Mysql Communications link failure in kubernetes sample - mysql

Step1:finish installing etcd and kubernetes with YUM in CentOS7 and shutdown firewall
Step2:modify related configuration item in /etc/sysconfig/docker
OPTIONS='--selinux-enabled=false --insecure-registry gcr.io'
Step3:modify related configuration item in /etc/kubernetes/apiserver
remove
ServiceAccount
in KUBE_ADMISSION_CONTROL configuration item
Step4:start all the related services of etcd and kubernetes
Step5:start ReplicationController for mysql db
kubectl create -f mysql-rc.yaml
apiVersion: v1
kind: ReplicationController
metadata:
name: mysql
spec:
replicas: 1
selector:
app: mysql
template:
metadata:
labels:
app: mysql
spec:
containers:
- name: mysql
image: hub.c.163.com/library/mysql
ports:
- containerPort: 3306
env:
- name: MYSQL_ROOT_PASSWORD
value: "123456"
Step6:start related mysql db service
kubectl create -f mysql-svc.yaml
kind: Service
metadata:
name: mysql
spec:
ports:
- port: 3306
selector:
app: mysql
Step7:start ReplicationController for myweb
kubectl create -f myweb-rc.yaml
apiVersion: v1
kind: ReplicationController
metadata:
name: myweb
spec:
replicas: 3
selector:
app: myweb
template:
metadata:
labels:
app: myweb
spec:
containers:
- name: myweb
image: docker.io/kubeguide/tomcat-app:v1
ports:
- containerPort: 8080
env:
- name: MYSQL_SERVICE_HOST
value: "mysql"
- name: MYSQL_SERVICE_PORT
value: "3306"
Step8:start related tomcat service
kubectl create -f myweb-svc.yaml
apiVersion: v1
kind: Service
metadata:
name: myweb
spec:
type: NodePort
ports:
- port: 8080
nodePort: 30001
selector:
app: myweb
When I visit from browser with nodeport(30001),I get the following Exception:
Error:com.mysql.jdbc.exceptions.jdbc4.CommunicationsException:
Communications link failure The last packet sent successfully to the
server was 0 milliseconds ago. The driver has not received any packets
from the server.
kubectl get ep
NAME ENDPOINTS AGE
kubernetes 192.168.57.129:6443 1d
mysql 172.17.0.2:3306 1d
myweb 172.17.0.3:8080,172.17.0.4:8080,172.17.0.5:8080 1d
kubectl get svc
NAME CLUSTER-IP EXTERNAL-IP PORT(S) AGE
kubernetes 10.254.0.1 <none> 443/TCP 1d
mysql 10.254.0.5 <none> 3306/TCP 1d
myweb 10.254.220.2 <nodes> 8080:30001/TCP 1d
From the interior of any tomcat container I can see the mysql env and the related mysql link code in JSP is as below:
Class.forName("com.mysql.jdbc.Driver");
String ip=System.getenv("MYSQL_SERVICE_HOST");
String port=System.getenv("MYSQL_SERVICE_PORT");
ip=(ip==null)?"localhost":ip;
port=(port==null)?"3306":port;
System.out.println("Connecting to database...");
conn = java.sql.DriverManager.getConnection("jdbc:mysql://"+ip+":"+port+"?useUnicode=true&characterEncoding=UTF-8", "root","123456");
[root#promote ~]# docker exec -it 1470cfaa1b1c /bin/bash
root#myweb-xswfb:/usr/local/tomcat# env |grep MYSQL_SERVICE
MYSQL_SERVICE_PORT=3306
MYSQL_SERVICE_HOST=mysql
root#myweb-xswfb:/usr/local/tomcat# ping mysql
ping: unknown host
Can someone tell me why I could not ping mysqldb hostname from inner tomcat server?Or how to locate the problem further?

I know the reason, it's the DNS problems. The web server cannot find the IP address of the mysql server. so it failed. Temp solution is change the web server's IP to the mysql db server. Hope can help you. Thank you.

