Open Infrastructure

h1. The ungleich kubernetes infrastructure and ungleich kubernetes manual

{{toc}}

h2. Status

This document is **pre-production**.

This document is to become the ungleich kubernetes infrastructure overview as well as the ungleich kubernetes manual.

h2. k8s clusters

| Cluster         | Purpose/Setup     | Maintainer   | Master(s)                                                | argo | rook | last verified |

| c0.k8s.ooo      | Dev               | -            | UNUSED                                                   |      |      |    2021-10-05 |

| c1.k8s.ooo      | Dev p6 VM         | Nico         | 2a0a-e5c0-2-11-0-62ff-fe0b-1a3d.k8s-1.place6.ungleich.ch |      |      |    2021-10-05 |

| c2.k8s.ooo      | Dev p7 HW         | Nico         | server47 server53 server54                               | x    | x    |    2021-10-05 |

| c3.k8s.ooo      | Test p7 PI        | -            | UNUSED                                                   |      |      |    2021-10-05 |

| c4.k8s.ooo      | Dev2 p7 HW        | Fran/Jin-Guk | server52 server53 server54                               |      |      |             - |

| c5.k8s.ooo      | Dev p6 VM Amal    | Nico/Amal    | 2a0a-e5c0-2-11-0-62ff-fe0b-1a46.k8s-1.place6.ungleich.ch |      |      |               |

| c6.k8s.ooo      | Dev p6 VM Jin-Guk | Jin-Guk      |                                                          |      |      |               |

| [[p6.k8s.ooo]]  | production        |              | server67 server69 server71                               | x    | x    |    2021-10-05 |

| [[p10.k8s.ooo]] | production        |              | server63 server65 server83                               | x    | x    |    2021-10-05 |

|                 |                   |              |                                                          |      |      |               |

h2. General architecture and components overview

* All k8s clusters are IPv6 only

* We use BGP peering to propagate podcidr and serviceCidr networks to our infrastructure

* The main public testing repository is "ungleich-k8s":https://code.ungleich.ch/ungleich-public/ungleich-k8s

** Private configurations are found in the **k8s-config** repository

h3. Cluster types

| **Type/Feature**            | **Development**                | **Production**         |

| Min No. nodes               | 3 (1 master, 3 worker)         | 5 (3 master, 3 worker) |

| Recommended minimum         | 4 (dedicated master, 3 worker) | 8 (3 master, 5 worker) |

| Separation of control plane | optional                       | recommended            |

| Persistent storage          | required                       | required               |

| Number of storage monitors  | 3                              | 5                      |

h2. General k8s operations

h3. Cheat sheet / external great references

* "kubectl cheatsheet":https://kubernetes.io/docs/reference/kubectl/cheatsheet/

h3. Get the cluster admin.conf

* On the masters of each cluster you can find the file @/etc/kubernetes/admin.conf@

* To be able to administrate the cluster you can copy the admin.conf to your local machine

* Multi cluster debugging can very easy if you name the config ~/cX-admin.conf (see example below)

<pre>

% scp root@server47.place7.ungleich.ch:/etc/kubernetes/admin.conf ~/c2-admin.conf

% export KUBECONFIG=~/c2-admin.conf    

% kubectl get nodes

NAME       STATUS                     ROLES                  AGE   VERSION

server47   Ready                      control-plane,master   82d   v1.22.0

server48   Ready                      control-plane,master   82d   v1.22.0

server49   Ready                      <none>                 82d   v1.22.0

server50   Ready                      <none>                 82d   v1.22.0

server59   Ready                      control-plane,master   82d   v1.22.0

server60   Ready,SchedulingDisabled   <none>                 82d   v1.22.0

server61   Ready                      <none>                 82d   v1.22.0

server62   Ready                      <none>                 82d   v1.22.0               

</pre>

h3. Installing a new k8s cluster

* Decide on the cluster name (usually *cX.k8s.ooo*), X counting upwards

** Using pXX.k8s.ooo for production clusters of placeXX

* Use cdist to configure the nodes with requirements like crio

* Decide between single or multi node control plane setups (see below)

** Single control plane suitable for development clusters

Typical init procedure:

* Single control plane: @kubeadm init --config bootstrap/XXX/kubeadm.yaml@

* Multi control plane (HA): @kubeadm init --config bootstrap/XXX/kubeadm.yaml --upload-certs@

h3. Deleting a pod that is hanging in terminating state

<pre>

kubectl delete pod <PODNAME> --grace-period=0 --force --namespace <NAMESPACE>

</pre>

(from https://stackoverflow.com/questions/35453792/pods-stuck-in-terminating-status)

h3. Listing nodes of a cluster

<pre>

[15:05] bridge:~% kubectl get nodes

NAME       STATUS   ROLES                  AGE   VERSION

server22   Ready    <none>                 52d   v1.22.0

server23   Ready    <none>                 52d   v1.22.2

server24   Ready    <none>                 52d   v1.22.0

server25   Ready    <none>                 52d   v1.22.0

server26   Ready    <none>                 52d   v1.22.0

server27   Ready    <none>                 52d   v1.22.0

server63   Ready    control-plane,master   52d   v1.22.0

server64   Ready    <none>                 52d   v1.22.0

server65   Ready    control-plane,master   52d   v1.22.0

server66   Ready    <none>                 52d   v1.22.0

server83   Ready    control-plane,master   52d   v1.22.0

server84   Ready    <none>                 52d   v1.22.0

server85   Ready    <none>                 52d   v1.22.0

server86   Ready    <none>                 52d   v1.22.0

</pre>

h3. Removing / draining a node

Usually @kubectl drain server@ should do the job, but sometimes we need to be more aggressive:

