Flux2 GitOps on Kubernetes

Manage Kubernetes Clusters with GitOps

The purpose of creating this repository is to use Flux GitOps to manage Kubernetes clusters. It includes everything required to deploy into a Kubernetes cluster, such as infrastructure's helm releases, application's manifests.

Tools Used for This Repo

Kubernetes Cluster = AKS/Kubeadm provisioned Kubernetes cluster on Azure.
Flux = Bootstrap and orchestrate the deployments.
Mozilla SOPA = SOPA encrypts Kubernetes secrets with OpenPGP to store secrets safely in a public or private Git repository.

Prerequisites

Kubernetes cluster
Kubectl installed
FluxCD installed, refer to FluxCD Installation
A Git repository with a personal token auth.
Mozilla SOPS installed, refer to Manage Kubernetes secrets with Mozilla SOPS

Repository Structure

This repository uses monorepo approach to store all Kubernetes manifests in a single Git repository. The structure is organized in this way.

|── clusters
|   ├── production
|   └── staging
|── infra
|   ├── base 
|   ├── production
|   └── staging
|── system
|   ├── base 
|   ├── production
|   └── staging
|── apps
|   ├── base 
|   ├── production
|   └── staging
|── 3rd
|   ├── base 
|   ├── production
|   └── staging

Top level

clusters directory has Flux bootstrap configuration per cluster (production/staging)
infra directory has platform level Kubernetes manifests related to storage, monitoring and ingress controller, currrently it has Prometheus, Memcached, Ingress Nginx, Cert-Manager, CSI driver and Velero.
system directory has system level Kubernetes manifests including, Linkerd, Istio, Jaeger, Redis, Postgres, Loki,Flagger and Chaos Mesh etc.
apps directory has application related manifests
3rd directory has 3rd application related manifests and it is used to kustomize configuration

The separation between infra, system, apps and 3rd makes it possible to define the order in which a cluster is reconciled, infra should keep untouched, system depends on infra, both apps and 3rd depend on system.

Under infra, system, apps and 3rd directories,

base directory serves as the base layer for staging and production environments. Each sub-directory under base has the Kubernetes manifests for an application with common configurations.
staging and production directories maps to staging and production environments, they are overlay layers of base, each sub-directory under them has customized configurations for same application under base directory.

How It Works

Flux enables application deployment (CD) through automatic reconciliation with pull-based mode.

Flux applies manifests stored at Git repository. It leverages kustomize for fetching, decrypting, building, validating and applying manifests.

Use podinfo for example.

apps/base/podinfo, it contains base Kubernetes manifests for podinfo application, including Namespace, Deployment, HorizontalPodAutoscaler, Service and Ingress.
apps/staging/podinfo creates an overlay on top of apps/base/podinfo, it merges resources from apps/base/podinfo, then customizes Ingress object with specific FQDN, encrypts it by using sops then writes output into ingress.enc.yaml. When Flux reconciles resources, ingress.enc.yaml is decrypted automatically and gets deployed along with other resources.

It is common that one Flux resource relies on another Flux resource, for example, one HelmRelease relies on the presence of a Custom Resource Definition installed by another HelmRelease, to those kind of dependency management, Flux provides below support

spec.dependsOn, available from Kustomization and HelmRelease, spec.dependsOn can only apply to same kind of resource, for example Kustomization depends on ``Kustomization`
spec.healthChecks, support cross resource dependency, for example, Kustomization can use spec.healthChecks to wait until HelmRelease is ready.

Sample case

apiVersion: kustomize.toolkit.fluxcd.io/v1beta2
kind: Kustomization
metadata:
  name: system
  namespace: flux-system
spec:
  interval: 10m0s
  # Kustomization depends on another Kustomization resource
  dependsOn:
    - name: infra
  # Kustomization depends on HelmRelease
  healthChecks:
  - apiVersion: helm.toolkit.fluxcd.io/v2beta1
    kind: HelmRelease
    name: prometheus
    namespace: monitoring
  - apiVersion: helm.toolkit.fluxcd.io/v2beta1
    kind: HelmRelease
    name: ingress-nginx
    namespace: ingress-nginx
  sourceRef:
    kind: GitRepository
    name: flux-system
  path: ./system/staging
  prune: true

NOTEs

Flux Installation

Follow this guide to install Flux.