Try to use a Headless Service http://kubernetes.io/v1.0/docs/user-guide/services.html#headless-services
by setting in your mysql Service
clusterIP: None
UPDATE
I have tried your yaml file.
Pods are running:
➜ kb get po
NAME READY STATUS RESTARTS AGE
mysql-ndtxn 1/1 Running 0 7m
myweb-j8xgh 1/1 Running 0 8m
myweb-qc7ws 1/1 Running 0 8m
myweb-zhzll 1/1 Running 0 8m
Services are:
kb get svc
NAME TYPE CLUSTER-IP EXTERNAL-IP PORT(S) AGE
kubernetes ClusterIP 10.96.0.1 <none> 443/TCP 1h
mysql ClusterIP 10.102.178.190 <none> 3306/TCP 20m
myweb NodePort 10.98.74.113 <none> 8080:30001/TCP 19m
Endpoints are:
kb get ep
NAME ENDPOINTS AGE
kubernetes 10.0.2.15:8443 1h
mysql 172.17.0.7:3306 20m
myweb 172.17.0.2:8080,172.17.0.4:8080,172.17.0.6:8080 19m
I exec bash on a tomcat pod and I can ping my service (it is resolved):
kb exec -ti myweb-zhzll -- bash
root#myweb-zhzll:/usr/local/tomcat# ping mysql
PING mysql.default.svc.cluster.local (10.102.178.190): 56 data bytes
^C--- mysql.default.svc.cluster.local ping statistics ---
I can ping the endpoint:
ping 172.17.0.7
PING 172.17.0.7 (172.17.0.7): 56 data bytes
64 bytes from 172.17.0.7: icmp_seq=0 ttl=64 time=0.181 ms
64 bytes from 172.17.0.7: icmp_seq=1 ttl=64 time=0.105 ms
64 bytes from 172.17.0.7: icmp_seq=2 ttl=64 time=0.119 ms
^C--- 172.17.0.7 ping statistics ---
Connecting to
http://192.168.99.100:30001/
I can see the tomcat page:
UPDATE 2
Here my screenshot... I see data in your database with no error.
I suggest to check your db configuration.

As a beginner, I did the same work with you and got the same problems.
This is my solution,maybe you can have a try:
Delete these configurations in myweb-rc.yaml, because it will override the system default values:
env:
- name: MYSQL_SERVICE_HOST
value: "mysql"
- name: MYSQL_SERVICE_PORT
value: "3306"
Change the mysql image tag in mysql-rc.yaml. use the low version mysql:
image: hub.c.163.com/library/mysql:5.5
Create the service first, then create the pod. refer to the following sequence:
kubectl create -f myweb-svc.yaml
kubectl create -f mysql-svc.yaml
kubectl create -f mysql-rc.yaml
kubectl create -f myweb-rc.yaml
You can refer to this doc:Discovering services
Good luck!

