DANDI JupyterHub

Dandihub provides a JupyterHub instance in the cloud to interact with the data stored in DANDI.

To use the hub, you will need to register for an account using the DANDI Web application. 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.

This information in this README is based on:

• this blog post and this corresponding repo
• this blog post on autoscaling and spot pricing

Note: The original MAST setup is now significantly outdated.

Deployment

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 step 5 in the group_vars/all file.

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).

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

   and then:

   • add the public dns name to the hosts file
   • install git in the CI instance

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

   openssl rand -hex 32 > ansible_password

   This is used to encrypt some of the values, such as GitHub tokens or the AWS certificate ID, using the following form:

   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

   Do this for:

   • client id
   • secret
   • certificate ARN (Amazon Resource Name)
   • dummy password (this is a string password you can use for testing without GitHub authentication)

5. Update the variables and some yaml files.

   Specifically, this involves:

   • group_vars/all
   • config.yaml.j2

   For the latter, this may involve adjusting authentication steps and profiles.

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

6. Create policy ig-policy and copy this ARN below:

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

Update z2jh.yaml to reflect the new policy ARN. Search for ig-policy in the file.

7. Startup and teardown.

To start up:

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

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

Description of 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

• To learn how to interact with the DANDI archive and for examples on how to use the DANDI Client in various use cases, see the handbook.

• To get help:

  • ask a question: https://github.com/dandi/helpdesk/discussions
  • file a feature request or bug report: https://github.com/dandi/helpdesk/issues/new/choose
  • contact the DANDI team: [email protected]