The ungleich kubernetes infrastructure » History » Revision 106
Revision 105 (Nico Schottelius, 06/02/2022 05:46 AM) → Revision 106/219 (Nico Schottelius, 06/14/2022 05:08 PM)
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 | v4 http proxy | last verified | | c0.k8s.ooo | Dev | - | UNUSED | | | 2021-10-05 | | c1.k8s.ooo | retired | | - | | | 2022-03-15 | | c2.k8s.ooo | Dev p7 HW | Nico | server47 server53 server54 | "argo":https://argocd-server.argocd.svc.c2.k8s.ooo | | 2021-10-05 | | c3.k8s.ooo | retired | - | - | | | 2021-10-05 | | c4.k8s.ooo | Dev2 p7 HW | Jin-Guk | server52 server53 server54 | | | - | | c5.k8s.ooo | retired | | - | | | 2022-03-15 | | c6.k8s.ooo | Dev p6 VM Jin-Guk | Jin-Guk | | | | | | [[p5.k8s.ooo]] | production | | server34 server36 server38 | "argo":https://argocd-server.argocd.svc.p5.k8s.ooo | - | | | [[p6.k8s.ooo]] | production | | server67 server69 server71 | "argo":https://argocd-server.argocd.svc.p6.k8s.ooo | 147.78.194.13 | 2021-10-05 | | [[p10.k8s.ooo]] | production | | server63 server65 server83 | "argo":https://argocd-server.argocd.svc.p10.k8s.ooo | 147.78.194.12 | 2021-10-05 | | nau fnnf | development | Nico | server75 | | | | 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. Allowing to schedule work on the control plane * Mostly for single node / test / development clusters * Just remove the master taint as follows <pre> kubectl taint nodes --all node-role.kubernetes.io/master- </pre> 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 serverXX </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 h3. Hardware Maintenance using ungleich-hardware Use the following manifest and replace the HOST with the actual host: <pre> apiVersion: v1 kind: Pod metadata: name: ungleich-hardware-HOST spec: containers: - name: ungleich-hardware image: ungleich/ungleich-hardware:0.0.5 args: - sleep - "1000000" volumeMounts: - mountPath: /dev name: dev securityContext: privileged: true nodeSelector: kubernetes.io/hostname: "HOST" volumes: - name: dev hostPath: path: /dev </pre> Also see: [[The_ungleich_hardware_maintenance_guide]] h3. Triggering a cronjob / creating a job from a cronjob To test a cronjob, we can create a job from a cronjob: <pre> kubectl create job --from=cronjob/volume2-daily-backup volume2-manual </pre> This creates a job volume2-manual based on the cronjob volume2-daily h2. Calico CNI h3. Calico Installation * We install "calico using helm":https://docs.projectcalico.org/getting-started/kubernetes/helm * This has the following advantages: ** Easy to upgrade ** Does not require os to configure IPv6/dual stack settings as the tigera operator figures out things on its own Usually plain calico can be installed directly using: <pre> helm repo add projectcalico https://docs.projectcalico.org/charts helm install calico projectcalico/tigera-operator --version v3.20.4 </pre> * Check the tags on https://github.com/projectcalico/calico/tags for the latest release h3. Installing calicoctl To be able to manage and configure calico, we need to "install calicoctl (we choose the version as a pod)":https://docs.projectcalico.org/getting-started/clis/calicoctl/install#install-calicoctl-as-a-kubernetes-pod <pre> kubectl apply -f https://docs.projectcalico.org/manifests/calicoctl.yaml </pre> Or version specific: <pre> kubectl apply -f https://github.com/projectcalico/calico/blob/v3.20.4/manifests/calicoctl.yaml # For 3.22 kubectl apply -f https://projectcalico.docs.tigera.io/archive/v3.22/manifests/calicoctl.yaml </pre> And making it easier accessible by alias: <pre> alias calicoctl="kubectl exec -i -n kube-system calicoctl -- /calicoctl" </pre> h3. Calico configuration By default our k8s clusters "BGP