How to use TopoLVM with Rancher/RKE

This document is a brief introduction of how to use TopoLVM on Rancher/RKE.

Rancher/RKE will be deployed on the following 4 instances of Google Compute Engine (GCE).

Hostname	Machine Type	Role	Requirement
`rancher`	`n1-standard-2`	Rancher Server	Allow HTTP/HTTPS
`master`	`n1-standard-2`	Kubernetes Master
`worker1`	`n1-standard-2`	Kubernetes Worker	Mount 1 SSD
`worker2`	`n1-standard-2`	Kubernetes Worker	Mount 1 SSD

If the gcloud command is not installed on your PC, please refer to this document and install Google Cloud SDK beforehand.

1. Run Rancher Server

Create GCE instance

Create a GCE instance for Rancher Server. This document uses the asia-northeast1-c zone, but you can choose any other zone you want.

ZONE=asia-northeast1-c
gcloud compute instances create rancher \
  --zone ${ZONE} \
  --machine-type n1-standard-2 \
  --image-project ubuntu-os-cloud \
  --image-family ubuntu-1804-lts \
  --boot-disk-size 200GB

Then, allow HTTP/HTTPS with the following commands.

Go to VM instances on the GCE dashboard and open the configuration page of rancher
Click EDIT at the top of the page
Enable Allow HTTP traffic and Allow HTTPS traffic under Firewalls
Click Save at the bottom of the page

Install Docker

Run the installation script.

gcloud compute ssh --zone ${ZONE} rancher -- "curl -sSLf https://get.docker.com | sudo sh"

Start Rancher

gcloud compute ssh --zone ${ZONE} rancher -- "sudo docker run -d --restart=unless-stopped -p 80:80 -p 443:443 rancher/rancher:v2.3.4"

Go to the external IP address of rancher which appears on the GCE dashboard with your favorite browser.

For simplicity, TLS certification is not prepared in this example. So, just allow insecure access and proceed next.

2. Deploy Kubernetes cluster

Create GCE instances for Master & Worker Nodes

Create master, worker1 and worker2. worker1 and worker2 mounts SSD at /dev/nvme0 to provision TopoLVM volumes.

gcloud compute instances create master \
  --zone ${ZONE} \
  --machine-type n1-standard-2 \
  --image-project ubuntu-os-cloud \
  --image-family ubuntu-1804-lts \
  --boot-disk-size 200GB

gcloud compute instances create worker1 \
  --zone ${ZONE} \
  --machine-type n1-standard-2 \
  --local-ssd interface=nvme \
  --image-project ubuntu-os-cloud \
  --image-family ubuntu-1804-lts

gcloud compute instances create worker2 \
  --zone ${ZONE} \
  --machine-type n1-standard-2 \
  --local-ssd interface=nvme \
  --image-project ubuntu-os-cloud \
  --image-family ubuntu-1804-lts

Install Docker

Run the installation script.

gcloud compute ssh --zone ${ZONE} master -- "curl -sSLf https://get.docker.com | sudo sh"
gcloud compute ssh --zone ${ZONE} worker1 -- "curl -sSLf https://get.docker.com | sudo sh"
gcloud compute ssh --zone ${ZONE} worker2 -- "curl -sSLf https://get.docker.com | sudo sh"

Deploy Kubernetes components with Rancher

Go to the Rancher dashboard and click Add Cluster -> From existing nodes (Custom) to see the configuration page. Overwrite some default values as follows.

Cluster Name: Write your cluster name
Cluster Options:
- Kubernetes Version: v1.16.4-rancher1-1
- Node Options:
  - Master:
    - Check Control Plane and etcd
    - Run the commands which will be displyed on the screen
  - Worker:
    - Check Worker
    - Run the commands which will be displyed on the screen

After finishing the configuration, click Done and wait for the cluster status to become Active.

3. Deploy cert-manager

You can run the kubectl command by downloading Kubeconfig File from the top right of the cluster dashboard.