Related

GKE Kubernetes MySQL Input/output error Ext4Error

I have deployed a MySQL database (statefulset) on Kubernetes zonal cluster, running as a service (GKE) in Google Cloud Platform.
The zonal cluster consist of 3 instances of type e2-medium.
The MySQL container cannot start due to the following error.
kubectl logs mysql-statefulset-0
2022-02-07 05:55:38+00:00 [Note] [Entrypoint]: Entrypoint script for MySQL Server 5.7.35-1debian10 started.
find: '/var/lib/mysql/': Input/output error
Last seen events.
4m57s Warning Ext4Error gke-cluster-default-pool-rnfh kernel-monitor, gke-cluster-default-pool-rnfh EXT4-fs error (device sdb): __ext4_find_entry:1532: inode #2: comm mysqld: reading directory lblock 0 40d 8062 gke-cluster-default-pool-rnfh
3m22s Warning BackOff pod/mysql-statefulset-0 spec.containers{mysql} kubelet, gke-cluster-default-pool-rnfh Back-off restarting failed container
Nodes.
kubectl get node -owide
gke-cluster-default-pool-ayqo Ready <none> 54d v1.21.5-gke.1302 So.Me.I.P So.Me.I.P Container-Optimized OS from Google 5.4.144+ containerd://1.4.8
gke-cluster-default-pool-rnfh Ready <none> 54d v1.21.5-gke.1302 So.Me.I.P So.Me.I.P Container-Optimized OS from Google 5.4.144+ containerd://1.4.8
gke-cluster-default-pool-sc3p Ready <none> 54d v1.21.5-gke.1302 So.Me.I.P So.Me.I.P Container-Optimized OS from Google 5.4.144+ containerd://1.4.8
I also noticed that rnfh node is out of memory.
kubectl top node
NAME CPU(cores) CPU% MEMORY(bytes) MEMORY%
gke-cluster-default-pool-ayqo 117m 12% 992Mi 35%
gke-cluster-default-pool-rnfh 180m 19% 2953Mi 104%
gke-cluster-default-pool-sc3p 179m 19% 1488Mi 52%
MySql mainfest
# HEADLESS SERVICE
apiVersion: v1
kind: Service
metadata:
name: mysql-headless-service
labels:
kind: mysql-headless-service
spec:
clusterIP: None
selector:
tier: mysql-db
ports:
- name: 'mysql-http'
protocol: 'TCP'
port: 3306
---
# STATEFUL SET
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: mysql-statefulset
spec:
selector:
matchLabels:
tier: mysql-db
serviceName: mysql-statefulset
replicas: 1
template:
metadata:
labels:
tier: mysql-db
spec:
terminationGracePeriodSeconds: 10
containers:
- name: my-mysql
image: my-mysql:latest
imagePullPolicy: Always
args:
- "--ignore-db-dir=lost+found"
ports:
- name: 'http'
protocol: 'TCP'
containerPort: 3306
volumeMounts:
- name: mysql-pvc
mountPath: /var/lib/mysql
env:
- name: MYSQL_ROOT_USER
valueFrom:
secretKeyRef:
name: mysql-secret
key: mysql-root-username
- name: MYSQL_ROOT_PASSWORD
valueFrom:
secretKeyRef:
name: mysql-secret
key: mysql-root-password
- name: MYSQL_USER
valueFrom:
configMapKeyRef:
name: mysql-config
key: mysql-username
- name: MYSQL_PASSWORD
valueFrom:
configMapKeyRef:
name: mysql-config
key: mysql-password
- name: MYSQL_DATABASE
valueFrom:
configMapKeyRef:
name: mysql-config
key: mysql-database
volumeClaimTemplates:
- metadata:
name: mysql-pvc
spec:
storageClassName: 'mysql-fast'
resources:
requests:
storage: 120Gi
accessModes:
- ReadWriteOnce
- ReadOnlyMany
MySQL storage class manifest:
apiVersion: storage.k8s.io/v1
kind: StorageClass
metadata:
name: mysql-fast
provisioner: kubernetes.io/gce-pd
parameters:
type: pd-ssd
reclaimPolicy: Retain
allowVolumeExpansion: true
volumeBindingMode: Immediate
Why Kubernetes is trying to schedule pod in out of memory node?
UPDATES
I've added requests and limits to MySQL manifest to improve the Qos Class. Now the Qos Class is Guaranteed.
Unfortunately, Kubernetes still trying to schedule to out of memory rnfh node.
kubectl describe po mysql-statefulset-0 | grep node -i
Node: gke-cluster-default-pool-rnfh/So.Me.I.P
kubectl describe po mysql-statefulset-0 | grep qos -i
QoS Class: Guaranteed
I ran a few more tests but I couldn't replicate this.
To answer this one correctly, we would need much more logs. Not sure if you still have them. If I could guess which was the root cause of this issue I would say it was connected with the PersistentVolume.
In one of the Github issue - Volume was remounted as read only after error #752 I found very similar behavior to OP's behavior.
You have created a special storageclass for your MySQL. You've set reclaimPolicy: Retain so PV was not removed. When Statefulset pod (with the same suffix -0) has been recreated (restarted due to error with connectivity, some issues on DB, hard to say) it tried to re-claim this Volume. In the mentioned Github issue, user had very similar situation. Also got inode #262147: comm mysqld: reading directory lblock issue, but in the bellow there was also entry [ +0.003695] EXT4-fs (sda): Remounting filesystem read-only. Maybe it changed permissions when re-mounted?
Another thing that your volumeClaimTemplates contained
accessModes:
- ReadWriteOnce
- ReadOnlyMany
So one PersistentVolume could be used as ReadWriteOnce by one node or only ReadOnlyMany by many nodes. There is a possibility that POD was recreated in different node with Read-Only assessMode.
[ +35.912075] EXT4-fs warning (device sda): htree_dirblock_to_tree:977: inode #2: lblock 0: comm mysqld: error -5 reading directory block
[ +6.294232] EXT4-fs error (device sda): ext4_find_entry:1436: inode #262147: comm mysqld: reading directory lblock ...
[ +0.005226] EXT4-fs error (device sda): ext4_find_entry:1436: inode #2: comm mysqld: reading directory lblock 0
[ +1.666039] EXT4-fs error (device sda): ext4_journal_check_start:61: Detected aborted journal
[ +0.003695] EXT4-fs (sda): Remounting filesystem read-only
It would fit to OP's comment:
Two days ago for reasons unknown to me Kubernetes restarted the container and was keep trying to run it on rnfa machine. The container was probably evicted from another node.
Another thing is that node or cluster might be updated (depending if the auto update option was turned on) which might enforce restart of the pod.
Issue with '/var/lib/mysql/': Input/output error might point to database corruption like mentioned here.
In general, the issue has been resolved by cordoning affected node. Additional information about the difference between cordon and drain can be found here.
Just as an addition, to assign pods to specific node or node with specified label, you can use Affinity

kubernetes mysql statefulset not taking new password, though password changes in env