Common steps to bootstrap Flux.

# https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-personal-access-token
export GITHUB_TOKEN=PERSONAL_ACCESS_TOKEN
# personal or organization account
export GITHUB_USER=ACCOUNT

# if account is organization, remove --personal
flux bootstrap github \
  --components-extra=image-reflector-controller,image-automation-controller \
  --owner=$GITHUB_USER \
  --repository=<YOUR_REPO> \
  --branch=main \
  --path=./clusters/staging \
  --read-write-key \
  --personal

Flux bootstrap doesn't care where the Git repository is, if the repository location is changed (e.g., transfer ownership to another organization), the only thing needs to do is re-run bootstrap and point --owner to new user/organization.

During bootstrap, Flux creates a secret named flux-system at flux-system namespace, it is used to read/write Git repository, for example, if Git repository provider is github, this secret is actually a github repository deploy key. This secret can be updated by deleting it and re-run bootstrap, this trick is useful when automate image update, as default bootstrap creates deploy key with read permission, automate image update requires write permission to commit changes, to do that, run kubectl -n flux-system delete secret flux-system and re-run bootstrap.

Flux Upgrade

Follow this guide to upgrade Flux.

Brief steps are listed in below

Run flux check --pre will tell you if a newer Flux version is available.
Run curl -s https://fluxcd.io/install.sh | sudo bash to install the updated flux cli

Run below commands to update Flux components

git clone https://<git-host>/<org>/<bootstrap-repo>
cd <bootstrap-repo>
flux install --components-extra image-reflector-controller,image-automation-controller --export > ./clusters/staging/flux-system/gotk-components.yaml
git add -A && git commit -m "Update $(flux -v) on staging"
git push

Wait for Flux to detect the changes or, tell it to do the upgrade immediately with:
```
flux reconcile ks flux-system --with-source
```

Manage Secrets and Sensitive Information

Flux natively supports Mozilla SOPS to encrypted files. To store Kubernetes secret safely or protect sensitive information over a public/private Git repository, here are common steps to Manage Kubernetes secrets with Mozilla SOPS

Install gnupg and SOPS
Generate a GPG key
Retrieve the GPG key fingerprint

Export the public and private keypair from your local GPG keyring and create a Kubernetes secret named sops-gpg in the flux-system namespace

gpg --export-secret-keys --armor GPG_KEY_FINGERPRINT |
kubectl create secret generic sops-gpg \
--namespace=flux-system \
--from-file=sops.asc=/dev/stdin

Update Kustomization resource files to decrypt secrets with SOPS

apiVersion: kustomize.toolkit.fluxcd.io/v1beta2
kind: Kustomization
metadata:
  name: apps
  namespace: flux-system
spec:
  # ...
  # SOPS decryption 
  decryption:
    provider: sops
    secretRef:
      name: sops-gpg

Under directory where Kubernetes manifests contain secret/sensitive data, create a file named .sops.yaml and add below content

creation_rules:
  - path_regex: .*.yaml
    encrypted_regex: ^(FIELD_TO_ENCRYPT_1|...|FIELD_TO_ENCRYPT_N)$
    pgp: GPG_KEY_FINGERPRINT

To protect from committing original file accidently, add a .gitignore file in same directory then add original file's name into it
Use command sops -e --input-type=yaml --output-type=yaml filename.yaml > filename.enc.yaml to encrypt the file
Start to reference filename.enc.yaml in other Kubernetes resource files

As a best practice, consider of exporting the public key to the repository so that other team members can use the same public key to encrypt the new files.

gpg --export --armor "${KEY_FP}" > ./clusters/staging/.sops.pub.asc

Check into the git

git add ./clusters/staging/.sops.pub.asc
git commit -am 'Share GPG public key for secrets generation'

Restore encryption and decryption key

sudo wget -qO /usr/local/bin/yq https://github.com/mikefarah/yq/releases/latest/download/yq_linux_amd64
sudo chmod a+x /usr/local/bin/yq
gpg --import ./clusters/staging/.sops.pub.asc
kubectl get secret sops-gpg -n flux-system -o yaml | yq -r '.data."sops.asc"' | base64 -d > .sops.asc
gpg --import .sops.asc