peer":https://docs.projectcalico.org/networking/bgp with an upstream router to propagate podcidr and servicecidr. Default settings in our infrastructure: * We use a full-mesh using the @nodeToNodeMeshEnabled: true@ option * We keep the original next hop so that *only* the server with the pod is announcing it (instead of ecmp) * We use private ASNs for k8s clusters * We do *not* use any overlay After installing calico and calicoctl the last step of the installation is usually: <pre> calicoctl create -f - < calico-bgp.yaml </pre> A sample BGP configuration: <pre> --- apiVersion: projectcalico.org/v3 kind: BGPConfiguration metadata: name: default spec: logSeverityScreen: Info nodeToNodeMeshEnabled: true asNumber: 65534 serviceClusterIPs: - cidr: 2a0a:e5c0:10:3::/108 serviceExternalIPs: - cidr: 2a0a:e5c0:10:3::/108 --- apiVersion: projectcalico.org/v3 kind: BGPPeer metadata: name: router1-place10 spec: peerIP: 2a0a:e5c0:10:1::50 asNumber: 213081 keepOriginalNextHop: true </pre> h2. ArgoCD / ArgoWorkFlow h3. Argocd Installation As there is no configuration management present yet, argocd is installed using <pre> kubectl create namespace argocd # Specific Version kubectl apply -n argocd -f https://raw.githubusercontent.com/argoproj/argo-cd/v2.3.2/manifests/install.yaml # OR: latest stable 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> h3. Accessing argocd In regular IPv6 clusters: * Navigate to https://argocd-server.argocd.CLUSTERDOMAIN In legacy IPv4 clusters <pre> kubectl --namespace argocd port-forward svc/argocd-server 8080:80 </pre> * Navigate to https://localhost:8080 h3. Using the argocd webhook to trigger changes * To trigger changes post json https://argocd.example.com/api/webhook h3. Deploying an application * Applications are deployed via git towards gitea (code.ungleich.ch) and then pulled by argo * Always include the *redmine-url* pointing to the (customer) ticket ** Also add the support-url if it exists Application sample <pre> apiVersion: argoproj.io/v1alpha1 kind: Application metadata: name: gitea-CUSTOMER namespace: argocd spec: destination: namespace: default server: 'https://kubernetes.default.svc' source: path: apps/prod/gitea repoURL: 'https://code.ungleich.ch/ungleich-intern/k8s-config.git' targetRevision: HEAD helm: parameters: - name: storage.data.storageClass value: rook-ceph-block-hdd - name: storage.data.size value: 200Gi - name: storage.db.storageClass value: rook-ceph-block-ssd - name: storage.db.size value: 10Gi - name: storage.letsencrypt.storageClass value: rook-ceph-block-hdd - name: storage.letsencrypt.size value: 50Mi - name: letsencryptStaging value: 'no' - name: fqdn value: 'code.verua.online' project: default syncPolicy: automated: prune: true selfHeal: true info: - name: 'redmine-url' value: 'https://redmine.ungleich.ch/issues/ISSUEID' - name: 'support-url' value: 'https://support.ungleich.ch/Ticket/Display.html?id=TICKETID' </pre> h2. Helm related operations and conventions 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> h3. Naming services and deployments in helm charts [Application labels] * We always have {{ .Release.Name }} to identify the current "instance" * Deployments: ** use @app: <what it is>@, f.i. @app: nginx@, @app: postgres@, ... * See more about standard labels on ** https://kubernetes.io/docs/concepts/overview/working-with-objects/common-labels/ ** https://helm.sh/docs/chart_best_practices/labels/ h2. Rook / Ceph Related Operations h3. Executing ceph commands Using the ceph-tools pod as follows: <pre> kubectl exec -n rook-ceph -ti $(kubectl -n rook-ceph get pods -l app=rook-ceph-tools -o jsonpath='{.items[*].metadata.name}') -- ceph -s </pre> 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. Inspecting