I have created statefulset of mysql using below yaml with this command:
kubectl apply -f mysql-statefulset.yaml
Yaml:
apiVersion: v1
kind: Service
metadata:
name: mysql-service
labels:
app: mysql
spec:
ports:
- port: 3306
name: db
clusterIP: None
selector:
app: mysql
---
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: mysql-sts
spec:
selector:
matchLabels:
app: mysql # has to match .spec.template.metadata.labels
serviceName: mysql-service
replicas: 3 # by default is 1
template:
metadata:
labels:
app: mysql # has to match .spec.selector.matchLabels
spec:
terminationGracePeriodSeconds: 10
containers:
- name: mysql
image: mysql
env:
- name: MYSQL_ROOT_PASSWORD
value: "okaoka"
ports:
- containerPort: 3306
name: db
volumeMounts:
- name: db-volume
mountPath: /var/lib/mysql
volumeClaimTemplates:
- metadata:
name: db-volume
spec:
accessModes: [ "ReadWriteOnce" ]
storageClassName: standard
resources:
requests:
storage: 1Gi
After that 3 pods and for each of them a pvc and pv was created. I successfully entered one of the pod using:
kubectl exec -it mysql-sts-0 sh
and then login in mysql using:
mysql -u root -p
after giving this command a:
Enter password:
came and I entered the password:
okaoka
and successfully could login. After that I exited from the pod.
Then I deleted the statefulset (as expected the pvc and pv were there even after the deletion of statefulset). After that I have applied a new yaml slightly changing the previous one, I changed the password in yaml, gave new password:
okaoka1234
and rest of the yaml were same as before. The yaml is given below, now after applying this yaml (only changed the password) by:
kubectl apply -f mysql-statefulset.yaml
it successfully created statefulset and 3 new pods (who binded with previous pvc and pv, as expected).
Changed Yaml:
apiVersion: v1
kind: Service
metadata:
name: mysql-service
labels:
app: mysql
spec:
ports:
- port: 3306
name: db
clusterIP: None
selector:
app: mysql
---
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: mysql-sts
spec:
selector:
matchLabels:
app: mysql # has to match .spec.template.metadata.labels
serviceName: mysql-service
replicas: 3 # by default is 1
template:
metadata:
labels:
app: mysql # has to match .spec.selector.matchLabels
spec:
terminationGracePeriodSeconds: 10
containers:
- name: mysql
image: mysql
env:
- name: MYSQL_ROOT_PASSWORD
value: "okaoka1234" # here is the change
ports:
- containerPort: 3306
name: db
volumeMounts:
- name: db-volume
mountPath: /var/lib/mysql
volumeClaimTemplates:
- metadata:
name: db-volume
spec:
accessModes: [ "ReadWriteOnce" ]
storageClassName: standard
resources:
requests:
storage: 1Gi
Now the problem is when I again entered a pod using:
kubectl exec -it mysql-sts-0 sh
then used:
mysql -u root -p
and again the:
Enter password:
came and this time when I gave my new password:
okaoka1234
it gave access denied.
When I printed the env (inside the pod) using:
printenv
then I could see that:
MYSQL_ROOT_PASSWORD=okaoka1234
that means in environment variable it changed and took the new password, but I could not logged in by the new password.
The interesting thing is that I could logged in by giving my previous password okaoka, I don't know why it is taking the previous password in this scenario not the new one which is even in the env (inside pod) also. Can anybody provide the logic behind this?
Most probably, the image that you are using in your StatefulSet, uses the environment variable as a way to initialize the password when it creates for the first time the structure on the persisted storage (on its pvc).
Given the fact that the pvc and pv are the same of the previous installation, that step is skipped, the database password is not updated, since the database structure is already found in the existing pvc.
After all, the root user is just a user of the database, its password is stored in the database. Unless the image applies any particular functionality at its start with its entrypoint, it makes sense to me that the password remain the same.
What image are you using? The docker hub mysql image or a custom one?
Update
Given the fact that you are using the mysql image on docker hub, let me quote a piece of the entrypoint (https://github.com/docker-library/mysql/blob/master/template/docker-entrypoint.sh)
# there's no database, so it needs to be initialized
if [ -z "$DATABASE_ALREADY_EXISTS" ]; then
docker_verify_minimum_env
# check dir permissions to reduce likelihood of half-initialized database
ls /docker-entrypoint-initdb.d/ > /dev/null
docker_init_database_dir "$#"
mysql_note "Starting temporary server"
docker_temp_server_start "$#"
mysql_note "Temporary server started."
docker_setup_db
docker_process_init_files /docker-entrypoint-initdb.d/*
mysql_expire_root_user
mysql_note "Stopping temporary server"
docker_temp_server_stop
mysql_note "Temporary server stopped"
echo
mysql_note "MySQL init process done. Ready for start up."
echo
fi
When the container starts, it makes some checks and if no database is found (and the database is expected to be on the path where the persisted pvc is mounted) a series of operations are performed, creating it, creating default users and so on.
Only in this case, the root user is created with the password specified in the environment (inside the function docker_setup_db)
Should a database already be available in the persisted path, which is your case since you let it mount the previous pvc, there's no initialization of the database, it already exists.
Everything in Kubernetes is working as expected, this is just the behaviour of the database and of the mysql image. The environment variable is used only for initialization, from what I can see in the entrypoint.
It is left to the root user to manually change the password, if desired, by using a mysql client.

