Elasticsearch statefulset does not create volumesClaims on rook-cephfs - elasticsearch

I am trying to deploy an elasticsearch statfulset and have the storage provisioned by rook-ceph storageclass.
The pod is in pending mode because of:
Warning FailedScheduling 87s default-scheduler 0/4 nodes are available: 4 pod has unbound immediate PersistentVolumeClaims.
The statefull set looks like this:
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: elasticsearch
namespace: rcc
labels:
app: elasticsearch
tier: backend
type: db
spec:
serviceName: es
replicas: 3
selector:
matchLabels:
app: elasticsearch
tier: backend
type: db
template:
metadata:
labels:
app: elasticsearch
tier: backend
type: db
spec:
terminationGracePeriodSeconds: 300
initContainers:
- name: fix-the-volume-permission
image: busybox
command:
- sh
- -c
- chown -R 1000:1000 /usr/share/elasticsearch/data
securityContext:
privileged: true
volumeMounts:
- name: data
mountPath: /usr/share/elasticsearch/data
- name: increase-the-vm-max-map-count
image: busybox
command:
- sysctl
- -w
- vm.max_map_count=262144
securityContext:
privileged: true
- name: increase-the-ulimit
image: busybox
command:
- sh
- -c
- ulimit -n 65536
securityContext:
privileged: true
containers:
- name: elasticsearch
image: docker.elastic.co/elasticsearch/elasticsearch-oss:7.7.1
ports:
- containerPort: 9200
name: http
- containerPort: 9300
name: tcp
resources:
requests:
memory: 4Gi
limits:
memory: 6Gi
env:
- name: cluster.name
value: elasticsearch
- name: node.name
valueFrom:
fieldRef:
fieldPath: metadata.name
- name: discovery.zen.ping.unicast.hosts
value: "elasticsearch-0.es.default.svc.cluster.local,elasticsearch-1.es.default.svc.cluster.local,elasticsearch-2.es.default.svc.cluster.local"
- name: ES_JAVA_OPTS
value: -Xms4g -Xmx4g
volumeMounts:
- name: data
mountPath: /usr/share/elasticsearch/data
volumeClaimTemplates:
- metadata:
name: data
spec:
accessModes:
- ReadWriteOnce
storageClassName: rook-cephfs
resources:
requests:
storage: 5Gi
and the reson of the pvc is not getting created is:
Normal FailedBinding 47s (x62 over 15m) persistentvolume-controller no persistent volumes available for this claim and no storage class is set
Any idea what I do wrong?

After adding rook-ceph-block storage class and changing the storageclass to that it worked without any issues.

Related

Run elasticsearch 7.17 on Openshift error chroot: cannot change root directory to '/': Operation not permitted

When starting the cluster Elasticsearch 7.17 in Openshift . Cluster writes an error
chroot: cannot change root directory to '/': Operation not permitted`
Kibana started ok.
Code :
`apiVersion: apps/v1
kind: StatefulSet
metadata:
name: elasticsearch
namespace: elasticsearch-pp
spec:
serviceName: elasticsearch
replicas: 3
selector:
matchLabels:
app: elasticsearch
template:
metadata:
labels:
app: elasticsearch
spec:
containers:
- name: elasticsearch
image: NEXUS/elasticsearch:7.17.7
env:
- name: cluster.name
value: k8s-logs
- name: node.name
valueFrom:
fieldRef:
fieldPath: metadata.name
- name: discovery.seed_hosts
value: "es-cluster-0.elasticsearch,es-cluster-1.elasticsearch,es-cluster-2.elasticsearch"
- name: cluster.initial_master_nodes
value: "es-cluster-0,es-cluster-1,es-cluster-2"
- name: ES_JAVA_OPTS
value: "-Xms4012m -Xmx4012m"
ports:
- containerPort: 9200
name: client
- containerPort: 9300
name: nodes
volumeMounts:
- name: data-cephfs
mountPath: /usr/share/elasticsearch/data
initContainers:
- name: fix-permissions
image: NEXUS/busybox
command: ["sh", "-c", "chown -R 1000:1000 /usr/share/elasticsearch/data"]
volumeMounts:
- name: data-cephfs
mountPath: /usr/share/elasticsearch/data
- name: increase-vm-max-map
image: NEXUS/busybox
imagePullPolicy: IfNotPresent
command: ["/bin/sh"]
args: ["-c", "sysctl -w vm.max_map_count=262144; echo vm.max_map_count=262144 >> /etc/sysctl.conf ; sysctl -p"]
# image: NEXUS/busybox
# command: ["sysctl", "-w", "vm.max_map_count=262144"]
- name: increase-fd-ulimit
image: NEXUS/busybox
command: ["sh", "-c", "ulimit -n 65536"]
serviceAccount: elk-anyuid
serviceAccountName: elk-anyuid
restartPolicy: Always
volumes:
- name: data-cephfs
persistentVolumeClaim:
claimName: data-cephfs `
I tried changing the cluster settings, disabled initContainers , the error persists