<pre>

kubectl drain --delete-emptydir-data --ignore-daemonsets server23

</pre>

h3. Readding a node after draining

<pre>

kubectl uncordon serverXX

</pre>

h3. (Re-)joining worker nodes after creating the cluster

* We need to have an up-to-date token

* We use different join commands for the workers and control plane nodes

Generating the join command on an existing control plane node:

<pre>

kubeadm token create --print-join-command

</pre>

h3. (Re-)joining control plane nodes after creating the cluster

* We generate the token again

* We upload the certificates

* We need to combine/create the join command for the control plane node

Example session:

<pre>

% kubeadm token create --print-join-command

kubeadm join p10-api.k8s.ooo:6443 --token xmff4i.ABC --discovery-token-ca-cert-hash sha256:longhash 

% kubeadm init phase upload-certs --upload-certs

[upload-certs] Storing the certificates in Secret "kubeadm-certs" in the "kube-system" Namespace

[upload-certs] Using certificate key:

CERTKEY

# Then we use these two outputs on the joining node:

kubeadm join p10-api.k8s.ooo:6443 --token xmff4i.ABC --discovery-token-ca-cert-hash sha256:longhash --control-plane --certificate-key CERTKEY

</pre>

Commands to be used on a control plane node:

<pre>

kubeadm token create --print-join-command

kubeadm init phase upload-certs --upload-certs

</pre>

Commands to be used on the joining node:

<pre>

JOINCOMMAND --control-plane --certificate-key CERTKEY

</pre>

SEE ALSO

* https://stackoverflow.com/questions/63936268/how-to-generate-kubeadm-token-for-secondary-control-plane-nodes

* https://blog.scottlowe.org/2019/08/15/reconstructing-the-join-command-for-kubeadm/

h3. How to fix etcd does not start when rejoining a kubernetes cluster as a control plane

If during the above step etcd does not come up, @kubeadm join@ can hang as follows:

<pre>

[control-plane] Creating static Pod manifest for "kube-apiserver"                                                              

[control-plane] Creating static Pod manifest for "kube-controller-manager"                                                     

[control-plane] Creating static Pod manifest for "kube-scheduler"                                                              

[check-etcd] Checking that the etcd cluster is healthy                                                                         

error execution phase check-etcd: etcd cluster is not healthy: failed to dial endpoint https://[2a0a:e5c0:10:1:225:b3ff:fe20:37

8a]:2379 with maintenance client: context deadline exceeded                                                                    

To see the stack trace of this error execute with --v=5 or higher         

</pre>

Then the problem is likely that the etcd server is still a member of the cluster. We first need to remove it from the etcd cluster and then the join works.

To fix this we do:

* Find a working etcd pod

* Find the etcd members / member list

* Remove the etcd member that we want to re-join the cluster

<pre>

# Find the etcd pods

kubectl -n kube-system get pods -l component=etcd,tier=control-plane

# Get the list of etcd servers with the member id 

kubectl exec -n kube-system -ti ETCDPODNAME -- etcdctl --endpoints '[::1]:2379' --cacert /etc/kubernetes/pki/etcd/ca.crt --cert  /etc/kubernetes/pki/etcd/server.crt --key /etc/kubernetes/pki/etcd/server.key member list

# Remove the member

kubectl exec -n kube-system -ti ETCDPODNAME -- etcdctl --endpoints '[::1]:2379' --cacert /etc/kubernetes/pki/etcd/ca.crt --cert  /etc/kubernetes/pki/etcd/server.crt --key /etc/kubernetes/pki/etcd/server.key member remove MEMBERID

</pre>

Sample session:

<pre>

[10:48] line:~% kubectl -n kube-system get pods -l component=etcd,tier=control-plane

NAME            READY   STATUS    RESTARTS     AGE

etcd-server63   1/1     Running   0            3m11s

etcd-server65   1/1     Running   3            7d2h

etcd-server83   1/1     Running   8 (6d ago)   7d2h

[10:48] line:~% kubectl exec -n kube-system -ti etcd-server65 -- etcdctl --endpoints '[::1]:2379' --cacert /etc/kubernetes/pki/etcd/ca.crt --cert  /etc/kubernetes/pki/etcd/server.crt --key /etc/kubernetes/pki/etcd/server.key member list

356891cd676df6e4, started, server65, https://[2a0a:e5c0:10:1:225:b3ff:fe20:375c]:2380, https://[2a0a:e5c0:10:1:225:b3ff:fe20:375c]:2379, false

