Template for deploying k3s backed by Flux

Template for deploying a single k3s cluster with k3sup backed by Flux and SOPS.

The purpose here is to showcase how you can deploy an entire Kubernetes cluster and show it off to the world using the GitOps tool Flux. When completed, your Git repository will be driving the state of your Kubernetes cluster. In addition with the help of the Flux SOPS integration you'll be able to commit GPG encrypted secrets to your public repo.

Overview

👋 Introduction

The following components will be installed in your k3s cluster by default. They are only included to get a minimum viable cluster up and running. You are free to add / remove components to your liking but anything outside the scope of the below components are not supported by this template.

Feel free to read up on any of these technologies before you get started to be more familiar with them.

flannel
local-path-provisioner
flux
metallb
cert-manager with Cloudflare DNS challenge
ingress-nginx
homer
system-upgrade-controller

📝 Prerequisites

💻 Nodes

Already provisioned Bare metal or VMs with any modern operating system like Ubuntu, Debian or CentOS.

🔧 Tools

📍 You need to install the required CLI tools listed below on your workstation.

Tool	Purpose	Minimum version	Required
k3sup	Tool to install k3s on your nodes	`0.10.2`	✅
kubectl	Allows you to run commands against Kubernetes clusters	`1.21.0`	✅
flux	Operator that manages your k8s cluster based on your Git repository	`0.12.3`	✅
SOPS	Encrypts k8s secrets with GnuPG	`3.7.1`	✅
GnuPG	Encrypts and signs your data	`2.2.27`	✅
pinentry	Allows GnuPG to read passphrases and PIN numbers	`1.1.1`	✅
direnv	Exports env vars based on present working directory	`2.28.0`	❌
pre-commit	Runs checks during `git commit`	`2.12.0`	❌
kustomize	Template-free way to customize application configuration	`4.1.0`	❌
helm	Manage Kubernetes applications	`3.5.4`	❌

⚠️ pre-commit

It is advisable to install pre-commit and the pre-commit hooks that come with this repository. sops-pre-commit will check to make sure you are not by accident commiting your secrets un-encrypted.

After pre-commit is installed on your machine run:

pre-commit install-hooks

📂 Repository structure

The Git repository contains the following directories under cluster and are ordered below by how Flux will apply them.

base directory is the entrypoint to Flux
crds directory contains custom resource definitions (CRDs) that need to exist globally in your cluster before anything else exists
core directory (depends on crds) are important infrastructure applications (grouped by namespace) that should never be pruned by Flux
apps directory (depends on core) is where your common applications (grouped by namespace) could be placed, Flux will prune resources here if they are not tracked by Git anymore

cluster
├── apps
│   ├── default
│   ├── networking
│   └── system-upgrade
├── base
│   └── flux-system
├── core
│   ├── cert-manager
│   ├── metallb-system
│   ├── namespaces
│   └── system-upgrade
└── crds
    └── cert-manager

🚀 Lets go!

Very first step will be to create a new repository by clicking the Use this template button on this page.

📍 In these instructions you will be exporting several environment variables to your current shell env. Make sure you stay with in your current shell to not lose any exported variables.

📍 All of the below commands are run on your local workstation, not on any of your cluster nodes.

🔐 Setting up GnuPG keys

📍 Here we will create a personal and a Flux GPG key. Using SOPS with GnuPG allows us to encrypt and decrypt secrets.

Create a Personal GPG Key, password protected, and export the fingerprint. It's strongly encouraged to back up this key somewhere safe so you don't lose it.