Keep getting error: "0/2 nodes are available: 2 pod has unbound immediate PersistentVolumeClaims."

I'm trying to setup an elasticsearch stateful set. I realise there a some similar questions that have been asked but none help in my circumstance.
The first version of setting up an elasticsearch stateful set worked fine with the following config:
apiVersion: v1
kind: PersistentVolume
metadata:
name: elasticsearch-volume
labels:
type: local
spec:
storageClassName: do-block-storage
capacity:
storage: 100M
accessModes:
- ReadWriteOnce
hostPath:
path: "/data/elasticsearch"
---
apiVersion: v1
kind: PersistentVolumeClaim # Create PVC
metadata:
name: elasticsearch-volume-claim # Sets PVC's name
labels:
app: elasticsearch # Defines app to create PVC for
spec:
storageClassName: do-block-storage
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 100M # Sets PVC's size
---
apiVersion: v1
kind: Service
metadata:
name: elasticsearch
spec:
type: ClusterIP
clusterIP: None
selector:
app: elasticsearch
ports:
- port: 9200 # To get at the elasticsearch container, just hit the service on 9200
targetPort: 9200 # routes to the exposed port on elasticsearch
---
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: elasticsearch # name of stateful
namespace: default
spec:
serviceName: elasticsearch
replicas: 1
selector:
matchLabels:
app: elasticsearch # should match service > spec.slector.app.
template:
metadata:
labels:
app: elasticsearch
spec:
volumes:
- name: elasticsearch-pvc
persistentVolumeClaim:
claimName: elasticsearch-volume-claim
containers:
- name: elasticsearch
image: docker.elastic.co/elasticsearch/elasticsearch:8.2.3
resources:
limits:
cpu: 100m
requests:
cpu: 100m
ports:
- containerPort: 9200
name: rest
protocol: TCP
- containerPort: 9300
name: inter-node
protocol: TCP
volumeMounts:
- name: elasticsearch-pvc
mountPath: /usr/share/elasticsearch/data
env:
- name: cluster.name
value: search
- name: node.name
valueFrom:
fieldRef:
fieldPath: metadata.name
- name: discovery.type
value: single-node
- name: ES_JAVA_OPTS
value: "-Xms512m -Xmx512m"
- name: xpack.security.enabled
value: "false"
initContainers:
- name: fix-permissions
image: busybox
command:
["sh", "-c", "chown -R 1000:1000 /usr/share/elasticsearch/data"]
securityContext:
privileged: true
volumeMounts:
- name: elasticsearch-pvc
mountPath: /usr/share/elasticsearch/data
- name: increase-vm-max-map
image: busybox
command: ["sysctl", "-w", "vm.max_map_count=262144"]
securityContext:
privileged: true
- name: increase-fd-ulimit
image: busybox
command: ["sh", "-c", "ulimit -n 65536"]
securityContext:
privileged: true
I then tried to implement a version of this with multiple replica's:
apiVersion: v1
kind: Service
metadata:
name: elasticsearch
spec:
type: ClusterIP
clusterIP: None
selector:
app: elasticsearch
ports:
- port: 9200 # To get at the elasticsearch container, just hit the service on 9200
targetPort: 9200 # routes to the exposed port on elasticsearch
---
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: es-cluster # name of stateful
spec:
serviceName: elasticsearch
replicas: 2
selector:
matchLabels:
app: elasticsearch # should match service > spec.slector.app.
