Production environment

This section is an overview of the repositories, projects, and systems used in a mybinder.org production deployment.

Reference: Google SRE book section on Production Environment

Repository structure

This repository contains a ‘meta chart’ (mybinder) that fully captures the state of the deployment on mybinder.org. Since it is a full helm chart, you can read the official helm chart structure document to know more about its structure.

Dependent charts

The core of the meta-chart pattern is to install a bunch of dependent charts, specified in mybinder/Chart.yaml. This contains both support charts like nginx-ingress, grafana, prometheus, but also the core application chart binderhub. Everything is version pinned here.

Configuration values

The following files fully capture the state of the deployment for staging:

1. mybinder/values.yaml - Common configuration values between prod & staging

2. secret/config/staging.yaml - Secret values specific to the staging deployment

3. config/staging.yaml - Non-secret values specific to the staging deployment

The following files fully capture the state of the production deployment:

1. mybinder/values.yaml - Common configuration values between prod & staging

2. secret/config/prod.yaml - Secret values specific to the production deployment

3. config/prod.yaml - Non-secret values specific to the production deployment

Important: For maintainability and consistency, we try to keep the contents of staging.yaml and prod.yaml super minimal - they should be as close to each other as possible. We want all common config in values.yaml so testing on staging gives us confidence it will work on prod. We also never share the same secrets between staging & prod for security boundary reasons.

Deployment nodes and pools

The staging cluster has one node pool, which makes things simple. The production cluster has two, one for “core” pods (the hub, etc.) and another dedicated to “user” pods (builds and user servers). This strategy helps protect our key services from potential issues caused by users and helps us drain user nodes when we need to.

Since ~only user pods should be running on the user nodes, cordoning that node should result in it being drained and reclaimed after the max-pod-age lifetime limit which often wouldn’t happen without manual intervention.

It is still not quite true that only user pods are running on the user nodes at this point. There can be some pods such as heapster and kube-dns that may run on user nodes, and need to be manually removed from the pod after cordoning before the autoscaler will allow culling.

In the future, when we implement a pod packing strategy and node taints, nodes could get reclaimed truly automatically without any intervention, but we are not there yet.

Users and core pods are assigned to their pools via a nodeSelector in config/prod.yaml. We use a custom label mybinder.org/node-purpose = core | user to select which node a pod should run on.

mybinder.org specific extra software

We sometimes want to run additional software for the mybinder deployment that does not already have a chart, or would be too cumbersome to use with a chart. For those cases, we can create kubernetes objects directly from the mybinder meta chart. You can see an example of this under mybinder/templates/redirector that is used to set up a simple nginx based HTTP redirector.

Related repositories

Related repositories used by the mybinder.org service are:

1. binderhub

   This contains the binderhub code (UI & hub management) & helm chart. To change the UI / UX or hub management aspects of mybinder.org, go to binderhub.

2. repo2docker

   This is used to do the actual building of git repositories into docker images, and can be used standalone too. If you want to change how a git repository is converted into a docker image to be run for the user, go to repo2docker.

The Deployment Helm Meta Chart

BinderHub is deployed using a Kubernetes Helm Chart, which is a specification for instructing Kubernetes how to deploy particular applications. Sometimes, applications depend on others in order to function properly, similar to how a package might depend on other packages (e.g., Pandas depends on Numpy). These dependencies are specified with a Helm “Meta Chart”.

For example, let’s say that you’d like to begin using Prometheus in your Kubernetes deployment. Since Prometheus has a helm chart for deploying it on Kubernetes, we can add it as a dependency in a Helm Meta Chart. We’d create a section called dependencies in mybinder/Chart.yaml and put the following in it:

dependencies:
  - name: prometheus
    version: 11.16.9
    repository: https://prometheus-community.github.io/helm-charts

This also allows us to pin a version of Prometheus, which improves reliability of the site.

Note

It is still possible to deploy each of these applications on their own without a Meta Helm Chart, this is simply a way of clustering dependencies together and simplifying the deployment structure.

Another benefit of Meta Charts is that you can use a single configuration file (config.yaml) with multiple Helm Charts. For example, look at the BinderHub Helm Chart. Note that there are multiple top-level sections (e.g., for jupyterhub and for prometheus) and that each section has a corresponding entry in the Helm Meta Chart. In this way, we can provide configuration for each dependency of BinderHub without needing a separate file for each, and we can deploy them all at the same time.

HTTPS configuration for mybinder.org

Using HTTPS requires having a signed certificate. BinderHub uses kube-lego, a tool that obtains and deploys a free Let’s Encrypt certificate automatically. This section describes how to use kube-lego to configure and deploy HTTPS support.

kube-lego provides 90 day SSL certificates for mybinder.org through the letsencrypt service. As the 90 day cycle nears its end, kube-lego will automatically request a new certificate and configure the kubernetes deployment to use it.

kube-lego is a kubernetes application, with its own Helm Chart that is referenced in the mybinder.org Meta Chart. This tells kubernetes which account to use for letsencrypt certification.

Once we have a letsencrypt account set up, we need to attach the SSL certificate to a particular ingress object. This is a Kubernetes object that controls how traffic is routed into the deployment. This is also done with the mybinder.org Helm Chart (see here for example).