export GPG_TTY=$(tty)
export PERSONAL_KEY_NAME="First name Last name (location) <email>"

gpg --batch --full-generate-key <<EOF
Key-Type: 1
Key-Length: 4096
Subkey-Type: 1
Subkey-Length: 4096
Expire-Date: 0
Name-Real: ${PERSONAL_KEY_NAME}
EOF

gpg --list-secret-keys "${PERSONAL_KEY_NAME}"
# pub   rsa4096 2021-03-11 [SC]
#       772154FFF783DE317KLCA0EC77149AC618D75581
# uid           [ultimate] k8s@home (Macbook) <k8s-at-home@gmail.com>
# sub   rsa4096 2021-03-11 [E]

export PERSONAL_KEY_FP=772154FFF783DE317KLCA0EC77149AC618D75581

Create a Flux GPG Key and export the fingerprint

export GPG_TTY=$(tty)
export FLUX_KEY_NAME="Cluster name (Flux) <email>"

gpg --batch --full-generate-key <<EOF
%no-protection
Key-Type: 1
Key-Length: 4096
Subkey-Type: 1
Subkey-Length: 4096
Expire-Date: 0
Name-Real: ${FLUX_KEY_NAME}
EOF

gpg --list-secret-keys "${FLUX_KEY_NAME}"
# pub   rsa4096 2021-03-11 [SC]
#       AB675CE4CC64251G3S9AE1DAA88ARRTY2C009E2D
# uid           [ultimate] Home cluster (Flux) <k8s-at-home@gmail.com>
# sub   rsa4096 2021-03-11 [E]

export FLUX_KEY_FP=AB675CE4CC64251G3S9AE1DAA88ARRTY2C009E2D

⛵ Installing k3s with k3sup

📍 Here we will be install k3s with k3sup. After completion, k3sup will drop a kubeconfig in your present working directory for use with interacting with your cluster with kubectl.

Ensure you are able to SSH into you nodes with using your private ssh key. This is how k3sup is able to connect to your remote node.
Install the master node

k3sup install \
    --host=node01.cluster.elcarpenter.com \
    --user=carpenam \
    --k3s-version=v1.21.5+k3s2 \
    --cluster \
    --k3s-extra-args="--disable servicelb --disable traefik --flannel-backend='none' --kubelet-arg='feature-gates=MixedProtocolLBService=true,GracefulNodeShutdown=true'"

Join other master nodes

k3sup join \
    --host=node01.cluster.elcarpenter.com \
    --server-host=node03.cluster.elcarpenter.com \
    --k3s-version=v1.21.8+k3s2 \
    --user=carpenam \
    --server \
    --k3s-extra-args="--disable servicelb --disable traefik --flannel-backend='none' --kubelet-arg='feature-gates=MixedProtocolLBService=true,GracefulNodeShutdown=true'"

Join other worker nodes

k3sup join \
    --host=node00.cluster.elcarpenter.com \
    --server-host=node03.cluster.elcarpenter.com \
    --k3s-version=v1.21.8+k3s2 \
    --user=carpenam

Verify the nodes are online

kubectl --kubeconfig=./kubeconfig get nodes
# NAME           STATUS   ROLES                       AGE     VERSION
# k8s-master-a   Ready    control-plane,master      4d20h   v1.20.5+k3s1
# k8s-worker-a   Ready    worker                    4d20h   v1.20.5+k3s1

Bootstrap Calico if this is a new cluster
Add udev rules for USB Devices
Disable hardware offloading for e1000e driver

sudo ethtool -K eno1 tso off gso off

Add udev rules For ??? USB Stick (Zigbee & ZWave)

SUBSYSTEM=="tty", ATTRS{idVendor}=="10c4", ATTRS{idProduct}=="8a2a", ATTRS{serial}=="813004F4", ENV{ID_USB_INTERFACE_NUM}=="00", SYMLINK+="zwave"
SUBSYSTEM=="tty", ATTRS{idVendor}=="10c4", ATTRS{idProduct}=="8a2a", ATTRS{serial}=="813004F4", ENV{ID_USB_INTERFACE_NUM}=="01", SYMLINK+="zigbee"

For Conbee

SUBSYSTEM=="tty", ATTRS{idVendor}=="1cf1", ATTRS{idProduct}=="0030", ATTRS{serial}=="DE2119158", SYMLINK+="conbee"

USB NIC Netplan Example

sudo nano /etc/netplan/10-usb-nic.yaml

network:
  ethernets:
    enx1:
      match:
        name: enx3*
      set-name: enx1
      addresses:
      - 10.10.200.69/24
      gateway4: 10.10.200.1
      nameservers:
        addresses:
        - 10.10.200.1
        - 1.1.1.1
        search:
        - cluster.FQDN
  version: 2

Modify /etc/sysctl.conf

net.ipv4.ip_forward=1
net.ipv6.conf.all.forwarding=1

net.ipv6.conf.all.disable_ipv6=1
net.ipv6.conf.default.disable_ipv6=1
net.ipv6.conf.lo.disable_ipv6=1

fs.inotify.max_user_watches = 5242880
fs.inotify.max_user_instances = 5120

☁️ Cloudflare API Token

📍 You may skip this step, however make sure to export dummy data on item 8 in the below list.