mariadb crashes inside kubernetes pod with hostpath volume

I'm trying to move a number of docker containers on a linux server to a test kubernets-based deployment running on a different linux machine where I've installed kubernetes as a k3s instance inside a vagrant virtual machine.
One of these containers is a mariadb container instance, with a bind volume mapped
This is the relevant portion of the docker-compose I'm using:
academy-db:
image: 'docker.io/bitnami/mariadb:10.3-debian-10'
container_name: academy-db
environment:
- ALLOW_EMPTY_PASSWORD=yes
- MARIADB_USER=bn_moodle
- MARIADB_DATABASE=bitnami_moodle
volumes:
- type: bind
source: ./volumes/moodle/mariadb
target: /bitnami/mariadb
ports:
- '3306:3306'
Note that this works correctly. (the container is used by another application container which connects to it and reads data from the db without problems).
I then tried to convert this to a kubernetes configuration, copying the volume folder to the destination machine and using the following kubernetes .yaml deployment files.
This includes a deployment .yaml, a persistent volume claim and a persistent volume, as well as a NodePort service to make the container accessible. For the data volume, I'm using a simple hostPath volume pointing to the contents copied from the docker-compose's bind mounts.
apiVersion: apps/v1
kind: Deployment
metadata:
name: academy-db
spec:
replicas: 1
selector:
matchLabels:
name: academy-db
strategy:
type: Recreate
template:
metadata:
labels:
name: academy-db
spec:
containers:
- env:
- name: ALLOW_EMPTY_PASSWORD
value: "yes"
- name: MARIADB_DATABASE
value: bitnami_moodle
- name: MARIADB_USER
value: bn_moodle
image: docker.io/bitnami/mariadb:10.3-debian-10
name: academy-db
ports:
- containerPort: 3306
resources: {}
volumeMounts:
- mountPath: /bitnami/mariadb
name: academy-db-claim
restartPolicy: Always
volumes:
- name: academy-db-claim
persistentVolumeClaim:
claimName: academy-db-claim
---
apiVersion: v1
kind: PersistentVolume
metadata:
name: academy-db-pv
labels:
type: local
spec:
capacity:
storage: 1Gi
accessModes:
- ReadWriteOnce
persistentVolumeReclaimPolicy: Retain
hostPath:
path: "<...full path to deployment folder on the server...>/volumes/moodle/mariadb"
---
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: academy-db-claim
spec:
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 1Gi
storageClassName: ""
volumeName: academy-db-pv
---
apiVersion: v1
kind: Service
metadata:
name: academy-db-service
spec:
type: NodePort
ports:
- name: "3306"
port: 3306
targetPort: 3306
selector:
name: academy-db
after applying the deployment, everything seems to work fine, in the sense that with kubectl get ... the pod and the volumes seem to be running correctly
kubectl get pods
NAME READY STATUS RESTARTS AGE
academy-db-5547cdbc5-65k79 1/1 Running 9 15d
.
.
.
kubectl get pv
NAME CAPACITY ACCESS MODES RECLAIM POLICY STATUS CLAIM STORAGECLASS REASON AGE
academy-db-pv 1Gi RWO Retain Bound default/academy-db-claim 15d
.
.
.
kubectl get pvc
NAME STATUS VOLUME CAPACITY ACCESS MODES STORAGECLASS AGE
academy-db-claim Bound academy-db-pv 1Gi RWO 15d
.
.
.
This is the pod's log:
kubectl logs pod/academy-db-5547cdbc5-65k79
mariadb 10:32:05.66
mariadb 10:32:05.66 Welcome to the Bitnami mariadb container
mariadb 10:32:05.66 Subscribe to project updates by watching https://github.com/bitnami/bitnami-docker-mariadb
mariadb 10:32:05.66 Submit issues and feature requests at https://github.com/bitnami/bitnami-docker-mariadb/issues
mariadb 10:32:05.66
mariadb 10:32:05.67 INFO ==> ** Starting MariaDB setup **
mariadb 10:32:05.68 INFO ==> Validating settings in MYSQL_*/MARIADB_* env vars
mariadb 10:32:05.68 WARN ==> You set the environment variable ALLOW_EMPTY_PASSWORD=yes. For safety reasons, do not use this flag in a production environment.
mariadb 10:32:05.69 INFO ==> Initializing mariadb database
mariadb 10:32:05.69 WARN ==> The mariadb configuration file '/opt/bitnami/mariadb/conf/my.cnf' is not writable. Configurations based on environment variables will not be applied for this file.
mariadb 10:32:05.70 INFO ==> Using persisted data
mariadb 10:32:05.71 INFO ==> Running mysql_upgrade
mariadb 10:32:05.71 INFO ==> Starting mariadb in background
and the describe pod command:
Name: academy-db-5547cdbc5-65k79
Namespace: default
Priority: 0
Node: zdmp-kube/192.168.33.99
Start Time: Tue, 22 Dec 2020 13:33:43 +0000
Labels: name=academy-db
pod-template-hash=5547cdbc5
Annotations: <none>
Status: Running
IP: 10.42.0.237
IPs:
IP: 10.42.0.237
Controlled By: ReplicaSet/academy-db-5547cdbc5
Containers:
academy-db:
Container ID: containerd://68af105f15a1f503bbae8a83f1b0a38546a84d5e3188029f539b9c50257d2f9a
Image: docker.io/bitnami/mariadb:10.3-debian-10
Image ID: docker.io/bitnami/mariadb#sha256:1d8ca1757baf64758e7f13becc947b9479494128969af5c0abb0ef544bc08815
Port: 3306/TCP
Host Port: 0/TCP
State: Running
Started: Thu, 07 Jan 2021 10:32:05 +0000
Last State: Terminated
Reason: Error
Exit Code: 1
Started: Thu, 07 Jan 2021 10:22:03 +0000
Finished: Thu, 07 Jan 2021 10:32:05 +0000
Ready: True
Restart Count: 9
Environment:
ALLOW_EMPTY_PASSWORD: yes
MARIADB_DATABASE: bitnami_moodle
MARIADB_USER: bn_moodle
MARIADB_PASSWORD: bitnami
Mounts:
/bitnami/mariadb from academy-db-claim (rw)
/var/run/secrets/kubernetes.io/serviceaccount from default-token-x28jh (ro)
Conditions:
Type Status
Initialized True
Ready True
ContainersReady True
PodScheduled True
Volumes:
academy-db-claim:
Type: PersistentVolumeClaim (a reference to a PersistentVolumeClaim in the same namespace)
ClaimName: academy-db-claim
ReadOnly: false
default-token-x28jh:
Type: Secret (a volume populated by a Secret)
SecretName: default-token-x28jh
Optional: false
QoS Class: BestEffort
Node-Selectors: <none>
Tolerations: node.kubernetes.io/not-ready:NoExecute for 300s
node.kubernetes.io/unreachable:NoExecute for 300s
Events:
Type Reason Age From Message
---- ------ ---- ---- -------
Normal Pulled 15d (x8 over 15d) kubelet Container image "docker.io/bitnami/mariadb:10.3-debian-10" already present on machine
Normal Created 15d (x8 over 15d) kubelet Created container academy-db
Normal Started 15d (x8 over 15d) kubelet Started container academy-db
Normal SandboxChanged 18m kubelet Pod sandbox changed, it will be killed and re-created.
Normal Pulled 8m14s (x2 over 18m) kubelet Container image "docker.io/bitnami/mariadb:10.3-debian-10" already present on machine
Normal Created 8m14s (x2 over 18m) kubelet Created container academy-db
Normal Started 8m14s (x2 over 18m) kubelet Started container academy-db
Later, though, I notice that the client application has problems in connecting. After some investigation I've concluded that though the pod is running, the mariadb process running inside it could have crashed just after startup. If I enter the container with kubectl exec and try to run for instance the mysql client I get:
kubectl exec -it pod/academy-db-5547cdbc5-65k79 -- /bin/bash
I have no name!#academy-db-5547cdbc5-65k79:/$ mysql
ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/opt/bitnami/mariadb/tmp/mysql.sock' (2)
Any idea of what could cause the problem, or how can I investigate further the issue? (Note: I'm not an expert in Kubernetes, but started only recently to learn it)
Edit: Following #Novo's comment, I tried to delete the volume folder and let mariadb recreate the deployment from scratch.
Now my pod doesn't even start, terminating in CrashLoopBackOff !
By comparing the pod logs I notice that in the previous mariabd log there was a message:
...
mariadb 10:32:05.69 WARN ==> The mariadb configuration file '/opt/bitnami/mariadb/conf/my.cnf' is not writable. Configurations based on environment variables will not be applied for this file.
mariadb 10:32:05.70 INFO ==> Using persisted data
mariadb 10:32:05.71 INFO ==> Running mysql_upgrade
mariadb 10:32:05.71 INFO ==> Starting mariadb in background
Now replaced with
...
mariadb 14:15:57.32 INFO ==> Updating 'my.cnf' with custom configuration
mariadb 14:15:57.32 INFO ==> Setting user option
mariadb 14:15:57.35 INFO ==> Installing database
Could it be that the issue is related with some access right problem to the volume folders in the host vagrant machine?
By default, hostPath directories are created with permission 755, owned by the user and group of the kubelet. To use the directory, you can try adding the following to your deployment:
spec:
securityContext:
fsGroup: <gid>
Where gid is the group used by the process in your container.
Also, you could fix the issue on the host itself by changing the permissions of the folder you want to mount into the container:
chown-R <uid>:<gid> /path/to/volume
where uid and gid are the userId and groupId from your app.
chmod -R 777 /path/to/volume
This should solve your issue.
But overall, a deployment is not what you want to create in this case, because deployments should not have state. For stateful apps, there are 'StatefulSets' in Kubernetes. Use those together with a 'VolumeClaimTemplate' plus spec.securityContext.fsgroup and k3s will create the persitent volume and the persistent volume claim for you, using it's default storage class, which is local storage (on your node).