Note that letsencrypt will send you an email if your SSL certificate is about to expire. If you get such an email, it might mean that the automatic kube-lego renewal process hasn’t worked properly. To debug this, we recommend running the standard Kubernetes debugging commands with the kube-lego object used with your deployment. For example:

kubectl --namespace=<my-namespace> logs <kube-lego-object>

Exceptions on the OVH cluster

On the OVH cluster all the binder components use a specific certificate on *.mybinder.ovh domain.

Traffic for ovh.mybinder.org is redirected with a CNAME on binder.mybinder.ovh. That’s why the OVH cluster should be able to serve 2 different certificates.

• The *.mybinder.ovh certificate is managed by ingresses in the ovh helm configuration.

• The ovh.mybinder.org certificate is managed by a specific ingress and kube-lego on the launch of deploy.py on the ovh stack.

Secrets

Since we use this repo for deployment, it needs credentials for things like our google cloud account, and secret tokens for our helm charts. Since this is a public repo, we don’t want these credentials to be readable in public! To solve this, we use git-crypt to store encrypted versions of files that should be kept secret. These files are in the secrets folder. git-crypt uses a shared secret to encrypt and decrypt files. For automated deployments, Travis has access to the git-crypt secret in an encrypted environment variable. If you don’t need to edit the secret files, then you don’t need the git-crypt secret, or to see the contents of the secret files. When you clone, you will just have the opaque, encrypted files. If you need access to view or edit the encrypted files, you will need the git-crypt secret. See below for a procedure to share the secret. Once you have unlocked the repo with git-crypt, you will be able to view and edit the encrypted files as if they were any other file. git- crypt handles the encryption and decryption transparently via git filters.

Sharing secrets

Sharing secrets is tricky! There is a handy tool called ssh-vault which allows you to securely share information via a mechanism we all have available here: ssh public keys on GitHub!

To securely share the git-crypt key, both parties should have git-crypt and ssh-vault. On mac, these are both available from homebrew:

brew install git-crypt ssh-vault

To encrypt the key with ssh-vault, pipe the key file through ssh-vault create. Assuming you are in a mybinder.org-deploy directory that is already setup with git-crypt:

[sender] $ cat .git/git-crypt/keys/default | ssh-vault -u receiver create

where receiver is the recipient’s GitHub username, e.g. willing or choldgraf.

The result should look something like this:

SSH-VAULT;AES256;30:40:9b:bd:16:26:f6:d2:1d:85:7a:dc:63:c9:e6:ae
LRCe3CrLL/isMhYVvA5gxZFCLCNyz64EepesTyKYklcMqUBZ1DML1rIXe4KBSudG
D9rbKP1PILGVaTHU2D2aSNJQUGNt3q+e3G8f5gpPJHvZeM9+mXKW4I3C8HfjU4sD
EKsm38ShYRAAtO5uTOToSd6j2vdakwEyO2YT7w2PTXiOL0VVeti7i9u+ENv1sxrg
oyAcN7tYA8Q/k3+zRy6ISJD8uEa/s9Igf99V0o7ocPpjON4oGsaLShuA8w0d3D+Y
kk0f1iBZ1k/0QoqPTL8JXjLh9Ba6o8TH6vi8rkZlmBrjDEg5cVlko/HadSnskQ/0
gW5CHn6XP0pIex59V9Tpiw==;dPQUIVgskPrYec3QqRqCrUkoRq1Ig5yOHihQJaS
EoTGNMwI=

The sender can deliver this encrypted copy to the receiver, via less secure transport mechanism, such as a gitter private message, SMS, email, etc.

The receiver can now decrypt the message with ssh-vault and use it to unlock the mybinder.org-deploy repo. Assuming the shared message has been saved to a file encrypted-key:

[receiver] $ cat encrypted-key | ssh-vault view | git-crypt unlock -
# remove the encrypted temporary file
[receiver] $ rm encrypted-key

If your ssh key requries a passphrase then the above might not work. Below is a method that works, but creates an intermediate file containing the human-readable text. Make sure this file is secure and not discoverable by others! If you have ssh-vault >= v0.12.4 you can run the following:

ssh-vault -o clear-git-crypt-key view encrypted-key
git-crypt unlock clear-git-crypt-key
rm clear-git-crypt-key

This solves the problem that ssh-vault prints the passphrase prompt to standard out as well as the decrypted key. Make sure to delete clear-git-crypt-key, which contains the clear text git-crypt key.

On a mac, you can use pbcopy and pbpaste to use the clipboard instead of creating files:

[sender] $ cat .git/git-crypt/keys/default | ssh-vault -u receiver create | pbcopy
# the encrypted message is in sender's clipboard
# deliver it to the receiver, and once it is in their clipboard:
[receiver] $ pbpaste | ssh-vault view | git-crypt unlock -

Who has the keys?

People who currently have the git-crypt secret include:

• @minrk at GitHub

• @yuvipanda at GitHub

• @choldgraf at GitHub

• @mael-le-gal at GitHub

• @sgibson91 at GitHub

• @bitnik at GitHub

• @arnim at GitHub

• @MridulS at GitHub

• @callummole at GitHub

• @rgaiacs at GitHub

• @consideRatio at GitHub

• add yourself here if you have it

Contact one of them if you need access to the git-crypt key.