OSBv2

An updated version of the Open Source Brain platform

Deploy

Prerequisites

The OSB deployment is built on top of CloudHarness. The deployment process is based on Python 3.7+ scripts. It is recommended to setup a virtual environment first.

With conda:

conda create --name osb python=3.7
conda activate osb

To install CloudHarness:

git clone https://github.com/MetaCell/cloud-harness.git
cd cloud-harness
pip install -r requirements.txt

Create deployment

CloudHarness scripts script automate the deployment process.

To update the Codefresh deployment, run:

harness-codefresh .

To manually create the helm chart to use on any Kubernetes deployment, run:

harness-deployment cloud-harness .

Cluster setup

The cert-manager must be installed in order to use letsencrypt generated certificates

To check if cert-manager is installed, run:

kubectl get pods -n cert-manager

If cert manager is installed, the command will return 3 lines.

To install the cert manager on a new cluster, run:

kubectl apply --validate=false -f https://github.com/jetstack/cert-manager/releases/download/v0.15.1/cert-manager-legacy.yaml

Install and upgrade with Helm

Create the namespace kubectl create ns osb2
Create the namespace kubectl create ns argo-workflows
Run helm install osb2 deployment/helm --namespace osb2 to install.
Run kubectl create rolebinding osb-admin-default --clusterrole=admin --serviceaccount=osb2:default -n osb2 to allow workflows to run on namespace osb2

To upgrade an existing deployment, use:

helm upgrade osb2 deployment/helm --namespace osb2 --install --reset-values [--force]

Install Argo (temporary)

Argo is not yet part of the helm chart (issue https://github.com/MetaCell/mnp/issues/31)

In order to install it in the cluster, run

kubectl create ns argo
kubectl apply -n argo -f https://raw.githubusercontent.com/argoproj/argo/v2.4.3/manifests/install.yaml
kubectl create rolebinding argo-workflows-default --clusterrole=admin --serviceaccount=argo-workflows:default -n argo-workflows
kubectl create rolebinding argo-workflows --clusterrole=admin --serviceaccount=argo-workflows:argo-workflows -n argo-workflows

Development setup

Minikube is recommended to setup locally. The procedure is different depending on where Minikube is installed. The simplest procedure is with Minikube hosted in the same machine where running the commands.

Initialize Minikube cluster

At least 6GB of ram and 4 processors are needed to run MNP

To create a new cluster, run

minikube start --memory="6000mb" --cpus=4 --disk-size=60000mb

Enable the ingress addon:

minikube addons enable ingress

Minikube on the host machine

Connect your docker registry with minikube with: eval $(minikube docker-env)

Then run:

harness-deployment cloud-harness . -l -b -d osb.local

Minikube on a different machine

With the registry on localhost:5000 run:

harness-deployment cloud-harness . -l -r localhost:5000 -b -d osb.local

See below to learn how to configure Minikube and forward the registry.

Setup kubectl

If Minikube is installed in a different machine, the following procedure will allow to connect kubectl.

Install kubectl in the client machine
copy ~/.minikube from the client to the server (skip cache and machines)
Copy ~/.kube/config from the Minikube server to the client machine (make a backup of the previous version) and adjust paths to match the home folder on the client machine

Kube configuration copy

If you don't want to replace the whole content of the configuration you can copy only the relevant entries in ~/.kube/config from the server to the client on clusters, context

Examples:

On clusters

- cluster:
    certificate-authority: /home/user/.minikube/ca.crt
    server: https://192.168.99.106:8443
  name: minikube

On context

- context:
    cluster: minikube
    user: minikube
  name: minikube

On users

- name: minikube
  user:
    client-certificate: /home/user/.minikube/client.crt
    client-key: /home/user/.minikube/client.key

Set default context:

current-context: minikube

Set up the Docker registry

In the case we are not building from the same machine as the cluster (which will always happen without Minikube), we need a way to share the registry.

Procedure to share localhost:5000 from a kube cluster

In the minikube installation:

minikube addons enable registry

In the machine running the infrastructure-generate script, run

kubectl port-forward --namespace kube-system $(kubectl get po -n kube-system --field-selector=status.phase=Running | grep registry | grep -v proxy | \awk '{print $1;}') 5000:5000

sanjayankur31 / OSBv2