How to connect mysql kubernetes container internally with nodejs k8s container?

I have created mysql k8s container and nodejs k8s container under same namespace.I can't able to connect mysql db.(sequalize)
I have tried to connect using '''http://mysql.e-commerce.svc.cluster.local:3306'''.But i got "SequelizeHostNotFoundError" error.
Here is my service and deployment yaml files.
kind: Service
metadata:
labels:
app: mysql
name: mysql
namespace: e-commerce
spec:
type: NodePort
ports:
- port: 3306
targetPort: 3306
nodePort: 30306
selector:
app: mysql
---
apiVersion: extensions/v1beta1
kind: Deployment
metadata:
name: mysql
namespace: e-commerce
spec:
replicas: 1
template:
metadata:
labels:
app: mysql
spec:
containers:
- image: mysql:5.6
name: mysql-container
env:
- name: MYSQL_ROOT_PASSWORD
value: password
ports:
- containerPort: 3306
name: mysql
volumeMounts:
- name: mysql-persistent-storage
mountPath: /var/lib/mysql
volumes:
- name: mysql-persistent-storage
persistentVolumeClaim:
claimName: mysql-pv-claim```
From the ClusterIP worked for me or better way to go with the host name of the local cluster service ex. db-mysql.default.svc.cluster.local. This way if you cluster restarts and your IP changes, then you got it covered.
You are trying to access database with http protocol, leave it or change with mysql://ip:3306. Some clients won't accept DNS name for databases so you can check ClusterIP of service and try that IP too.
As mentioned by community member FL3SH you can change your spec.type to clusterIP.
You can reproduce this task using stable helm chart wordpress/mysql.
For newly created pods:
mysql-mariadb-0
mysql-wordpress
and services:
mysql-mariadb
mysql-wordpress
After successfully deployment you can verify if your service is working from the mysql-wordpress pod by running:
kubectl exec -it mysql-wordpress-7cb4958654-tqxm6 -- /bin/bash
In addition, you can install additional tools like nslooukp, telnet:
apt-get update && apt-get install dnsutils telnet
Services and connectivity with db you can test by running f.e. those commands:
nslookup mysql-mariadb
telnet mysql-mariadb 3306
mysql -uroot -hmysql-mariadb -p<your_db_password>
example output:
nslookup mysql-mariadb
Server: 10.125.0.10
Address: 10.125.0.10#53
Non-authoritative answer:
Name: mysql-mariadb.default.svc.cluster.local
Address: 10.125.0.76
mysql -u root -hmysql-mariadb -p<your_db_password>
Welcome to the MariaDB monitor. Commands end with ; or \g.
Your MariaDB connection id is 2068
Server version: 10.1.40-MariaDB Source distribution
You should be able to connect using service name or using ip address.
Inside this helm chart you can find also template for statefulset in order to create mysql pods.
Update
From the second pod f.e. ubuntu run this example - Node.js Mysql, install nodes.js and create connection to the database demo_db_connection.js
example:
var mysql = require('mysql');
var con = mysql.createConnection({
host: "mysql-mariadb",
user: "root",
password: "yourpassword"
});
con.connect(function(err) {
if (err) throw err;
console.log("Connected!");
});
run it:
root#ubuntu:~/test# node demo_db_connection.js
Connected!
Try with:
kind: Service
metadata:
labels:
app: mysql
name: mysql
namespace: e-commerce
spec:
clusterIP: None
type: ClusterIP
ports:
- port: 3306
targetPort: 3306
selector:
app: mysql
with the same connection string.