volumeClaimTemplates:
- metadata:
name: elasticsearch-pvc
labels:
app: elasticsearch
spec:
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 100M
storageClassName: do-block-storage
template:
metadata:
labels:
app: elasticsearch
spec:
# volumes:
# - name: elasticsearch-pvc
# persistentVolumeClaim:
# claimName: elasticsearch-volume-claim
containers:
- name: elasticsearch
image: docker.elastic.co/elasticsearch/elasticsearch:8.2.3
resources:
limits:
cpu: 100m
requests:
cpu: 100m
ports:
- containerPort: 9200
name: rest
protocol: TCP
- containerPort: 9300
name: inter-node
protocol: TCP
volumeMounts:
- name: elasticsearch-pvc
mountPath: /usr/share/elasticsearch/data
env:
- name: cluster.name
value: search
- name: node.name
valueFrom:
fieldRef:
fieldPath: metadata.name
- name: discovery.seed_hosts
value: "es-cluster-0.elasticsearch,es-cluster-1.elasticsearch,es-cluster-2.elasticsearch"
- name: cluster.initial_master_nodes
value: "es-cluster-0,es-cluster-1,es-cluster-2"
- name: ES_JAVA_OPTS
value: "-Xms512m -Xmx512m"
initContainers:
- name: fix-permissions
image: busybox
command:
["sh", "-c", "chown -R 1000:1000 /usr/share/elasticsearch/data"]
securityContext:
privileged: true
volumeMounts:
- name: elasticsearch-pvc
mountPath: /usr/share/elasticsearch/data
- name: increase-vm-max-map
image: busybox
command: ["sysctl", "-w", "vm.max_map_count=262144"]
securityContext:
privileged: true
- name: increase-fd-ulimit
image: busybox
command: ["sh", "-c", "ulimit -n 65536"]
securityContext:
privileged: true
However I ran into the error: 0/2 nodes are available: 2 pod has unbound immediate PersistentVolumeClaims.
I subsequently reduced the replica's to just 1 and manually created the PV in case DO was having an issue creating the PVC without a PV (even though DO should dynamically create the PVC and PV because it works with the postgres multi-replica stateful set which I set up in exactly the same way):
apiVersion: v1
kind: PersistentVolume
metadata:
name: es-volume-1
spec:
capacity:
storage: 100M
accessModes:
- ReadWriteOnce
persistentVolumeReclaimPolicy: Retain
storageClassName: do-block-storage
hostPath:
path: "/data/elasticsearch"
nodeAffinity:
required:
nodeSelectorTerms:
- matchExpressions:
- key: kubernetes.io/hostname
operator: In
values:
- es-cluster-0
This again yielded the error: 0/2 nodes are available: 2 pod has unbound immediate PersistentVolumeClaims.
After spending a while de-bugging I gave up and decided to revert back to my single replica elasticsearch stateful set using the method I had originally used.
But once again I got the error 0/2 nodes are available: 2 pod has unbound immediate PersistentVolumeClaims.!!!
I don't have a clue what's going on here. Why am I getting this error even though I'm only trying to create a single replica and I have manually defined the PV and PVC which worked fine before??
Turns out the issue was indeed Digital Ocean specific. In the second attempt when I tried to create multiple replica's I had to use dynamic volume provisioning via volumeClaimTemplates and set the storage class to do-block-storage which as it turns out has a minimum limit of 1Gi!
Alas when I updated to 1Gi it all started working.