...Be aware you will not have a valid SSL cert until cert-manager is configured correctly

In order to use cert-manager with the Cloudflare DNS challenge you will need to create a API token.

Head over to Cloudflare and create a API token by going here.
Click the blue Create Token button
Scroll down and create a Custom Token by choosing Get started
Give your token a name like cert-manager
Under Permissions give Edit access to Zone : Zone and Zone : DNS
Under Zone Resources set it to Include : All Zones
Click Continue to summary and then Create Token
Export this token and your Cloudflare email address to an environment variable on your system to be used in the following steps

export BOOTSTRAP_CLOUDFLARE_EMAIL="k8s-at-home@gmail.com"
export BOOTSTRAP_CLOUDFLARE_TOKEN="kpG6iyg3FS_du_8KRShdFuwfbwu3zMltbvmJV6cD"

🔹 GitOps with Flux

📍 Here we will be installing flux after some quick bootstrap steps.

Verify Flux can be installed

flux --kubeconfig=./kubeconfig check --pre
# ► checking prerequisites
# ✔ kubectl 1.21.0 >=1.18.0-0
# ✔ Kubernetes 1.20.5+k3s1 >=1.16.0-0
# ✔ prerequisites checks passed

Pre-create the flux-system namespace

kubectl --kubeconfig=./kubeconfig create namespace flux-system --dry-run=client -o yaml | kubectl --kubeconfig=./kubeconfig apply -f -

Add the Flux GPG key in-order for Flux to decrypt SOPS secrets

gpg --export-secret-keys --armor "${FLUX_KEY_FP}" |
kubectl --kubeconfig=./kubeconfig create secret generic sops-gpg \
    --namespace=flux-system \
    --from-file=sops.asc=/dev/stdin

Export more environment variables for application configuration

# The repo you created from this template
export BOOTSTRAP_GITHUB_REPOSITORY="https://github.com/k8s-at-home/home-cluster"
# Choose one of your domains or use a made up one
export BOOTSTRAP_DOMAIN="k8s-at-home.com"
# Pick a range of unused IPs that are on the same network as your nodes
export BOOTSTRAP_METALLB_LB_RANGE="169.254.1.10-169.254.1.20"
# The load balancer IP for ingress-nginx, choose from one of the available IPs above
export BOOTSTRAP_INGRESS_NGINX_LB="169.254.1.10"

Create required files based on ALL exported environment variables.

envsubst < ./tmpl/.sops.yaml > ./.sops.yaml
envsubst < ./tmpl/cluster-secrets.yaml > ./cluster/base/cluster-secrets.yaml
envsubst < ./tmpl/cluster-settings.yaml > ./cluster/base/cluster-settings.yaml
envsubst < ./tmpl/gotk-sync.yaml > ./cluster/base/flux-system/gotk-sync.yaml
envsubst < ./tmpl/secret.enc.yaml > ./cluster/core/cert-manager/secret.enc.yaml

Verify all the above files have the correct information present
Encrypt cluster/cluster-secrets.yaml and cert-manager/secret.enc.yaml with SOPS

export GPG_TTY=$(tty)
sops --encrypt --in-place ./cluster/base/cluster-secrets.yaml
sops --encrypt --in-place ./cluster/core/cert-manager/secret.enc.yaml

📍 Variables defined in cluster-secrets.yaml and cluster-settings.yaml will be usable anywhere in your YAML manifests under ./cluster

Verify all the above files are encrypted with SOPS
Push you changes to git

git add -A
git commit -m "initial commit"
git push

Install Flux

📍 Due to race conditions with the Flux CRDs you will have to run the below command twice. There should be no errors on this second run.