Kubernetes service dns resolution returning wrong IP

I have a simple MYSQL pod sitting behind a MYSQL service.
Additionally I have another pod that is running a python process that is trying to connect to the MYSQL pod.
If I try connecting to the IP address of the MYSQL pod manually from the python pod, everything is A-OK. However if I try connecting to the MYSQL service then I get an error that I can't connect to MYSQL.
grant#grant-Latitude-E7450:~/k8s/objects$ kubectl describe pod mysqlpod
Name: mysqlpod
Namespace: default
Node: minikube/192.168.99.100
Start Time: Fri, 20 Jan 2017 11:10:50 -0600
Labels: <none>
Status: Running
IP: 172.17.0.4
Controllers: <none>
grant#grant-Latitude-E7450:~/k8s/objects$ kubectl describe service mysqlservice
Name: mysqlservice
Namespace: default
Labels: <none>
Selector: db=mysqllike
Type: ClusterIP
IP: None
Port: <unset> 3306/TCP
Endpoints: 172.17.0.5:3306
Session Affinity: None
No events.
grant#grant-Latitude-E7450:~/k8s/objects$ kubectl describe pod basic-python-model
Name: basic-python-model
Namespace: default
Node: minikube/192.168.99.100
Start Time: Fri, 20 Jan 2017 12:01:50 -0600
Labels: db=mysqllike
Status: Running
IP: 172.17.0.5
Controllers: <none>
If I attach to my python container and do an nslookup of the mysqlservice, then I'm actually getting the wrong IP. As you saw above the IP of the mysqlpod is 172.17.0.4 while nslookup mysqlservice is resolving to 172.17.0.5.
grant#grant-Latitude-E7450:~/k8s/objects$ k8s exec -it basic-python-model bash
[root#basic-python-model /]# nslookup mysqlservice
Server: 10.0.0.10
Address: 10.0.0.10#53
Name: mysqlservice.default.svc.cluster.local
Address: 172.17.0.5
I'm fairly new to kubernetes, but I've been banging my head on this issue for a few hours and I can't seem to understand what I'm doing wrong.
So this was the exact correct behavior but I just misconfigured my pods.
For future people who are stuck:
The selector defined in a kubernetes service must match the label of the pod(s) you wish to serve. IE) In my MySqlService.yaml file I have the name selector for "mysqlpod":
apiVersion: v1
kind: Service
metadata:
name: mysqlservice
spec:
clusterIP: None
ports:
- port: 3306
targetPort: 3306
selector:
name: mysqlpod
Thus in my MySqlPod.yaml file I need an exactly matching label.
kind: Pod
apiVersion: v1
metadata:
name: mysqlpod
labels:
name: mysqlpod
spec:
...
For anyone coming again here, please check #gnicholas answer, but also make sure that clusterIP: None is correctly set.
I happened to indent clusterIP: None too much in the .yml file and the command was ignored by Kubernetes therefore clusterIP was mistakenly assigned causing the wrong IP issue.
Be aware that the validation won't throw any error, but will silently ignore it.