Setting up elastic search cluster on kubernetes pods can't talk to each other by hostname

Trying to setup elasticsearch cluster on kube, the problem i am having is that each pod isn't able to talk to the others by the respective hostnames, but the ip address works.
So for example i'm trying to currently setup 3 master nodes, es-master-0, es-master-1 and es-master-2 , if i log into one of the containers and ping another based on the pod ip it's fine, but i i try to ping say es-master-1 from es-master-0 based on the hostname it can't find it.
Clearly missing something here. Currently launching this config to try get it working:
apiVersion: v1
kind: Service
metadata:
name: ed
labels:
component: elasticsearch
role: master
spec:
selector:
component: elasticsearch
role: master
ports:
- name: transport1
port: 9300
protocol: TCP
clusterIP: None
---
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: es-master
labels:
component: elasticsearch
role: master
spec:
selector:
matchLabels:
component: elasticsearch
role: master
serviceName: ed
replicas: 3
template:
metadata:
labels:
component: elasticsearch
role: master
spec:
affinity:
nodeAffinity:
requiredDuringSchedulingIgnoredDuringExecution:
nodeSelectorTerms:
- matchExpressions:
- { key: es-master, operator: In, values: [ "true" ] }
initContainers:
- name: init-sysctl
image: busybox:1.27.2
command:
- sysctl
- -w
- vm.max_map_count=262144
securityContext:
privileged: true
dnsPolicy: "None"
dnsConfig:
options:
- name: ndots
value: "6"
nameservers:
- 10.85.0.10
searches:
- ed.es.svc.cluster.local
- es.svc.cluster.local
- svc.cluster.local
- cluster.local
- home
- node1
containers:
- name: es-master
image: docker.elastic.co/elasticsearch/elasticsearch:7.17.5
imagePullPolicy: Always
securityContext:
privileged: true
env:
- name: ES_JAVA_OPTS
value: -Xms2048m -Xmx2048m
resources:
requests:
cpu: "0.25"
limits:
cpu: "2"
ports:
- containerPort: 9300
name: transport1
livenessProbe:
tcpSocket:
port: transport1
initialDelaySeconds: 60
periodSeconds: 10
volumeMounts:
- name: storage
mountPath: /data
- name: config
mountPath: /usr/share/elasticsearch/config/elasticsearch.yml
subPath: elasticsearch.yml
volumes:
- name: config
configMap:
name: es-master-config
volumeClaimTemplates:
- metadata:
name: storage
spec:
storageClassName: "local-path"
accessModes: [ ReadWriteOnce ]
resources:
requests:
storage: 2Gi
It's clearly somehow not resolving the hostnames
For pod to pod communication you can use k8s service which you had defined.