the logs of the rook-ceph-operator <pre> kubectl -n rook-ceph logs -f -l app=rook-ceph-operator </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 * More specifically: https://github.com/rook/rook/blob/release-1.7/cluster/examples/kubernetes/ceph/osd-purge.yaml * Then delete the related deployment Set osd id in the osd-purge.yaml and apply it. OSD should be down before. <pre> apiVersion: batch/v1 kind: Job metadata: name: rook-ceph-purge-osd namespace: rook-ceph # namespace:cluster labels: app: rook-ceph-purge-osd spec: template: metadata: labels: app: rook-ceph-purge-osd spec: serviceAccountName: rook-ceph-purge-osd containers: - name: osd-removal image: rook/ceph:master # TODO: Insert the OSD ID in the last parameter that is to be removed # The OSD IDs are a comma-separated list. For example: "0" or "0,2". # If you want to preserve the OSD PVCs, set `--preserve-pvc true`. # # A --force-osd-removal option is available if the OSD should be destroyed even though the # removal could lead to data loss. args: - "ceph" - "osd" - "remove" - "--preserve-pvc" - "false" - "--force-osd-removal" - "false" - "--osd-ids" - "SETTHEOSDIDHERE" env: - name: POD_NAMESPACE valueFrom: fieldRef: fieldPath: metadata.namespace - name: ROOK_MON_ENDPOINTS valueFrom: configMapKeyRef: key: data name: rook-ceph-mon-endpoints - name: ROOK_CEPH_USERNAME valueFrom: secretKeyRef: key: ceph-username name: rook-ceph-mon - name: ROOK_CEPH_SECRET valueFrom: secretKeyRef: key: ceph-secret name: rook-ceph-mon - name: ROOK_CONFIG_DIR value: /var/lib/rook - name: ROOK_CEPH_CONFIG_OVERRIDE value: /etc/rook/config/override.conf - name: ROOK_FSID valueFrom: secretKeyRef: key: fsid name: rook-ceph-mon - name: ROOK_LOG_LEVEL value: DEBUG volumeMounts: - mountPath: /etc/ceph name: ceph-conf-emptydir - mountPath: /var/lib/rook name: rook-config volumes: - emptyDir: {} name: ceph-conf-emptydir - emptyDir: {} name: rook-config restartPolicy: Never </pre> Deleting the deployment: <pre> [18:05] bridge:~% kubectl -n rook-ceph delete deployment rook-ceph-osd-6 deployment.apps "rook-ceph-osd-6" deleted </pre> h2. Harbor * We user "Harbor":https://goharbor.io/ for caching and as an image registry. Internal app reference: apps/prod/harbor. * The admin password is in the password store, auto generated per cluster * At the moment harbor only authenticates against the internal ldap tree h3. LDAP configuration * The url needs to be ldaps://... * uid = uid * rest standard h2. Monitoring / Prometheus * Via "kube-prometheus":https://github.com/prometheus-operator/kube-prometheus/ Access via ... * http://prometheus-k8s.monitoring.svc:9090 * http://grafana.monitoring.svc:3000 * http://alertmanager.monitoring.svc:9093 h3. Prometheus Options * "helm/kube-prometheus-stack":https://github.com/prometheus-community/helm-charts/tree/main/charts/kube-prometheus-stack ** Includes dashboards and co. * "manifest based kube-prometheus":https://github.com/prometheus-operator/kube-prometheus ** Includes dashboards and co. * "Prometheus Operator (mainly CRD manifest":https://github.com/prometheus-operator/prometheus-operator h2. Nextcloud h3. How to get the nextcloud credentials * The initial username is set to "nextcloud" * The password is autogenerated and saved in a kubernetes secret <pre> kubectl get secret RELEASENAME-nextcloud -o jsonpath="{.data.PASSWORD}" | base64 -d; echo "" </pre> h3. How to fix "Access through untrusted domain" * Nextcloud stores the initial domain configuration * If the FQDN is changed, it will show the error message "Access through untrusted domain" * To fix, edit /var/www/html/config/config.php and correct the domain * Then delete the pods 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