I'm trying to deploy postgres using Kubernetes. This step works well.
But now I need to customised the pg_hba.conf file. So the idea is to use a configMap to mount the personal file.
Here are my deployment file:
apiVersion: v1
kind: ConfigMap
metadata:
name: pg-hba-configmap
data:
pg_hba.conf: |+
# TYPE DATABASE USER ADDRESS METHOD
# Some personal settings here
---
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: db
spec:
selector:
matchLabels:
app: db
serviceName: db
replicas: 1
template:
metadata:
labels:
app: db
spec:
nodeSelector:
db: 'true'
containers:
- name: db
image: kartoza/postgis:10.0-2.4
volumeMounts:
- name: data-volume
mountPath: /var/lib/postgresql
- name: pg-hba-config-volume
mountPath: /var/lib/postgresql/10/main/pg_hba.conf
subPath: pg_hba.conf
volumes:
- name: data-volume
hostPath:
path: /data/db
- name: pg-hba-config-volume
configMap:
name: pg-hba-configmap
But this doesn't work. The db is in Error state. In logs, I can see this:
chown: changing ownership of '/var/lib/postgresql/10/main/pg_hba.conf': Read-only file system
Also, on the server where is mounted the database, I only have this:
root#server:/data/db/10/main# ls -l
total 0
-rwxr-xr-x 1 root root 0 Oct 8 08:49 pg_hba.conf
I should have all the database here. It's like if all the folder was overwritten.
What am I doing wrong here and how can I mount my customised config ?
Thanks
Related
I have kubernetes cluster with two replicas of a PostgreSQL database in it, and I wanted to see the values stored in the database.
When I exec myself into one of the two postgres pod (kubectl exec --stdin --tty [postgres_pod] -- /bin/bash) and check the database from within, I have only a partial part of the DB. The rest of the DB data is on the other Postgres pod, and I don't see any directory created by the persistent volumes with all the database stored.
So in short I create 4 tables; in one postgres pod I have 4 tables but 2 are empty, in the other postgres pod there are 3 tables and the tables that were empty in the first pod, here are filled with data.
Why the pods don't have the same data in it?
How can I access and download the entire database?
PS. I deploy the cluster using HELM in minikube.
Here are the YAML files:
---
apiVersion: v1
kind: ConfigMap
metadata:
name: postgres-config
labels:
app: postgres
data:
POSTGRES_DB: database-pg
POSTGRES_USER: postgres
POSTGRES_PASSWORD: postgres
PGDATA: /data/pgdata
---
kind: PersistentVolume
apiVersion: v1
metadata:
name: postgres-pv-volume
labels:
type: local
app: postgres
spec:
storageClassName: manual
capacity:
storage: 1Gi
accessModes:
- ReadWriteMany
hostPath:
path: "/mnt/data"
---
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
name: postgres-pv-claim
spec:
storageClassName: manual
accessModes:
- ReadWriteMany
resources:
requests:
storage: 1Gi
---
apiVersion: v1
kind: Service
metadata:
name: postgres
labels:
app: postgres
spec:
ports:
- name: postgres
port: 5432
nodePort: 30432
type: NodePort
selector:
app: postgres
---
apiVersion: apps/v1
kind: StatefulSet
metadata:
name: postgres
spec:
serviceName: postgres-service
selector:
matchLabels:
app: postgres
replicas: 2
template:
metadata:
labels:
app: postgres
spec:
containers:
- name: postgres
image: postgres:13.2
volumeMounts:
- name: postgres-disk
mountPath: /data
# Config from ConfigMap
envFrom:
- configMapRef:
name: postgres-config
volumeClaimTemplates:
- metadata:
name: postgres-disk
spec:
accessModes: ["ReadWriteOnce"]
---
apiVersion: apps/v1
kind: Deployment
metadata:
name: postgres
labels:
app: postgres
spec:
selector:
matchLabels:
app: postgres
replicas: 2
template:
metadata:
labels:
app: postgres
spec:
containers:
- name: postgres
image: postgres:13.2
imagePullPolicy: IfNotPresent
envFrom:
- configMapRef:
name: postgres-config
volumeMounts:
- mountPath: /var/lib/postgresql/data
name: postgredb
volumes:
- name: postgredb
persistentVolumeClaim:
claimName: postgres-pv-claim
---
I found a solution to my problem of downloading the volume directory, however when I run multiple replicasets of postgres, the tables of the DB are still scattered between the pods.
Here's what I did to download the postgres volume:
First of all, minikube supports some specific directories for volume appear:
minikube is configured to persist files stored under the following directories, which are made in the Minikube VM (or on your localhost if running on bare metal). You may lose data from other directories on reboots.