Then, deploy cert-manager on the Kubernetes cluster.

kubectl apply --validate=false -f https://github.com/jetstack/cert-manager/releases/download/v0.12.0/cert-manager.yaml

Add a label to Namespace resources for the TopoLVM webhook to avoid unnecessary validation.

kubectl label namespace kube-system topolvm.cybozu.com/webhook=ignore
kubectl label namespace cert-manager topolvm.cybozu.com/webhook=ignore

4. Install `lvmd`

Create VG (VolumeGroup) on worker1 and worker2.

gcloud compute ssh --zone ${ZONE} worker1 -- sudo vgcreate myvg1 /dev/nvme0n1
gcloud compute ssh --zone ${ZONE} worker2 -- sudo vgcreate myvg1 /dev/nvme0n1

Install lvmd on worker1 and worker2.

gcloud compute ssh --zone ${ZONE} worker1

# Install lvmd
TOPOLVM_VERSION=0.6.0
sudo mkdir -p /opt/sbin
curl -sSLf https://github.com/topolvm/topolvm/releases/download/v${TOPOLVM_VERSION}/lvmd-${TOPOLVM_VERSION}.tar.gz | sudo tar xzf - -C /opt/sbin

# Put configuration file
sudo mkdir -p /etc/topolvm
sudo curl -sSL -o /etc/topolvm/lvmd.yaml https://raw.githubusercontent.com/topolvm/topolvm/v${TOPOLVM_VERSION}/deploy/lvmd-config/lvmd.yaml

# Register service
sudo curl -sSL -o /etc/systemd/system/lvmd.service https://raw.githubusercontent.com/topolvm/topolvm/v${TOPOLVM_VERSION}/deploy/systemd/lvmd.service
sudo systemctl enable lvmd
sudo systemctl start lvmd
exit

gcloud compute ssh --zone ${ZONE} worker2

# Install lvmd
TOPOLVM_VERSION=0.6.0
sudo mkdir -p /opt/sbin
curl -sSLf https://github.com/topolvm/topolvm/releases/download/v${TOPOLVM_VERSION}/lvmd-${TOPOLVM_VERSION}.tar.gz | sudo tar xzf - -C /opt/sbin

# Put configuration file
sudo mkdir -p /etc/topolvm
sudo curl -sSL -o /etc/topolvm/lvmd.yaml https://raw.githubusercontent.com/topolvm/topolvm/v${TOPOLVM_VERSION}/deploy/lvmd-config/lvmd.yaml

# Register service
sudo curl -sSL -o /etc/systemd/system/lvmd.service https://raw.githubusercontent.com/topolvm/topolvm/v${TOPOLVM_VERSION}/deploy/systemd/lvmd.service
sudo systemctl enable lvmd
sudo systemctl start lvmd
exit

5. Deploy TopoLVM

Before deploying TopoLVM, install kustomize by following the link below. https://kubernetes-sigs.github.io/kustomize/installation/

TOPOLVM_VERSION=0.6.0
kustomize build https://github.com/topolvm/topolvm/deploy/manifests/overlays/daemonset-scheduler?ref=v${TOPOLVM_VERSION} | kubectl apply -f -
kubectl apply -f https://raw.githubusercontent.com/topolvm/topolvm/v${TOPOLVM_VERSION}/deploy/manifests/base/certificates.yaml

6. Configure `topolvm-scheduler`

Update `topolvm-scheduler` manifest

First, master has the following label and taint.

Label
1. node-role.kubernetes.io/controlplane=true
2. node-role.kubernetes.io/etcd=true
Taints
1. node-role.kubernetes.io/controlplane=true:NoSchedule
2. node-role.kubernetes.io/etcd=true:NoExecute

To locate topolvm-scheduler onto master, update node affinity and toleration.

$ kubectl edit daemonset topolvm-scheduler -n topolvm-system
# Edit as follows
 apiVersion: apps/v1
 kind: DaemonSet
...
 spec:
...
   template:
...
     spec:
       affinity:
         nodeAffinity:
           requiredDuringSchedulingIgnoredDuringExecution:
             nodeSelectorTerms:
             - matchExpressions:
-              - key: node-role.kubernetes.io/master
+              - key: node-role.kubernetes.io/controlplane
                 operator: Exists
...
       tolerations:
       - key: CriticalAddonsOnly
         operator: Exists
-      - effect: NoSchedule
-        key: node-role.kubernetes.io/master
+      - key: node-role.kubernetes.io/controlplane
+        operator: Exists
+      - key: node-role.kubernetes.io/etcd
+        operator: Exists
...

