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simple ClickHouse instance with PVC Installation is failing while starting pod #1464

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Rajpratik71 opened this issue Jul 24, 2024 · 20 comments

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@Rajpratik71
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Operator install is success.

When tried to deploy "ClickHouse" Instance using below yaml

apiVersion: "clickhouse.altinity.com/v1"
kind: "ClickHouseInstallation"
metadata:
  name: "clickhouse-olap"
spec:
  defaults:
    templates:
      dataVolumeClaimTemplate: data-volume-template
      logVolumeClaimTemplate: log-volume-template
  configuration:
    clusters:
      - name: "clickhouse-olap"
        layout:
          shardsCount: 1
          replicasCount: 1
  templates:
    volumeClaimTemplates:
      - name: data-volume-template
        spec:
          accessModes:
            - ReadWriteOnce
          resources:
            requests:
              storage: 100Gi
      - name: log-volume-template
        spec:
          accessModes:
            - ReadWriteOnce
          resources:
            requests:
              storage: 100Gi

getting below error while starting the pod

pratikraj@Pratiks-MacBook-Pro common % oc -n clickhouse get po,svc,pvc,ClickHouseInstallation                          
NAME                                            READY   STATUS             RESTARTS       AGE
pod/chi-clickhouse-olap-clickhouse-olap-0-0-0   1/2     CrashLoopBackOff   10 (72s ago)   27m

NAME                                              TYPE        CLUSTER-IP   EXTERNAL-IP   PORT(S)                      AGE
service/chi-clickhouse-olap-clickhouse-olap-0-0   ClusterIP   None         <none>        9000/TCP,8123/TCP,9009/TCP   22m
service/clickhouse-clickhouse-olap                ClusterIP   None         <none>        8123/TCP,9000/TCP            12m

NAME                                                                                   STATUS   VOLUME                                     CAPACITY   ACCESS MODES   STORAGECLASS      AGE
persistentvolumeclaim/data-volume-template-chi-clickhouse-olap-clickhouse-olap-0-0-0   Bound    pvc-6e2da356-cd7d-4c39-98be-a047235b1fc4   100Gi      RWO            rook-ceph-block   27m
persistentvolumeclaim/log-volume-template-chi-clickhouse-olap-clickhouse-olap-0-0-0    Bound    pvc-f2bd4c06-32ef-411f-aeb8-1b6b417fc457   100Gi      RWO            rook-ceph-block   27m

NAME                                                             CLUSTERS   HOSTS   STATUS      HOSTS-COMPLETED   AGE
clickhouseinstallation.clickhouse.altinity.com/clickhouse-olap   1          1       Completed                     28m
pratikraj@Pratiks-MacBook-Pro common % 
pratikraj@Pratiks-MacBook-Pro common % 
pratikraj@Pratiks-MacBook-Pro common % oc -n clickhouse logs -f --tail=10 pod/chi-clickhouse-olap-clickhouse-olap-0-0-0
Defaulted container "clickhouse" out of: clickhouse, clickhouse-log
Code: 36. DB::Exception: Group 0 is not found in the system. (BAD_ARGUMENTS) (version 24.6.2.17 (official build))
Couldn't create necessary directory: /var/lib/clickhouse/
pratikraj@Pratiks-MacBook-Pro common % 
@Slach
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Slach commented Jul 24, 2024

Let's check, is /var/lib/clickhouse present in pod mounts ?
Could you share?
oc -n clickhouse getpod chi-clickhouse-olap-clickhouse-olap-0-0-0 -o yaml