/data
/var/lib/minikube
/var/lib/docker
/tmp/hostpath_pv
/tmp/hostpath-provisioner
So I've changed the mount path to be under the /data directory. This made the database volume visible.
After this I ssh'ed into minikube and copied the database volume to a new directory (I used /home/docker as the user of minikube is docker).
sudo cp -R /data/pgdata /home/docker
The volume pgdata was still owned by root (access denied error) so I changed it to be owned by docker. For this I also set a new password which I knew:
sudo passwd docker # change password for docker user
sudo chown -R docker: /home/docker/pgdata # change owner from root to docker
Then you can exit and copy the directory into you local machine:
exit
scp -r $(minikube ssh-key) docker#$(minikube ip):/home/docker/pgdata [your_local_path].
NOTE
Mario's advice, which is to use pgdump is probably a better solution to copy a database. I still wanted to download the volume directory to see if it has the full database, when the pods have only a part of all the tables. In the end it turned out it doesn't.
I'm trying to deploy Postgresql on Azure Kubernetes with data persistency. So I'm using PVC.
I searched lots of posts on here, most of them offered yaml files like below, but it's giving the error below;
chmod: changing permissions of '/var/lib/postgresql/data/pgdata': Operation not permitted
The files belonging to this database system will be owned by user "postgres".
This user must also own the server process.
The database cluster will be initialized with locale "en_US.utf8".
The default database encoding has accordingly been set to "UTF8".
The default text search configuration will be set to "english".
Data page checksums are disabled.
initdb: error: could not change permissions of directory "/var/lib/postgresql/data/pgdata": Operation not permitted
fixing permissions on existing directory /var/lib/postgresql/data/pgdata ...
deployment yaml file is below;
apiVersion: apps/v1
kind: Deployment
metadata:
name: postgresql
spec:
replicas: 1
selector:
matchLabels:
app: postgresql
template:
metadata:
labels:
app: postgresql
spec:
containers:
- name: postgresql
image: postgres:13.2
securityContext:
runAsUser: 999
imagePullPolicy: "IfNotPresent"
ports:
- containerPort: 5432
envFrom:
- secretRef:
name: postgresql-secret
volumeMounts:
- mountPath: /var/lib/postgresql/data
name: postgredb-kap
volumes:
- name: postgredb-kap
persistentVolumeClaim:
claimName: postgresql-pvc
Secret yaml is below;
apiVersion: v1
kind: Secret
metadata:
name: postgresql-secret
type: Opaque
data:
POSTGRES_DB: a2V5sd4=
POSTGRES_USER: cG9zdGdyZXNhZG1pbg==
POSTGRES_PASSWORD: c234Rw==
PGDATA: L3Za234dGF0YQ==
pvc and sc yaml files are below:
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
name: postgresql-pvc
labels:
app: postgresql
spec:
storageClassName: postgresql-sc
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 5Gi
---
allowVolumeExpansion: true
apiVersion: storage.k8s.io/v1
kind: StorageClass
metadata:
name: postgresql-sc
mountOptions:
- dir_mode=0777
- file_mode=0777
- uid=1000
- gid=1000
parameters:
skuName: Standard_LRS
provisioner: kubernetes.io/azure-file
reclaimPolicy: Retain
So when I use the mountpath like "- mountPath: /var/lib/postgresql/", it's working. I can reach the DB and it's good. But when I delete the pod and recreating, there is no DB! So no data persistency.
Can you please help, what am I missing here?
Thanks!
One thing you could try is to change uid=1000,gid=1000 in mount options to 999 since this is the uid of postgres user in postgres conatiner (I didn't test this).
Another solution that will for certain solve this issue involves init conatainers.
Postgres container requires to start as root to be able to chown pgdata dir since its mounted as root dir. After it does this, it drops root permisions and runs as postgres user.
But you can use init container (running as root) to chmod the volume dir so that you can run main container as non-root.