ElasticSearch Kubernetes Setup with Skaffold

I love elastic search so on my new project I have been trying to make it work on Kubernetes and skaffold
this is the yaml file I wrote:
apiVersion: apps/v1
kind: Deployment
metadata:
name: eks-depl
spec:
replicas: 1
selector:
matchLabels:
app: eks
template:
metadata:
labels:
app: eks
spec:
containers:
- name: eks
image: elasticsearch:7.17.0
---
apiVersion: v1
kind: Service
metadata:
name: eks-srv
spec:
selector:
app: eks
ports:
- name: db
protocol: TCP
port: 9200
targetPort: 9200
- name: monitoring
protocol: TCP
port: 9300
targetPort: 9300
After I run skaffold dev it shows to be working by Kubernetes but after a few seconds it crashes and goes down.
I can't understand what I am doing wrong.
After I have updated my config files as Mr. Harsh Manvar it worked like a charm but currently I am facing another issue. The client side says the following....
Btw I am using ElasticSearch version 7.11.1 and Client side module "#elastic/elasticsearch^7.11.1"
Here is example YAML file you should consider running if you are planning to run the single Node elasticsearch cluster on the Kubernetes
apiVersion: apps/v1
kind: StatefulSet
metadata:
labels:
app: elasticsearch
component: elasticsearch
release: elasticsearch
name: elasticsearch
namespace: default
spec:
podManagementPolicy: OrderedReady
replicas: 1
revisionHistoryLimit: 10
selector:
matchLabels:
app: elasticsearch
component: elasticsearch
release: elasticsearch
serviceName: elasticsearch
template:
metadata:
labels:
app: elasticsearch
component: elasticsearch
release: elasticsearch
spec:
containers:
- env:
- name: cluster.name
value: es_cluster
- name: ELASTIC_PASSWORD
value: xyz-xyz
- name: discovery.type
value: single-node
- name: path.repo
value: backup/es-backup
- name: ES_JAVA_OPTS
value: -Xms512m -Xmx512m
- name: bootstrap.memory_lock
value: "false"
- name: xpack.security.enabled
value: "true"
image: elasticsearch:7.3.2
imagePullPolicy: IfNotPresent
name: elasticsearch
ports:
- containerPort: 9200
name: http
protocol: TCP
- containerPort: 9300
name: transport
protocol: TCP
resources:
limits:
cpu: 451m
memory: 1250Mi
requests:
cpu: 250m
memory: 1000Mi
securityContext:
privileged: true
runAsUser: 1000
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
volumeMounts:
- mountPath: /usr/share/elasticsearch/data
name: elasticsearch-data
dnsPolicy: ClusterFirst
initContainers:
- command:
- sh
- -c
- chown -R 1000:1000 /usr/share/elasticsearch/data
- sysctl -w vm.max_map_count=262144
- chmod 777 /usr/share/elasticsearch/data
- chomod 777 /usr/share/elasticsearch/data/node
- chmod g+rwx /usr/share/elasticsearch/data
- chgrp 1000 /usr/share/elasticsearch/data
image: busybox:1.29.2
imagePullPolicy: IfNotPresent
name: set-dir-owner
resources: {}
securityContext:
privileged: true
terminationMessagePath: /dev/termination-log
terminationMessagePolicy: File
volumeMounts:
- mountPath: /usr/share/elasticsearch/data
name: elasticsearch-data
restartPolicy: Always
schedulerName: default-scheduler
securityContext: {}
terminationGracePeriodSeconds: 10
updateStrategy:
type: OnDelete
volumeClaimTemplates:
- metadata:
creationTimestamp: null
name: elasticsearch-data
spec:
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 10Gi
volumeMode: Filesystem
i would also recommand checking out the helm charts of the elasticsearch :
1 . https://github.com/elastic/helm-charts/tree/master/elasticsearch
2. https://github.com/helm/charts/tree/master/stable/elasticsearch
you can expose the above stateful set using the service and use the further with the application.