@Rajpratik71
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It is there

pratikraj@Pratiks-MacBook-Pro common % oc get pod -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0 -o yaml
apiVersion: v1
kind: Pod
metadata:
  annotations:
    k8s.ovn.org/pod-networks: '{"default":{"ip_addresses":["10.254.22.217/22"],"mac_address":"0a:58:0a:fe:16:d9","gateway_ips":["10.254.20.1"],"routes":[{"dest":"10.254.0.0/16","nextHop":"10.254.20.1"},{"dest":"172.30.0.0/16","nextHop":"10.254.20.1"},{"dest":"100.64.0.0/16","nextHop":"10.254.20.1"}],"ip_address":"10.254.22.217/22","gateway_ip":"10.254.20.1"}}'
    k8s.v1.cni.cncf.io/network-status: |-
      [{
          "name": "ovn-kubernetes",
          "interface": "eth0",
          "ips": [
              "10.254.22.217"
          ],
          "mac": "0a:58:0a:fe:16:d9",
          "default": true,
          "dns": {}
      }]
    openshift.io/scc: restricted-v2
    seccomp.security.alpha.kubernetes.io/pod: runtime/default
  creationTimestamp: "2024-07-24T19:42:43Z"
  generateName: chi-clickhouse-olap-clickhouse-olap-0-0-
  labels:
    clickhouse.altinity.com/app: chop
    clickhouse.altinity.com/chi: clickhouse-olap
    clickhouse.altinity.com/cluster: clickhouse-olap
    clickhouse.altinity.com/namespace: clickhouse
    clickhouse.altinity.com/ready: "yes"
    clickhouse.altinity.com/replica: "0"
    clickhouse.altinity.com/shard: "0"
    controller-revision-hash: chi-clickhouse-olap-clickhouse-olap-0-0-6d59bbb7c
    statefulset.kubernetes.io/pod-name: chi-clickhouse-olap-clickhouse-olap-0-0-0
  name: chi-clickhouse-olap-clickhouse-olap-0-0-0
  namespace: clickhouse
  ownerReferences:
  - apiVersion: apps/v1
    blockOwnerDeletion: true
    controller: true
    kind: StatefulSet
    name: chi-clickhouse-olap-clickhouse-olap-0-0
    uid: 3410fc06-876c-4748-814c-c4b511685b60
  resourceVersion: "1682310"
  uid: 25afed6c-7481-4284-99a3-97caf8516279
spec:
  containers:
  - image: clickhouse/clickhouse-server:latest
    imagePullPolicy: Always
    livenessProbe:
      failureThreshold: 10
      httpGet:
        path: /ping
        port: http
        scheme: HTTP
      initialDelaySeconds: 60
      periodSeconds: 3
      successThreshold: 1
      timeoutSeconds: 1
    name: clickhouse
    ports:
    - containerPort: 9000
      name: tcp
      protocol: TCP
    - containerPort: 8123
      name: http
      protocol: TCP
    - containerPort: 9009
      name: interserver
      protocol: TCP
    readinessProbe:
      failureThreshold: 3
      httpGet:
        path: /ping
        port: http
        scheme: HTTP
      initialDelaySeconds: 10
      periodSeconds: 3
      successThreshold: 1
      timeoutSeconds: 1
    resources: {}
    securityContext:
      allowPrivilegeEscalation: false
      capabilities:
        drop:
        - ALL
      runAsNonRoot: true
      runAsUser: 1000730000
    terminationMessagePath: /dev/termination-log
    terminationMessagePolicy: File
    volumeMounts:
    - mountPath: /etc/clickhouse-server/config.d/
      name: chi-clickhouse-olap-common-configd
    - mountPath: /etc/clickhouse-server/users.d/
      name: chi-clickhouse-olap-common-usersd
    - mountPath: /etc/clickhouse-server/conf.d/
      name: chi-clickhouse-olap-deploy-confd-clickhouse-olap-0-0
    - mountPath: /var/lib/clickhouse
      name: data-volume-template
    - mountPath: /var/log/clickhouse-server
      name: log-volume-template
    - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
      name: kube-api-access-r2djq
      readOnly: true
  - args:
    - while true; do sleep 30; done;
    command:
    - /bin/sh
    - -c
    - --
    image: registry.access.redhat.com/ubi8/ubi-minimal:latest
    imagePullPolicy: Always
    name: clickhouse-log
    resources: {}
    securityContext:
      allowPrivilegeEscalation: false
      capabilities:
        drop:
        - ALL
      runAsNonRoot: true
      runAsUser: 1000730000
    terminationMessagePath: /dev/termination-log
    terminationMessagePolicy: File
    volumeMounts:
    - mountPath: /var/lib/clickhouse
      name: data-volume-template
    - mountPath: /var/log/clickhouse-server
      name: log-volume-template
    - mountPath: /var/run/secrets/kubernetes.io/serviceaccount
      name: kube-api-access-r2djq
      readOnly: true
  dnsPolicy: ClusterFirst
