.org/10.5281/zenodo.5903364

License

Covalent is licensed under the GNU Affero GPL 3.0 License. Covalent may be distributed under other licenses upon request. See the LICENSE file or contact the support team for more details.