Here is an example:
initContainers:
- name: init
image: alpine
command: ["sh", "-c", "chown 999:999 /var/lib/postgresql/data"]
volumeMounts:
- mountPath: /var/lib/postgresql/data
name: postgredb-kap
Based on the helpful answer from Matt. For bitnami postgresql the initContainer also works but with a slightly different configuration:
initContainers:
- name: init
image: alpine
command: ["sh", "-c", "chown 1001:1001 /bitnami/postgresql"]
volumeMounts:
- mountPath: /bitnami/postgresql
name: postgres-volume
I’m getting started with kubernetes, and I want to create a simple app with a single webserver & postgres database. The problem I’m running into is the deployment of the postgres is giving me permission errors. The following are discussions around this:
https://github.com/docker-library/postgres/issues/116
https://github.com/docker-library/postgres/issues/103
https://github.com/docker-library/postgres/issues/696
Can't get either Postgres permissions or PVC working in AKS
Kubernetes - Pod which encapsulates DB is crashing
Mount local directory into pod in minikube
https://serverfault.com/questions/981459/minikube-using-a-storageclass-to-provision-data-outside-of-tmp
EDIT
spec:
OSX - 10.15.4
minikube - v1.9.2
kubernetes - v1.18.2
minikube setup
minikube start --driver=virtualbox --cpus=2 --memory=5120 --kubernetes-version=v1.18.2 --container-runtime=docker --mount=true --mount-string=/Users/holmes/kubernetes/pgdata:/data/pgdata
The permission error: chmod: changing permissions of '/var/lib/postgresql/data': Operation not permitted
I am trying to mount a local OS directory into minikube to be used with the postgres deployment/pod/container volume mount.
After I run the above setup I ssh into minikube (minikube ssh) and check the permissions
# minikube: /
drwxr-xr-x 3 root root 4096 May 13 19:31 data
# minikube: /data
drwx------ 1 docker docker 96 May 13 19:27 pgdata
By running the script below the chmod permission error surfaces. If I change the --mount-string=/Users/holmes/kubernetes/pgdata:/data (leave out /pgdata) and then minikube ssh to create the pgdata directory:
mkdir -p /data/pgdata
chmod 777 /data/pgdata
I get a different set of permissions before deployment
# minikube: /
drwx------ 1 docker docker 96 May 13 20:10 data
# minikube: /data
drwxrwxrwx 1 docker docker 64 May 13 20:25 pgdata
and after deployment
# minikube: /
drwx------ 1 docker docker 128 May 13 20:25 data
# minikube: /data
drwx------ 1 docker docker 64 May 13 20:25 pgdata
Not sure why this changes, and the chmod permission error persists. It seems like the above reference links are bouncing around different methods on different machines on different vms which I don’t understand nor can I get this to work. Can someone walk me getting this to work? Super confused going through all the above discussions.
postgres.yaml
apiVersion: v1
kind: Namespace
metadata:
name: data-block
---
apiVersion: v1
kind: ConfigMap
metadata:
name: postgres-config
namespace: data-block
labels:
type: starter
data:
POSTGRES_DB: postgres
POSTGRES_USER: postgres
POSTGRES_PASSWORD: docker
---
apiVersion: v1
kind: PersistentVolume
metadata:
name: postgres-pv
namespace: data-block
labels:
app: postgres
spec:
capacity:
storage: 2Gi
accessModes:
- ReadWriteOnce
hostPath:
path: /data/pgdata
---
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: postgres-pv-claim
namespace: data-block
labels:
app: postgres
spec:
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 1Gi
storageClassName: ""
---
apiVersion: apps/v1
kind: Deployment
metadata:
name: postgres
namespace: data-block
spec:
replicas: 1
selector:
matchLabels:
app: postgres
template:
metadata:
labels:
app: postgres
spec:
containers:
- name: postgres
image: postgres:12.2
ports:
- containerPort: 5432
envFrom:
- configMapRef:
name: postgres-config
volumeMounts:
- name: postgres-vol
mountPath: /var/lib/postgresql/data
volumes:
- name: postgres-vol
persistentVolumeClaim:
claimName: postgres-pv-claim
UPDATE
I went ahead and updated the deployment script to a simple pod. The goal is map the postgres /var/lib/postgresql/data to my local file directory /Users/<my-path>/database/data to persist the data.
---
apiVersion: v1
kind: Pod
metadata:
name: postgres-pod
namespace: data-block
labels:
name: postgres-pod
spec:
containers:
- name: postgres
image: postgres:12.3
imagePullPolicy: IfNotPresent
ports:
- name: postgres-port
containerPort: 5432
envFrom:
- configMapRef:
name: postgres-env-config
- secretRef:
name: postgres-secret
volumeMounts:
- name: postgres-vol
mountPath: /var/lib/postgresql/data
volumes:
- name: postgres-vol
hostPath:
path: /Users/<my-path>/database/data
restartPolicy: Never
The error: initdb: error: could not access directory "/var/lib/postgresql/data": Permission denied
How to go about mounting the local file directory?