  enableServiceLinks: true
  hostAliases:
  - hostnames:
    - chi-clickhouse-olap-clickhouse-olap-0-0
    ip: 127.0.0.1
  hostname: chi-clickhouse-olap-clickhouse-olap-0-0-0
  imagePullSecrets:
  - name: default-dockercfg-v9z72
  nodeName: worker1.gi-tracing-poc.cp.fyre.ibm.com
  preemptionPolicy: PreemptLowerPriority
  priority: 0
  restartPolicy: Always
  schedulerName: default-scheduler
  securityContext:
    fsGroup: 1000730000
    seLinuxOptions:
      level: s0:c27,c14
    seccompProfile:
      type: RuntimeDefault
  serviceAccount: default
  serviceAccountName: default
  subdomain: chi-clickhouse-olap-clickhouse-olap-0-0
  terminationGracePeriodSeconds: 30
  tolerations:
  - effect: NoExecute
    key: node.kubernetes.io/not-ready
    operator: Exists
    tolerationSeconds: 300
  - effect: NoExecute
    key: node.kubernetes.io/unreachable
    operator: Exists
    tolerationSeconds: 300
  volumes:
  - name: data-volume-template
    persistentVolumeClaim:
      claimName: data-volume-template-chi-clickhouse-olap-clickhouse-olap-0-0-0
  - name: log-volume-template
    persistentVolumeClaim:
      claimName: log-volume-template-chi-clickhouse-olap-clickhouse-olap-0-0-0
  - configMap:
      defaultMode: 420
      name: chi-clickhouse-olap-common-configd
    name: chi-clickhouse-olap-common-configd
  - configMap:
      defaultMode: 420
      name: chi-clickhouse-olap-common-usersd
    name: chi-clickhouse-olap-common-usersd
  - configMap:
      defaultMode: 420
      name: chi-clickhouse-olap-deploy-confd-clickhouse-olap-0-0
    name: chi-clickhouse-olap-deploy-confd-clickhouse-olap-0-0
  - name: kube-api-access-r2djq
    projected:
      defaultMode: 420
      sources:
      - serviceAccountToken:
          expirationSeconds: 3607
          path: token
      - configMap:
          items:
          - key: ca.crt
            path: ca.crt
          name: kube-root-ca.crt
      - downwardAPI:
          items:
          - fieldRef:
              apiVersion: v1
              fieldPath: metadata.namespace
            path: namespace
      - configMap:
          items:
          - key: service-ca.crt
            path: service-ca.crt
          name: openshift-service-ca.crt
status:
  conditions:
  - lastProbeTime: null
    lastTransitionTime: "2024-07-24T19:42:44Z"
    status: "True"
    type: Initialized
  - lastProbeTime: null
    lastTransitionTime: "2024-07-24T19:42:44Z"
    message: 'containers with unready status: [clickhouse]'
    reason: ContainersNotReady
    status: "False"
    type: Ready
  - lastProbeTime: null
    lastTransitionTime: "2024-07-24T19:42:44Z"
    message: 'containers with unready status: [clickhouse]'
    reason: ContainersNotReady
    status: "False"
    type: ContainersReady
  - lastProbeTime: null
    lastTransitionTime: "2024-07-24T19:42:44Z"
    status: "True"
    type: PodScheduled
  containerStatuses:
  - containerID: cri-o://3a9e1ba9e1cb22a9f9a3b962500d244fe0717c8471848c177f60ac059fec089c
    image: docker.io/clickhouse/clickhouse-server:latest
    imageID: docker.io/clickhouse/clickhouse-server@sha256:00d808c094fa0e790b662f4ee5b7a7476c990c79907c997ac2a1484a8833ab70
    lastState:
      terminated:
        containerID: cri-o://3a9e1ba9e1cb22a9f9a3b962500d244fe0717c8471848c177f60ac059fec089c
        exitCode: 1
        finishedAt: "2024-07-24T20:19:41Z"
        reason: Error
        startedAt: "2024-07-24T20:19:40Z"
    name: clickhouse
    ready: false
    restartCount: 12
    started: false
    state:
      waiting:
        message: back-off 5m0s restarting failed container=clickhouse pod=chi-clickhouse-olap-clickhouse-olap-0-0-0_clickhouse(25afed6c-7481-4284-99a3-97caf8516279)
        reason: CrashLoopBackOff
  - containerID: cri-o://b2c34c6fcabcbe6aa3b97512ea692bb3453ae012b09404a9d2c29456b9885760
    image: registry.access.redhat.com/ubi8/ubi-minimal:latest
    imageID: registry.access.redhat.com/ubi8/ubi-minimal@sha256:a6e546ff72e0eca114e0bfee08aa5b1bba726fc3986a8fa1e453629e054c4357
    lastState: {}
    name: clickhouse-log
    ready: true
    restartCount: 0
    started: true
    state:
      running:
        startedAt: "2024-07-24T19:42:49Z"
  hostIP: 10.17.60.70
  phase: Running
  podIP: 10.254.22.217
  podIPs:
  - ip: 10.254.22.217
  qosClass: BestEffort
  startTime: "2024-07-24T19:42:44Z"