371b8a07185dee7e, started, server63, https://[2a0a:e5c0:10:1:225:b3ff:fe20:378a]:2380, https://[2a0a:e5c0:10:1:225:b3ff:fe20:378a]:2379, false

5942bc58307f8af9, started, server83, https://[2a0a:e5c0:10:1:3e4a:92ff:fe79:bb98]:2380, https://[2a0a:e5c0:10:1:3e4a:92ff:fe79:bb98]:2379, false

[10:48] line:~% kubectl exec -n kube-system -ti etcd-server65 -- etcdctl --endpoints '[::1]:2379' --cacert /etc/kubernetes/pki/etcd/ca.crt --cert  /etc/kubernetes/pki/etcd/server.crt --key /etc/kubernetes/pki/etcd/server.key member remove 371b8a07185dee7e

Member 371b8a07185dee7e removed from cluster e3c0805f592a8f77

</pre>

SEE ALSO

* We found the solution using https://stackoverflow.com/questions/67921552/re-installed-node-cannot-join-kubernetes-cluster

h2. ArgoCD / ArgoFlow

h3. Argocd Installation

As there is no configuration management present yet, argocd is installed using

<pre>

kubectl create namespace argocd

kubectl apply -n argocd -f https://raw.githubusercontent.com/argoproj/argo-cd/stable/manifests/install.yaml

</pre>

* See https://argo-cd.readthedocs.io/en/stable/

h3. Get the argocd credentials

<pre>

kubectl -n argocd get secret argocd-initial-admin-secret -o jsonpath="{.data.password}" | base64 -d; echo ""

</pre>

h2. Helm related operations

We use helm charts extensively.

* In production, they are managed via argocd

* In development, helm chart can de developed and deployed manually using the helm utility.

h3. Installing a helm chart

One can use the usual pattern of

<pre>

helm install <releasename> <chartdirectory>

</pre>

However often you want to reinstall/update when testing helm charts. The following pattern is "better", because it allows you to reinstall, if it is already installed:

<pre>

helm upgrade --install <releasename> <chartdirectory>

</pre>

h2. Rook / Ceph Related Operations

h3. Inspecting the logs of a specific server

<pre>

# Get the related pods

kubectl -n rook-ceph get pods -l app=rook-ceph-osd-prepare 

...

# Inspect the logs of a specific pod

kubectl -n rook-ceph logs -f rook-ceph-osd-prepare-server23--1-444qx

</pre>

h3. Triggering server prepare / adding new osds

The rook-ceph-operator triggers/watches/creates pods to maintain hosts. To trigger a full "re scan", simply delete that pod:

<pre>

kubectl -n rook-ceph delete pods -l app=rook-ceph-operator

</pre>

This will cause all the @rook-ceph-osd-prepare-..@ jobs to be recreated and thus OSDs to be created, if new disks have been added.

h3. Removing an OSD

* See "Ceph OSD Management":https://rook.io/docs/rook/v1.7/ceph-osd-mgmt.html

h2. Infrastructure versions

h3. ungleich kubernetes infrastructure v5 (2021-10)

Clusters are configured / setup in this order:

* Bootstrap via kubeadm

* "Networking via calico + BGP (non ECMP) using helm":https://docs.projectcalico.org/getting-started/kubernetes/helm

* "ArgoCD for CD":https://argo-cd.readthedocs.io/en/stable/

** "rook for storage via argocd":https://rook.io/

** haproxy for in IPv6-cluster-IPv4-to-IPv6 proxy via argocd

** "kubernetes-secret-generator for in cluster secrets":https://github.com/mittwald/kubernetes-secret-generator

** "ungleich-certbot managing certs and nginx":https://hub.docker.com/repository/docker/ungleich/ungleich-certbot

h3. ungleich kubernetes infrastructure v4 (2021-09)

* rook is configured via manifests instead of using the rook-ceph-cluster helm chart

* The rook operator is still being installed via helm

h3. ungleich kubernetes infrastructure v3 (2021-07)

* rook is now installed via helm via argocd instead of directly via manifests

h3. ungleich kubernetes infrastructure v2 (2021-05)

* Replaced fluxv2 from ungleich k8s v1 with argocd

** argocd can apply helm templates directly without needing to go through Chart releases

* We are also using argoflow for build flows

* Planned to add "kaniko":https://github.com/GoogleContainerTools/kaniko for image building

h3. ungleich kubernetes infrastructure v1 (2021-01)

We are using the following components:

* "Calico as a CNI":https://www.projectcalico.org/ with BGP, IPv6 only, no encapsulation

** Needed for basic networking

* "kubernetes-secret-generator":https://github.com/mittwald/kubernetes-secret-generator for creating secrets

** Needed so that secrets are not stored in the git repository, but only in the cluster

* "ungleich-certbot":https://hub.docker.com/repository/docker/ungleich/ungleich-certbot

** Needed to get letsencrypt certificates for services

* "rook with ceph rbd + cephfs":https://rook.io/ for storage

** rbd for almost everything, *ReadWriteOnce*

** cephfs for smaller things, multi access *ReadWriteMany*

** Needed for providing persistent storage

* "flux v2":https://fluxcd.io/

** Needed to manage resources automatically