Adding the scheduler extender

Download the scheduler extender configuration files on the master instance.

They must be placed under /etc/kubernetes on master because kube-scheduler, deployed with Rancher, is configured to mount the directory.

gcloud compute ssh --zone ${ZONE} master

TOPOLVM_VERSION=0.6.0
sudo mkdir -p /etc/kubernetes/scheduler
sudo curl -sSL -o /etc/kubernetes/scheduler/scheduler-policy.cfg https://raw.githubusercontent.com/topolvm/topolvm/v${TOPOLVM_VERSION}/deploy/scheduler-config/scheduler-policy.cfg
sudo curl -sSL -o /etc/kubernetes/scheduler/scheduler-config.yaml https://raw.githubusercontent.com/topolvm/topolvm/v${TOPOLVM_VERSION}/docs/rancher/scheduler-config.yaml
exit

On the Rancher dashboard, click Edit and update Cluster Options with Edit as YAML to tell Kubernetes where the scheduler extension configuration is.

   services:
     ...
     kube-api:
       always_pull_images: false
       pod_security_policy: false
       service_node_port_range: 30000-32767
     kube-controller: {}
     kubelet:
       fail_swap_on: false
       generate_serving_certificate: false
     kubeproxy: {}
# Add extra_args
-    scheduler: {}
+    scheduler:
+      extra_args:
+        config: /etc/kubernetes/scheduler/scheduler-config.yaml
   ssh_agent_auth: false

Then click Save to finish the configuration.

7. Provision volume with TopoLVM

Congratulations!! You finally deployed TopoLVM on RKE.

To confirm TopoLVM is working, create PVC and mount it on a Pod.

kubectl apply -f - << EOF
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
  name: topolvm-pvc
spec:
  accessModes:
  - ReadWriteOnce
  resources:
    requests:
      storage: 1Gi
  storageClassName: topolvm-provisioner
---
apiVersion: v1
kind: Pod
metadata:
  name: my-pod
  labels:
    app.kubernetes.io/name: my-pod
spec:
  containers:
  - name: ubuntu
    image: quay.io/cybozu/ubuntu:18.04
    command: ["/usr/local/bin/pause"]
    volumeMounts:
    - mountPath: /test1
      name: my-volume
  volumes:
    - name: my-volume
      persistentVolumeClaim:
        claimName: topolvm-pvc
EOF

8. Cleanup

Do not forget to delete GCE instances.

gcloud --quiet compute instances delete rancher --zone ${ZONE}
gcloud --quiet compute instances delete master --zone ${ZONE}
gcloud --quiet compute instances delete worker1 --zone ${ZONE}
gcloud --quiet compute instances delete worker2 --zone ${ZONE}

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How to use TopoLVM with Rancher/RKE

1. Run Rancher Server

Create GCE instance

Install Docker

Start Rancher

2. Deploy Kubernetes cluster

Create GCE instances for Master & Worker Nodes

Install Docker

Deploy Kubernetes components with Rancher

3. Deploy cert-manager

4. Install `lvmd`

5. Deploy TopoLVM

6. Configure `topolvm-scheduler`

Update `topolvm-scheduler` manifest

Adding the scheduler extender

7. Provision volume with TopoLVM

8. Cleanup

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How to use TopoLVM with Rancher/RKE

1. Run Rancher Server

Create GCE instance

Install Docker

Start Rancher

2. Deploy Kubernetes cluster

Create GCE instances for Master & Worker Nodes

Install Docker

Deploy Kubernetes components with Rancher

3. Deploy cert-manager

4. Install lvmd

5. Deploy TopoLVM

6. Configure topolvm-scheduler

Update topolvm-scheduler manifest

Adding the scheduler extender

7. Provision volume with TopoLVM

8. Cleanup

4. Install `lvmd`

6. Configure `topolvm-scheduler`

Update `topolvm-scheduler` manifest