@Slach
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Slach commented Jul 25, 2024

Which component responsible for second container with sleep 30 and securityContext?
I don't see where exactly you configure it, looks like these customizations added outside from clickhouse-operator?

I think the root reason is

    securityContext:
      allowPrivilegeEscalation: false
      capabilities:
        drop:
        - ALL
      runAsNonRoot: true
      runAsUser: 1000730000

to strict security context

could we change it to following according to internal docker image uid?

    securityContext:
      runAsUser: 101
      runAsGroup: 101
      fsGroup: 101
      allowPrivilegeEscalation: false
      capabilities:
        drop: [ "ALL" ]
        add: [ "CAP_NICE", "CAP_IPC_LOCK" ]

If we can't change securityContext

could we add

  env:
  - name: CLIKCHOUSE_UID
    value: 1000730000  

to podTemplate?

Something like that should work

spec:
  defaults:
    templates:
      podTemlate: custom-uid

  templates:
    podTemplates:
    - name: custom-uid
      spec:
        containers:
        - name: clickhouse
          image: clickhouse/clickhouse-server:latest
          env:
          - name: CLIKCHOUSE_UID
            value: 1000730000  
          - name: CLIKCHOUSE_GID
            value: 1000730000              

@Rajpratik71
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Tried below snippet but adding below snippet resulted in pending instance creation

spec:
  defaults:
    templates:
      podTemlate: custom-uid

  templates:
    podTemplates:
    - name: custom-uid
      spec:
        containers:
        - name: clickhouse
          image: clickhouse/clickhouse-server:latest
          env:
          - name: CLIKCHOUSE_UID
            value: 1000730000  
          - name: CLIKCHOUSE_GID
            value: 1000730000              

even after 3 mins it remains in pending state

image

while without the above snippet , it got created in few sec.

image

@Slach
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Slach commented Jul 25, 2024

which clickhouse-opeator version do you use
could you share?

oc get pods --all-namespaces -l app=clickhouse-operator -o jsonpath="{.items[*].spec.containers[*].image}"

@Rajpratik71
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altinity/clickhouse-operator:0.23.6 altinity/metrics-exporter:0.23.6

@Slach
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Slach commented Jul 25, 2024

apply changes from #1464 (comment)
again

and when status will InProgress

share
oc describe chi -n clickhouse clickhouse-olap

Events Section

@Rajpratik71
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No success.