kubectl --kubeconfig=./kubeconfig apply --kustomize=./cluster/base/flux-system
# namespace/flux-system configured
# customresourcedefinition.apiextensions.k8s.io/alerts.notification.toolkit.fluxcd.io created
# customresourcedefinition.apiextensions.k8s.io/buckets.source.toolkit.fluxcd.io created
# customresourcedefinition.apiextensions.k8s.io/gitrepositories.source.toolkit.fluxcd.io created
# customresourcedefinition.apiextensions.k8s.io/helmcharts.source.toolkit.fluxcd.io created
# customresourcedefinition.apiextensions.k8s.io/helmreleases.helm.toolkit.fluxcd.io created
# customresourcedefinition.apiextensions.k8s.io/helmrepositories.source.toolkit.fluxcd.io created
# customresourcedefinition.apiextensions.k8s.io/kustomizations.kustomize.toolkit.fluxcd.io created
# customresourcedefinition.apiextensions.k8s.io/providers.notification.toolkit.fluxcd.io created
# customresourcedefinition.apiextensions.k8s.io/receivers.notification.toolkit.fluxcd.io created
# serviceaccount/helm-controller created
# serviceaccount/kustomize-controller created
# serviceaccount/notification-controller created
# serviceaccount/source-controller created
# clusterrole.rbac.authorization.k8s.io/crd-controller-flux-system created
# clusterrolebinding.rbac.authorization.k8s.io/cluster-reconciler-flux-system created
# clusterrolebinding.rbac.authorization.k8s.io/crd-controller-flux-system created
# service/notification-controller created
# service/source-controller created
# service/webhook-receiver created
# deployment.apps/helm-controller created
# deployment.apps/kustomize-controller created
# deployment.apps/notification-controller created
# deployment.apps/source-controller created
# unable to recognize "./cluster/base/flux-system": no matches for kind "Kustomization" in version "kustomize.toolkit.fluxcd.io/v1beta1"
# unable to recognize "./cluster/base/flux-system": no matches for kind "GitRepository" in version "source.toolkit.fluxcd.io/v1beta1"
# unable to recognize "./cluster/base/flux-system": no matches for kind "HelmRepository" in version "source.toolkit.fluxcd.io/v1beta1"
# unable to recognize "./cluster/base/flux-system": no matches for kind "HelmRepository" in version "source.toolkit.fluxcd.io/v1beta1"
# unable to recognize "./cluster/base/flux-system": no matches for kind "HelmRepository" in version "source.toolkit.fluxcd.io/v1beta1"
# unable to recognize "./cluster/base/flux-system": no matches for kind "HelmRepository" in version "source.toolkit.fluxcd.io/v1beta1"

🎉 Congratulations you have a Kubernetes cluster managed by Flux, your Git repository is driving the state of your cluster.

📣 Post installation

Verify Flux

kubectl --kubeconfig=./kubeconfig get pods -n flux-system
# NAME                                       READY   STATUS    RESTARTS   AGE
# helm-controller-5bbd94c75-89sb4            1/1     Running   0          1h
# kustomize-controller-7b67b6b77d-nqc67      1/1     Running   0          1h
# notification-controller-7c46575844-k4bvr   1/1     Running   0          1h
# source-controller-7d6875bcb4-zqw9f         1/1     Running   0          1h

Verify ingress

If your cluster is not accessible to outside world you can update your hosts file to verify the ingress controller is working.

echo "${BOOTSTRAP_INGRESS_NGINX_LB} ${BOOTSTRAP_DOMAIN} homer.${BOOTSTRAP_DOMAIN}" | sudo tee -a /etc/hosts

Head over to your browser and you should be able to access https://homer.${BOOTSTRAP_DOMAIN}

direnv

This is a great tool to export environment variables depending on what your present working directory is, head over to their installation guide and don't forget to hook it into your shell!

When this is done you no longer have to use --kubeconfig=./kubeconfig in your kubectl, flux or helm commands.