Pin Specific Version in GitOps

There are a few good reasons you may want to pin a specific version in GitOps:

Reproducibility - Pinning specific versions (e.g. tags, commits) ensures you can redeploy the exact same app version repeatedly. This is great for testing or diagnosing issues with a specific build.
Stability - You may want to pin a known good, stable version of an app to a production environment. This prevents unexpected changes or regressions from syncing.
Compliance - In regulated environments like healthcare, you often need to lock down specific approved versions of an application. Pinning versions can satisfy compliance requirements.
Rollbacks - If a bad version is deployed, you can easily rollback by pointing the GitOps config back to a previous good version.
Promotions - You can promote versions through environments by updating the pinned version as you move from dev to staging to production.
Testing - Pinning versions allows you to safely test specific builds in lower environments without impacting production.
Independent environments - Pinning uniques versions lets you isolate environments and prevent bad changes from spreading across dev, staging, prod. So in summary, version pinning gives you control, stability and reproducibilty. It's a best practice for using GitOps to manage a change management workflow across environments.

The repo includes a sample of pinning a specific version, refer to postgres sample system/base/postgres and system/staging/postgres for details, in staging, we pinned postgres version to a specific version number 12.5.2, this is done through adding a patch section into kustomization.yaml

patches:
  - path: release.yaml
    target:
      kind: HelmRelease

Webhook Receivers

Flux can be configured to receive changes in Git and trigger a cluster reconciliation every time a source changes. To expose the webhook receiver endpoint, we can create an Ingress

When use cert-manager to request certificate for Ingress used by Webhook Receivers, certificate request won't be succeeded, cert-manager and ingress controller will keep reporting 504 error, below is sample log from cert-manager

E1208 06:37:38.717038 1 sync.go:190] cert-manager/challenges "msg"="propagation check failed" "error"="wrong status code '504', expected '200'" "dnsName"="flux-webhook.example.com" "resource_kind"="Challenge" "resource_name"="flux-webhook-tls-vmb44-803982081-2270031681" "resource_namespace"="flux-system" "resource_version"="v1" "type"="HTTP-01"

This is because network policy created at flux-system namespace allow-webhooks during flux bootstrap, only allows inbound traffic to pod with label app=notification-controller, when cert-manager notices an ingress object is created at flux-system namespace, it creates a pod named with cm-acme-http-solver-xxxxx in same namespace, as there is no network policy to allow inbound traffic to this pod, HTTP01 challenges fails. To work around this issue, consider of adding a new network policy to allow inbound HTTP01 challenges, below is an example

# Filename allow-acme-solver.yaml
apiVersion: networking.k8s.io/v1
kind: NetworkPolicy
metadata:
  name: allow-acme-solver
spec:
  ingress:
  - from:
    - namespaceSelector: {}
  podSelector:
    matchLabels:
      acme.cert-manager.io/http01-solver: "true"
  policyTypes:
  - Ingress

Automate Image Updates to Git

This article Automate image updates to Git provides detailed steps to configure image update, when creates ImageUpdateAutomation to write image update to Git repository, a few things need to take care

All three resources ImageRepository, ImagePolicy and ImageUpdateAutomation must be in same namespace, this is because currently ImageUpdateAutomation will only list ImagePolicy in same namespace.
Point path field to the manifest directory where the update is going to write. For example, GitRepository might point to ./cluster/staging, but the deployment.yaml file is at ./apps/staging/echo-mirror, the path field should set to ./apps/staging/echo-mirror.
Add namespace under sourceRef if GitRepository resource is created at different namespace. For example, GitRepository flux-system is created at flux-system namespace, while ImageUpdateAutomation echo-mirror is created at echo-mirror namespace, a namespace field has to be added so ImageUpdateAutomation can find GitRepository correctly.

Below is an example

apiVersion: image.toolkit.fluxcd.io/v1beta1
kind: ImageUpdateAutomation
metadata:
  name: echo
spec:
  interval: 1m0s
  sourceRef:
    kind: GitRepository
    name: flux-system
    # Reference GitRepository namespace 
    namespace: flux-system 
  git:
    checkout:
      ref:
        branch: main
    commit:
      author:
        email: fluxcdbot@users.noreply.github.com
        name: fluxcdbot
      messageTemplate: '{{range .Updated.Images}}{{println .}}{{end}}'
    push:
      branch: main
  update:
    # Point to manifest directory
    path: ./apps/staging/echo-mirror 
    strategy: Setters

Prometheus Monitoring

ETCD, Kube Controller Manager and Kube Scheduler Monitoring

From community issue

From kubernetes master node, updating etcd.yaml in /etc/kubernetes/manifests/ to use the --listen-metrics-urls=http://0.0.0.0:2381 for ETCD.

