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DANDI JupyterHub

This repository spins up a Kubernetes cluster on AWS using ansible, boto and kops, and then uses the jupyterhub helm chart to deploy a JupyterHub instance in the cluster.

This project is deployed at Dandihub which a JupyterHub instance in the cloud that allows users to interact with the data stored in DANDI.

Usage

To use the hub, you will need to register for an account using the DANDI Web application (https://dandiarchive.org) using your GitHub account.

NOTE: Note that Dandihub is not intended for significant computation, but provides a place to introspect Dandisets and to perform some analysis and visualization of data.

Deployment

This information in this README is based on:

Note: The original MAST setup is now significantly outdated.

Follow the steps below to deploy DANDI JupyterHub.

Note: Be sure to perform all the operations in the same AWS zone that you will use in group_vars/all file. (US-east-2 Ohio)

  1. Create an https certificate for your domain using AWS cert manager. It's free to attach this certificate to load balancers, and JupyterHub also allows proxy offloading to this certificate.

  2. Create the GitHub OAuth App id/token: GitHub settings -> Developer settings -> Oauth Apps. We have done this via a bot GitHub user account (e.g. dandibot). You will need to set Homepage URL (e.g., https://hub.dandiarchive.org) and the Authorization callback URL (e.g. https://hub.dandiarchive.org/hub/oauth_callback). This can be set to a subdomain, just be sure to set this to the same value as ingress in group_vars/all and also set up the CNAME route via Route 53.

  3. Set up an AWS CI instance with these authorized roles (see this blog post for more details):

    • AmazonEC2FullAccess
    • AmazonSQSFullAccess
    • IAMFullAccess
    • AmazonS3FullAccess
    • AmazonVPCFullAccess
    • AmazonElasticFileSystemFullAccess
    • AmazonRoute53FullAccess
    • AmazonEventBridgeFullAccess

  4. Add the public dns name to the hosts file (This is an Ansible Inventory file.)

  5. SSH into the ec2 instance (using the pem key downloaded in previous step) and install git in the CI instance sudo yum install git -y

  6. Update the variables in group_vars/all

  7. Install ansible locally and create a password for ansible to encrypt some of the ansible variables:

    openssl rand -hex 32 > ansible_password

  8. Encrypt strings using ansible-vault

    ansible-vault encrypt_string --vault-password-file ansible_password

    This will prompt for input.

    • Paste the string to encrypt without a carriage return
    • Hit Ctrl-d twice
    • Copy the encrypted string into the relevant section of group_vars/all
    • NOTE: Use bash rather than a non-standard shell to prevent truncation.
Required vault values:
   - github_client_id (From GH OAuth app)
   - github_client_secret (From GH OAuth app)
   - aws_certificate_arn (From aws certificate manager)
   - dummypass (a string password you can use for testing without GitHub authentication
         by uncommenting the relevant dummypass options in `config.yaml.j2`)
   - danditoken (used to authenticate github users against registered dandi users)

1. Also note that `namespace` has to be unique across any JH
   instances created with this setup.

   1. Ensure `z2jh.yaml` uses the `ig-policy` in the file. (This
      is not necessary to change if there is already an instance of the
      policy in AWS. If you need to create `ig-policy` use the following:

           ```
           {
               "Version": "2012-10-17",
               "Statement": [
                   {
                       "Effect": "Allow",
                       "Action": [
                           "autoscaling:DescribeAutoScalingGroups",
                           "autoscaling:DescribeAutoScalingInstances",
                           "autoscaling:DescribeLaunchConfigurations",
                           "autoscaling:DescribeScalingActivities",
                           "autoscaling:DescribeTags",
                           "ec2:DescribeInstanceTypes",
                           "ec2:DescribeLaunchTemplateVersions"
                       ],
                       "Resource": ["*"]
                   },
                   {
                       "Effect": "Allow",
                       "Action": [
                           "autoscaling:SetDesiredCapacity",
                           "autoscaling:TerminateInstanceInAutoScalingGroup",
                           "ec2:DescribeImages",
                           "ec2:GetInstanceTypesFromInstanceRequirements",
                           "eks:DescribeNodegroup"
                       ],
                       "Resource": ["*"]
                   }
               ]
           }
           ```

  1. Run the playbook!

    ansible-playbook -i hosts z2jh.yml -v --vault-password-file ansible_password

  2. To tear down:

    ansible-playbook -i hosts teardown.yml -v --vault-password-file ansible_password -t all-fixtures

To remove kubernetes without removing shared EFS:

ansible-playbook -i hosts teardown.yml -v --vault-password-file ansible_password -t kubernetes

Pushing Changes to GitHub

  • Inside z2jh-aws-ansible, do rm -rf * and then git stash. This will restore the submodule to its pre-modification step.
  • Step outside, commit changes, and either push or send a PR to Dandihub.

Files

  • group_vars/all: ansible file contains variables for various templates
  • cluster-autoscaler-multi-asg.yaml.j2: k8s cluster autoscaler spec
  • config.yaml.j2: z2jh jupyterhub configuration
  • hosts: ansible provides IP of control host
  • nodes[1-3].yaml.j2: k8s node specs for on-demand nodes in multiple zones
  • pod.yaml.j2: k8s pod for introspecting shared storage
  • pv_efs.yaml.j2: k8s persistent volume spec for EFS
  • pvc_efs.yaml.j2: k8s persistent volume claim for EFS
  • spot-ig.yaml.j2: k8s non-GPU spec for compute nodes
  • spot-ig-gpu.yaml.j2: k8s GPU spec for compute nodes
  • storageclass.yaml.j2: k8s EFS storageclass
  • teardown.yml: ansible file for tearing down the cluster
  • z2jh.yml: ansible file for starting up the cluster

Resources