Even after 65m , no update .

pratikraj@Pratiks-MacBook-Pro common % oc -n clickhouse get po,svc,pvc,ClickHouseInstallation
NAME                                                             CLUSTERS   HOSTS   STATUS   HOSTS-COMPLETED   AGE
clickhouseinstallation.clickhouse.altinity.com/clickhouse-olap                                                 65m
pratikraj@Pratiks-MacBook-Pro common % 
pratikraj@Pratiks-MacBook-Pro common % oc describe chi -n clickhouse clickhouse-olap         
Name:         clickhouse-olap
Namespace:    clickhouse
Labels:       <none>
Annotations:  <none>
API Version:  clickhouse.altinity.com/v1
Kind:         ClickHouseInstallation
Metadata:
  Creation Timestamp:  2024-07-25T12:47:20Z
  Generation:          1
  Resource Version:    3999789
  UID:                 20e63d44-dc3d-4b29-a850-6b688637655f
Spec:
  Configuration:
    Clusters:
      Layout:
        Replicas Count:  1
        Shards Count:    1
      Name:              clickhouse-olap
  Defaults:
    Templates:
      Data Volume Claim Template:  data-volume-template
      Log Volume Claim Template:   log-volume-template
  Templates:
    Pod Templates:
      Name:  custom-uid
      Spec:
        Containers:
          Env:
            Name:   CLIKCHOUSE_UID
            Value:  1000730000
            Name:   CLIKCHOUSE_GID
            Value:  1000730000
          Image:    clickhouse/clickhouse-server:latest
          Name:     clickhouse
    Volume Claim Templates:
      Name:  data-volume-template
      Spec:
        Access Modes:
          ReadWriteOnce
        Resources:
          Requests:
            Storage:  100Gi
      Name:           log-volume-template
      Spec:
        Access Modes:
          ReadWriteOnce
        Resources:
          Requests:
            Storage:  100Gi
Events:               <none>
pratikraj@Pratiks-MacBook-Pro common % 
pratikraj@Pratiks-MacBook-Pro common % 

One thing i notice that "podTemlate: custom-uid" is not missing in respective section.

@Slach
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Slach commented Jul 25, 2024

check clickhouse-operator logs

oc logs --all-namespaces -l app=clickhouse-operator --container clickhouse-operator --since=2h
if not work

check

oc get pods --all-namespaces -l app=clickhouse-operator

and
oc logs -n <your-namespace-where-operator-installed> deployment/clickhouse-operator --container clickhouse-operator --since=2h

@Slach
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Slach commented Jul 25, 2024

also check
oc get sts -n clickhouse

@Rajpratik71
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In operator log , got the issue

W0726 03:29:44.109340       1 reflector.go:533] pkg/client/informers/externalversions/factory.go:132: failed to list *v1.ClickHouseInstallation: json: cannot unmarshal number into Go struct field EnvVar.items.spec.templates.podTemplates.spec.containers.env.value of type string
E0726 03:29:44.109373       1 reflector.go:148] pkg/client/informers/externalversions/factory.go:132: Failed to watch *v1.ClickHouseInstallation: failed to list *v1.ClickHouseInstallation: json: cannot unmarshal number into Go struct field EnvVar.items.spec.templates.podTemplates.spec.containers.env.value of type string

which is fixed by adding quotes in env values.

But again same issue while starting the pod

pratikraj@Pratiks-MacBook-Pro common % 
pratikraj@Pratiks-MacBook-Pro common % oc -n clickhouse get po,svc,pvc,ClickHouseInstallation             
NAME                                            READY   STATUS             RESTARTS         AGE
pod/chi-clickhouse-olap-clickhouse-olap-0-0-0   1/2     CrashLoopBackOff   18 (2m46s ago)   70m

NAME                                              TYPE        CLUSTER-IP   EXTERNAL-IP   PORT(S)                      AGE
service/chi-clickhouse-olap-clickhouse-olap-0-0   ClusterIP   None         <none>        9000/TCP,8123/TCP,9009/TCP   65m
service/clickhouse-clickhouse-olap                ClusterIP   None         <none>        8123/TCP,9000/TCP            55m

NAME                                                                                   STATUS   VOLUME                                     CAPACITY   ACCESS MODES   STORAGECLASS      AGE
persistentvolumeclaim/data-volume-template-chi-clickhouse-olap-clickhouse-olap-0-0-0   Bound    pvc-6f901528-fc9d-468f-a1c6-5d0d1ef687a4   100Gi      RWO            rook-ceph-block   70m
persistentvolumeclaim/log-volume-template-chi-clickhouse-olap-clickhouse-olap-0-0-0    Bound    pvc-6952669c-93ff-4e31-8e74-c6819fa3668f   100Gi      RWO            rook-ceph-block   70m