VSCode SOPS extension

VSCode SOPS is a neat little plugin for those using VSCode. It will automatically decrypt you SOPS secrets when you click on the file in the editor and encrypt them when you save and exit the file.

👉 Debugging

Manually sync Flux with your Git repository

flux --kubeconfig=./kubeconfig reconcile source git flux-system
# ► annotating GitRepository flux-system in flux-system namespace
# ✔ GitRepository annotated
# ◎ waiting for GitRepository reconciliation
# ✔ GitRepository reconciliation completed
# ✔ fetched revision main/943e4126e74b273ff603aedab89beb7e36be4998

Show the health of you kustomizations

kubectl --kubeconfig=./kubeconfig get kustomization -A
# NAMESPACE     NAME          READY   STATUS                                                             AGE
# flux-system   apps          True    Applied revision: main/943e4126e74b273ff603aedab89beb7e36be4998    3d19h
# flux-system   core          True    Applied revision: main/943e4126e74b273ff603aedab89beb7e36be4998    4d6h
# flux-system   crds          True    Applied revision: main/943e4126e74b273ff603aedab89beb7e36be4998    4d6h
# flux-system   flux-system   True    Applied revision: main/943e4126e74b273ff603aedab89beb7e36be4998    4d6h

Show the health of your main Flux GitRepository

flux --kubeconfig=./kubeconfig get sources git
# NAME           READY	MESSAGE                                                            REVISION                                         SUSPENDED
# flux-system    True 	Fetched revision: main/943e4126e74b273ff603aedab89beb7e36be4998    main/943e4126e74b273ff603aedab89beb7e36be4998    False

Show the health of your HelmReleases

flux --kubeconfig=./kubeconfig get helmrelease -A
# NAMESPACE   	    NAME                  	READY	MESSAGE                         	REVISION	SUSPENDED
# cert-manager	    cert-manager          	True 	Release reconciliation succeeded	v1.3.0  	False
# default        	homer                 	True 	Release reconciliation succeeded	4.2.0   	False
# networking  	    ingress-nginx       	True 	Release reconciliation succeeded	3.29.0  	False

Show the health of your HelmRepositorys

flux --kubeconfig=./kubeconfig get sources helm -A
# NAMESPACE  	NAME                 READY	MESSAGE                                                   	REVISION                                	SUSPENDED
# flux-system	bitnami-charts       True 	Fetched revision: 0ec3a3335ff991c45735866feb1c0830c4ed85cf	0ec3a3335ff991c45735866feb1c0830c4ed85cf	False
# flux-system	ingress-nginx-charts True 	Fetched revision: 45669a3117fc93acc09a00e9fb9b4445e8990722	45669a3117fc93acc09a00e9fb9b4445e8990722	False
# flux-system	jetstack-charts      True 	Fetched revision: 7bad937cc82a012c9ee7d7a472d7bd66b48dc471	7bad937cc82a012c9ee7d7a472d7bd66b48dc471	False
# flux-system	k8s-at-home-charts   True 	Fetched revision: 1b24af9c5a1e3da91618d597f58f46a57c70dc13	1b24af9c5a1e3da91618d597f58f46a57c70dc13	False

Flux has a wide range of CLI options available be sure to run flux --help to view more!

🤖 Automation

Renovate is a very useful tool that when configured will start to create PRs in your Github repository when Docker images, Helm charts or anything else that can be tracked has a newer version. The configuration for renovate is located here.
system-upgrade-controller will watch for new k3s releases and upgrade your nodes when new releases are found.

There's also a couple Github workflows included in this repository that will help automate some processes.

Flux upgrade schedule - workflow to upgrade Flux.
Renovate schedule - workflow to annotate HelmRelease's which allows Renovate to track Helm chart versions.

❔ What's next

The world is your cluster, try installing another application or if you have a NAS and want storage back by that check out the helm charts for democratic-csi, csi-driver-nfs or nfs-subdir-external-provisioner.

If you plan on exposing your ingress to the world from your home. Checkout our rough guide to run a k8s CronJob to update DDNS.

🤝 Thanks

Big shout out to all the authors and contributors to the projects that we are using in this repository.

dcplaya/k8s-at-home