From kubernetes master node, updating kube-controller-manager.yaml and kube-scheduler.yaml in /etc/kubernetes/manifests/ to use the --bind-address 0.0.0.0 for both the scheduler and the controller manager.

Restart pods

kubectl delete pod -l component=etcd -n kube-system
kubectl delete pod -l component=kube-controller-manager -n kube-system
kubectl delete pod -l component=kube-scheduler -n kube-system

Above steps will relaunch the the pods with the correct bind address, but these settings will not survive a kubeadm upgrade.

In order to persist the settings, the kubeadm-config configmap in the kube-system namespace should also be edited to include the following:

kubectl edit cm kubeadm-config -n kube-system

    controllerManager:
      extraArgs:
        bind-address: 0.0.0.0
    scheduler:
      extraArgs:
        bind-address: 0.0.0.0
    etcd:
      local:
        extraArgs:
          listen-metrics-urls: http://0.0.0.0:2381

Kube Proxy Monitoring

kubectl edit cm/kube-proxy -n kube-system

...
kind: KubeProxyConfiguration
## Change from
## metricsBindAddress: 127.0.0.1:10249
## Change to
metricsBindAddress: 0.0.0.0:10249
...

kubectl delete pod -l k8s-app=kube-proxy -n kube-system

Prometheus Alerting Rules

Awesome Prometheus Alerts

Grafana Dashboards

kube-prometheus-stack helm chart includes a collection of Grafana dashboards, besides of those default dashboards, here is a list of used Grafana dashboards in this repository

NGINX Ingress controller (https://raw.githubusercontent.com/kubernetes/ingress-nginx/main/deploy/grafana/dashboards/nginx.json) Request Handling Performance

Redis, requires Redis Grafana Plugin to be installed

Memcached

PostgreSQL

Grafana Loki Dashboard for NGINX Service Mesh

Velero Backup

# Start the sample nginx app
kubectl apply -f https://raw.githubusercontent.com/vmware-tanzu/velero/main/examples/nginx-app/with-pv.yaml
# Create a backup
velero backup create nginx-backup --include-namespaces nginx-example
# Verify backup is completed
velero backup describe nginx-backup
# Simulate a disaster
kubectl delete namespaces nginx-example
# Restore your lost resources
velero restore create --from-backup nginx-backup
# Delete backup
velero backup delete nginx-backup
# Delete sample ngix app again
kubectl delete namespaces nginx-example

Workload Identity

# environment variables for issuer configuration
export SUBSCRIPTION_ID=<REPLACE_ME>
export AZURE_STORAGE_ACCOUNT=<REPLACE ME>
export AZURE_STORAGE_CONTAINER=<REPLACE ME>
export RESOURCE_GROUP="AZWI"
export LOCATION="eastus"

# setup public OIDC issuer URL using Azure blob storage and upload a minimal discovery document to the storage account.
az group create --name "${RESOURCE_GROUP}" --location "${LOCATION}"
az storage account create --resource-group "${RESOURCE_GROUP}" --name "${AZURE_STORAGE_ACCOUNT}"
az storage container create --name "${AZURE_STORAGE_CONTAINER}" --public-access container

cat <<EOF > openid-configuration.json
{
  "issuer": "https://${AZURE_STORAGE_ACCOUNT}.blob.core.windows.net/${AZURE_STORAGE_CONTAINER}/",
  "jwks_uri": "https://${AZURE_STORAGE_ACCOUNT}.blob.core.windows.net/${AZURE_STORAGE_CONTAINER}/openid/v1/jwks",
  "response_types_supported": [
    "id_token"
  ],
  "subject_types_supported": [
    "public"
  ],
  "id_token_signing_alg_values_supported": [
    "RS256"
  ]
}
EOF