NAME                                                             CLUSTERS   HOSTS   STATUS      HOSTS-COMPLETED   AGE
clickhouseinstallation.clickhouse.altinity.com/clickhouse-olap   1          1       Completed                     70m
pratikraj@Pratiks-MacBook-Pro common % 
pratikraj@Pratiks-MacBook-Pro common % oc logs -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0    
Defaulted container "clickhouse" out of: clickhouse, clickhouse-log
Code: 36. DB::Exception: Group 0 is not found in the system. (BAD_ARGUMENTS) (version 24.6.2.17 (official build))
Couldn't create necessary directory: /var/lib/clickhouse/
pratikraj@Pratiks-MacBook-Pro common % 
pratikraj@Pratiks-MacBook-Pro common % 

@Slach
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Slach commented Jul 26, 2024

need to figure out, which component added security context in your OpenShift?

@Slach
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Slach commented Jul 26, 2024

oc exec -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0 --container clickhouse-log -- ls -la /var/lib/clickhouse

oc exec -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0 --container clickhouse-log -- whoami

@Rajpratik71
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need to figure out, which component added security context in your OpenShift?

I think default "PodSecurityPolicy" is enabled. I don't have any other security / policy enforcer tool installed.

@Rajpratik71
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oc exec -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0 --container clickhouse-log -- ls -la /var/lib/clickhouse

oc exec -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0 --container clickhouse-log -- whoami
pratikraj@Pratiks-MacBook-Pro ~ % 
pratikraj@Pratiks-MacBook-Pro ~ % oc exec -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0 --container clickhouse-log -- ls -la /var/lib/clickhouse
total 20
drwxrwsrwx. 3 root 1000730000  4096 Jul 26 03:31 .
drwxr-xr-x. 1 root root          24 Jul 26 03:31 ..
drwxrws---. 2 root 1000730000 16384 Jul 26 03:31 lost+found
pratikraj@Pratiks-MacBook-Pro ~ % 
pratikraj@Pratiks-MacBook-Pro ~ % 
pratikraj@Pratiks-MacBook-Pro ~ % oc exec -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0 --container clickhouse-log -- whoami
1000730000
pratikraj@Pratiks-MacBook-Pro ~ % 
pratikraj@Pratiks-MacBook-Pro ~ % 

@Slach
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Slach commented Jul 29, 2024

let's apply CLICKHOUSE_DO_NOT_CHOWN=1

spec:
  defaults:
    templates:
      podTemlate: custom-uid

  templates:
    podTemplates:
    - name: custom-uid
      spec:
        containers:
        - name: clickhouse
          image: clickhouse/clickhouse-server:latest
          env:
          - name: CLIKCHOUSE_UID
            value: "1000730000"  
          - name: CLIKCHOUSE_GID
            value: "1000730000"
          - name: CLICKHOUSE_DO_NOT_CHOWN
            value: "1"

@Rajpratik71
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same issue

@alex-zaitsev
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@Rajpratik71 , is it resolved? What is a reason of CrashLoopBackOff? (you should be able to see it in container logs)

Do you need clickhouse-logs container, btw? It is rarely useful

@Rajpratik71
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@Rajpratik71 , is it resolved? What is a reason of CrashLoopBackOff? (you should be able to see it in container logs)

Do you need clickhouse-logs container, btw? It is rarely useful

@alex-zaitsev same issue.

getting below in log

pratikraj@Pratiks-MacBook-Pro common % oc logs -n clickhouse chi-clickhouse-olap-clickhouse-olap-0-0-0    
Defaulted container "clickhouse" out of: clickhouse, clickhouse-log
Code: 36. DB::Exception: Group 0 is not found in the system. (BAD_ARGUMENTS) (version 24.6.2.17 (official build))
Couldn't create necessary directory: /var/lib/clickhouse/
pratikraj@Pratiks-MacBook-Pro common % 

@alex-zaitsev
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@Rajpratik71 , have you tried adding security context as suggested above?

    securityContext:
      runAsUser: 101
      runAsGroup: 101
      fsGroup: 101
      allowPrivilegeEscalation: false

Could you post here full CHI spec deleting sensitive data?

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