You are declaring the PGDATA field that maybe the cause of the issue. I faced the same error, this comes because there's as LOST+FOUND folder already in that directory however, the container wants it to be a empty dir. Giving the subPath field solves this issue. Please try this it should solve the issue and you need not need any PGDATA field. Try omitting it from your configmap and add subPath to some folder. Please go through following manifests.
https://github.com/mendix/kubernetes-howto/blob/master/postgres-deployment.yaml
https://www.bmc.com/blogs/kubernetes-postgresql/
it's a statefulset that usually you should go with and not a deployment when it comes to Database deployment.
- name: postgredb
mountPath: /var/lib/postgresql/data
#setting subPath will fix your issue it can be pgdata or
postgres or any other folder name according to your
choice.
subPath: postgres
So I'm just trying to get a web app running on GKE experimentally to familiarize myself with Kubernetes and GKE.
I have a statefulSet (Postgres) with a persistent volume/ persistent volume claim which is mounted to the Postgres pod as expected. The problem I'm having is having the Postgres data endure. If I mount the PV at var/lib/postgres the data gets overridden with each pod update. If I mount at var/lib/postgres/data I get the warning:
initdb: directory "/var/lib/postgresql/data" exists but is not empty
It contains a lost+found directory, perhaps due to it being a mount point.
Using a mount point directly as the data directory is not recommended.
Create a subdirectory under the mount point.
Using Docker alone having the volume mount point at var/lib/postgresql/data works as expected and data endures, but I don't know what to do now in GKE. How does one set this up properly?
Setup file:
---
apiVersion: v1
kind: PersistentVolumeClaim
metadata:
name: sm-pd-volume-claim
spec:
storageClassName: "standard"
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 1G
---
apiVersion: "apps/v1"
kind: "StatefulSet"
metadata:
name: "postgis-db"
namespace: "default"
labels:
app: "postgis-db"
spec:
serviceName: "postgis-db"
replicas: 1
selector:
matchLabels:
app: "postgis-db"
template:
metadata:
labels:
app: "postgis-db"
spec:
terminationGracePeriodSeconds: 25
containers:
- name: "postgis"
image: "mdillon/postgis"
ports:
- containerPort: 5432
name: postgis-port
volumeMounts:
- name: sm-pd-volume
mountPath: /var/lib/postgresql/data
volumes:
- name: sm-pd-volume
persistentVolumeClaim:
claimName: sm-pd-volume-claim
You are getting this error because the postgres pod has tried to mount the data directory on / folder. It is not recommended to do so.
You have to create subdirectory to resolve this issues on the statefulset manifest yaml files.
volumeMounts:
- name: sm-pd-volume
mountPath: /var/lib/postgresql/data
subPath: data
I'm trying to setup PostgreSQL on Minikube with data path being my host folder mounted on Minikube (I'd like to keep my data on host).
With the kubernetes object created (below) I get permission error, the same one as here How to solve permission trouble when running Postgresql from minikube? although the question mentioned doesn't answer the issue. It advises to mount minikube's VM dir instead.
---
apiVersion: apps/v1
kind: Deployment
metadata:
name: postgres
labels:
app: postgres
spec:
replicas: 1
selector:
matchLabels:
app: postgres
template:
metadata:
labels:
app: postgres
spec:
containers:
- name: postgres
image: postgres
volumeMounts:
- mountPath: /var/lib/postgresql/data
name: storage
env:
- name: POSTGRES_PASSWORD
value: user
- name: POSTGRES_USER
value: pass
- name: POSTGRES_DB
value: k8s
volumes:
- name: storage
hostPath:
path: /data/postgres
Is there any other way to do that other than building own image on top of Postgres and playing with the permissions somehow? I'm on macOS with Minikube 0.30.0 and I'm experiencing that with both Virtualbox and hyperkit drivers for Minikube.
Look at these lines from here : hostPath
the files or directories created on the underlying hosts are only writable by root. You either need to run your process as root in a privileged Container or modify the file permissions on the host to be able to write to a hostPath volume
So, either you have to run as root or you have to change the file permission of /data/postgres directory.
However, you can run your Postgres container as root without rebuilding docker image.
You have to add following to your container:
securityContext:
runAsUser: 0
Your yaml should look like this:
apiVersion: apps/v1
kind: Deployment
metadata:
name: postgres
labels:
app: postgres
spec:
replicas: 1
selector:
matchLabels:
app: postgres
template:
metadata:
labels:
app: postgres
spec:
containers:
- name: postgres
image: postgres
volumeMounts:
- mountPath: /var/lib/postgresql/data
name: storage
env:
- name: POSTGRES_PASSWORD
value: user
- name: POSTGRES_USER
value: pass
- name: POSTGRES_DB
value: k8s
securityContext:
runAsUser: 0
volumes:
- name: storage
hostPath:
path: /data/postgres