az storage blob upload \
  --container-name "${AZURE_STORAGE_CONTAINER}" \
  --account-name "${AZURE_STORAGE_ACCOUNT}" \
  --file openid-configuration.json \
  --name .well-known/openid-configuration

azwi jwks --public-keys /etc/kubernetes/pki/sa.pub --output-file jwks.json

az storage blob upload \
  --container-name "${AZURE_STORAGE_CONTAINER}" \
  --account-name "${AZURE_STORAGE_ACCOUNT}" \
  --file jwks.json \  
  --name openid/v1/jwks

export SERVICE_ACCOUNT_ISSUER=https://$AZURE_STORAGE_ACCOUNT.blob.core.windows.net/$AZURE_STORAGE_CONTINERAINER

sed -i "s#service-account-issuer=https://kubernetes.default.svc.cluster.local#service-account-issuer=$SERVICE_ACCOUNT_ISSUER#g" /etc/kubernetes/manifests/kube-apiserver.yaml


# install workload-identity-webhook helm chart
export AZURE_TENANT_ID="$(az account show -s "${SUBSCRIPTION_ID}" --query tenantId -o tsv)"
helm install workload-identity-webhook azure-workload-identity/workload-identity-webhook \ 
   --namespace azure-workload-identity-system \
   --set azureTenantID="${AZURE_TENANT_ID}"

# environment variables for the Azure Key Vault resource
export KEYVAULT_NAME="azwi-kv-eus"
export KEYVAULT_SECRET_NAME="azwi-secret"
export USER_ASSIGNED_IDENTITY_NAME="azwi-k8sea"
export SERVICE_ACCOUNT_NAMESPACE="azwi"
export SERVICE_ACCOUNT_NAME="workload-identity-sa"

az keyvault create --resource-group "${RESOURCE_GROUP}" \
   --location "${LOCATION}" \        
   --name "${KEYVAULT_NAME}"

az keyvault secret set --vault-name "${KEYVAULT_NAME}" \
   --name "${KEYVAULT_SECRET_NAME}" \
   --value "Hello\!"

az identity create --name "${USER_ASSIGNED_IDENTITY_NAME}" --resource-group "${RESOURCE_GROUP}"  --location "${LOCATION}"

export USER_ASSIGNED_IDENTITY_CLIENT_ID="$(az identity show --name "${USER_ASSIGNED_IDENTITY_NAME}" --resource-group "${RESOURCE_GROUP}" --query 'clientId' -o tsv)"

az keyvault set-policy --name "${KEYVAULT_NAME}" \
  --secret-permissions get \
  --spn "${USER_ASSIGNED_IDENTITY_CLIENT_ID}"

kubectl create ns $SERVICE_ACCOUNT_NAMESPACE

cat <<EOF | kubectl apply -f -
apiVersion: v1
kind: ServiceAccount
metadata:
  annotations:
    azure.workload.identity/client-id: ${APPLICATION_CLIENT_ID:-$USER_ASSIGNED_IDENTITY_CLIENT_ID}
  labels:
    azure.workload.identity/use: "true"
  name: ${SERVICE_ACCOUNT_NAME}
  namespace: ${SERVICE_ACCOUNT_NAMESPACE}
EOF

az identity federated-credential create \
  --name "k8sea-federated-credential" \
  --identity-name "${USER_ASSIGNED_IDENTITY_NAME}" \
  --resource-group "${RESOURCE_GROUP}" \
  --issuer "${SERVICE_ACCOUNT_ISSUER}" \
  --subject "system:serviceaccount:${SERVICE_ACCOUNT_NAMESPACE}:${SERVICE_ACCOUNT_NAME}"

export KEYVAULT_URL="$(az keyvault show -g ${RESOURCE_GROUP} -n ${KEYVAULT_NAME} --query properties.vaultUri -o tsv)"

cat <<EOF | kubectl apply -f -
apiVersion: v1
kind: Pod
metadata:
  name: azwi
  namespace: ${SERVICE_ACCOUNT_NAMESPACE}
  labels:
    azure.workload.identity/use: "true"
spec:
  serviceAccountName: ${SERVICE_ACCOUNT_NAME}
  containers:
    - image: ghcr.io/azure/azure-workload-identity/msal-go
      name: oidc
      env:
      - name: KEYVAULT_URL
        value: ${KEYVAULT_URL}
      - name: SECRET_NAME
        value: ${KEYVAULT_SECRET_NAME}
  nodeSelector:
    kubernetes.io/os: linux
EOF