kubelet does not create symlinks to /var/log/containers

I am trying to set up EFK stack on my k8s cluster using ansible repo.
When i tried to browse kibana dashboard it shows me next output:
After making some research, i found out that i don't have any log detected by Fluentd.
I am running k8s 1.2.4 on minions and 1.2.0 on master.
What i succeeded to understand, is that kubelet creates /var/log/containers directory, and make symlinks from all containers running in the cluster into it. After that Fluentd mounts share /var/log volume from the minion and have eventually access to all logs containers. So , it can send these logs to elastic search.
In my case i had /var/log/containers created, but it is empty, even /var/lib/docker/containers does not contain any log file.
I used to use the following controllers and services for EFK stack setup:
es-controller.yaml
apiVersion: v1
kind: ReplicationController
metadata:
name: elasticsearch-logging-v1
namespace: kube-system
labels:
k8s-app: elasticsearch-logging
version: v1
kubernetes.io/cluster-service: "true"
spec:
replicas: 2
selector:
k8s-app: elasticsearch-logging
version: v1
template:
metadata:
labels:
k8s-app: elasticsearch-logging
version: v1
kubernetes.io/cluster-service: "true"
spec:
containers:
- image: gcr.io/google_containers/elasticsearch:v2.4.1
name: elasticsearch-logging
resources:
# need more cpu upon initialization, therefore burstable class
limits:
cpu: 1000m
requests:
cpu: 100m
ports:
- containerPort: 9200
name: db
protocol: TCP
- containerPort: 9300
name: transport
protocol: TCP
volumeMounts:
- name: es-persistent-storage
mountPath: /data
env:
- name: "NAMESPACE"
valueFrom:
fieldRef:
fieldPath: metadata.namespace
volumes:
- name: es-persistent-storage
emptyDir: {}
es-service.yaml
apiVersion: v1
kind: Service
metadata:
name: elasticsearch-logging
namespace: kube-system
labels:
k8s-app: elasticsearch-logging
kubernetes.io/cluster-service: "true"
kubernetes.io/name: "Elasticsearch"
spec:
ports:
- port: 9200
protocol: TCP
targetPort: db
selector:
k8s-app: elasticsearch-logging
fluentd-es.yaml
apiVersion: v1
kind: Pod
metadata:
name: fluentd-es-v1.20
namespace: kube-system
labels:
k8s-app: fluentd-es
version: v1.20
spec:
containers:
- name: fluentd-es
image: gcr.io/google_containers/fluentd-elasticsearch:1.20
command:
- '/bin/sh'
- '-c'
- '/usr/sbin/td-agent 2>&1 >> /var/log/fluentd.log'
resources:
limits:
cpu: 100m
volumeMounts:
- name: varlog
mountPath: /var/log
- name: varlibdockercontainers
mountPath: /var/lib/docker/containers
readOnly: true
terminationGracePeriodSeconds: 30
volumes:
- name: varlog
hostPath:
path: /var/log
- name: varlibdockercontainers
hostPath:
path: /var/lib/docker/containers
kibana-controller.yaml
apiVersion: extensions/v1beta1
kind: Deployment
metadata:
name: kibana-logging
namespace: kube-system
labels:
k8s-app: kibana-logging
kubernetes.io/cluster-service: "true"
spec:
replicas: 1
selector:
matchLabels:
k8s-app: kibana-logging
template:
metadata:
labels:
k8s-app: kibana-logging
spec:
containers:
- name: kibana-logging
image: gcr.io/google_containers/kibana:v4.6.1
resources:
# keep request = limit to keep this container in guaranteed class
limits:
cpu: 100m
requests:
cpu: 100m
env:
- name: "ELASTICSEARCH_URL"
value: "http://elasticsearch-logging:9200"
ports:
- containerPort: 5601
name: ui
protocol: TCP
kibana-service.yaml
apiVersion: v1
kind: Service
metadata:
name: kibana-logging
namespace: kube-system
labels:
k8s-app: kibana-logging
kubernetes.io/cluster-service: "true"
kubernetes.io/name: "Kibana"
spec:
type: NodePort
ports:
- port: 5601
protocol: TCP
targetPort: ui
selector:
k8s-app: kibana-logging
update:
I changed fluentd-es.yaml as following:
apiVersion: v1
kind: Pod
metadata:
name: fluentd-elasticsearch
namespace: kube-system
labels:
k8s-app: fluentd-logging
spec:
containers:
- name: fluentd-elasticsearch
image: gcr.io/google_containers/fluentd-elasticsearch:1.15
resources:
limits:
memory: 200Mi
requests:
cpu: 100m
memory: 200Mi
volumeMounts:
- name: varlog
mountPath: /var/log
- name: varlibdockercontainers
mountPath: /var/lib/docker/containers
readOnly: true
terminationGracePeriodSeconds: 30
volumes:
- name: varlog
hostPath:
path: /var/log
- name: varlibdockercontainers
hostPath:
path: /var/lib/docker/containers
But when i run a pod "named gateway", i got in the fluentd log the next error:
/var/log/containers/gateway-c3cuu_default_gateway-d5966a86e7cb1519329272a0b900182be81f55524227db2f524e6e23cd75ba04.log unreadable. It is excluded and would be examined next time.
Finally i found out what was causing the issue.
when installing docker from CentOS 7 repo, there is an option (--log-driver=journald) which force docker to run log output to journald. The default behavior is to write these logs to json.log files.So, the only thing i had to do, delete the last mentioned option from /etc/sysconfig/docker.

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