# clean up
kubectl delete -n "${SERVICE_ACCOUNT_NAMESPACE}"
az group delete --name "${RESOURCE_GROUP}"

{
  "alg": "RS256",
  "kid": "xnML5UVEOmaXhc6C961EArSm86kIdXfjTisuL2q6JV0"
}.{
  "aud": [
    "https://k8sea.blob.core.windows.net/oidc"
  ],
  "exp": 1702294296,
  "iat": 1670758296,
  "iss": "https://k8sea.blob.core.windows.net/oidc",
  "kubernetes.io": {
    "namespace": "azwi",
    "pod": {
      "name": "azwi",
      "uid": "72ed5f47-e3a0-48a4-94dc-ea955b765097"
    },
    "serviceaccount": {
      "name": "workload-identity-sa",
      "uid": "a410f479-480a-4a6f-aa31-0fd0ec78b6af"
    },
    "warnafter": 1670761903
  },
  "nbf": 1670758296,
  "sub": "system:serviceaccount:azwi:workload-identity-sa"
}.[Signature]

Troubleshooting

Fix "upgrade retries exhausted"

If seeing below errors flux get helmreleases -A NAMESPACE NAME REVISION SUSPENDED READY MESSAGE

dapr-system                   	dapr                     	1.10.7  	False    	False  	upgrade retries exhausted

Try using those commands to fix the issue

flux suspend hr <helmreleae name> -n <namespace>
flux resume hr <helmreleae name> -n <namespace>

Helm upgrade failed: another operation (install/upgrade/rollback) is in progress

If seeing below errors when running flux get helmreleases -A

<helm release>                       	<namespace>                  	        	False    	False	Helm upgrade failed: another operation (install/upgrade/rollback) is in progress

The issue is documented at this link

A quick solution to solve this issue will be

Remove the helmrelease from kustomization.yaml
Add the helmrelease back to kustomization.yaml

Forcefully delete namespace

When a Helm release is deleted from Flux, the associated namespace can get stuck in a terminating state indefinitely due to dependency issues, preventing the namespace from being fully cleaned up. This can cause the Kustomization deployment to remain in an unsuccessful state. To resolve this, forcefully delete the stuck namespace with the following script

kubectl proxy --port=8001 &

NAMESPACE=
kubectl get ns $NAMESPACE -o json | \
  jq '.spec.finalizers=[]' | \
  curl -X PUT http://localhost:8001/api/v1/namespaces/$NAMESPACE/finalize -H "Content-Type: application/json" --data @-

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README.md

README.md

Flux2 GitOps on Kubernetes

Manage Kubernetes Clusters with GitOps

Tools Used for This Repo

Prerequisites

Repository Structure

How It Works

NOTEs

Flux Installation

Flux Upgrade

Manage Secrets and Sensitive Information

Pin Specific Version in GitOps

Webhook Receivers

Automate Image Updates to Git

Prometheus Monitoring

ETCD, Kube Controller Manager and Kube Scheduler Monitoring

Kube Proxy Monitoring

Prometheus Alerting Rules

Grafana Dashboards

Velero Backup

Workload Identity

Troubleshooting

Fix "upgrade retries exhausted"

Helm upgrade failed: another operation (install/upgrade/rollback) is in progress

Forcefully delete namespace

Files

README.md

Latest commit

History

README.md

File metadata and controls

Flux2 GitOps on Kubernetes

Manage Kubernetes Clusters with GitOps

Tools Used for This Repo

Prerequisites

Repository Structure

How It Works

NOTEs

Flux Installation

Flux Upgrade

Manage Secrets and Sensitive Information

Pin Specific Version in GitOps

Webhook Receivers

Automate Image Updates to Git

Prometheus Monitoring

ETCD, Kube Controller Manager and Kube Scheduler Monitoring

Kube Proxy Monitoring

Prometheus Alerting Rules

Grafana Dashboards

Velero Backup

Workload Identity

Troubleshooting

Fix "upgrade retries exhausted"

Helm upgrade failed: another operation (install/upgrade/rollback) is in progress

Forcefully delete namespace