Configure Kubernetes bitnami/mariadb container to mount minikube volume - docker

Question

I've been hitting errors when trying to set up a dev platform in Kubernetes & minikube. The config is creating a service, persistentVolume, persistentVolumeClaim & deployment.
The deployment is creating a single pod with a single container based on bitnami/mariadb:latest
I am mounting a local volume into the minikube vm via:
minikube mount <source-path>:/data
This local volume is mounting correctly and can be inspected when I ssh into the minikube vm via: minikube ssh
I now run:
kubectl create -f mariadb-deployment.yaml
to fire up the platform, the yaml config:
kind: Service
apiVersion: v1
metadata:
name: mariadb-deployment
labels:
app: supertubes
spec:
ports:
- port: 3306
selector:
app: supertubes
tier: mariadb
type: LoadBalancer
---
kind: PersistentVolume
apiVersion: v1
metadata:
name: local-db-pv
labels:
type: local
tier: mariadb
app: supertubes
spec:
storageClassName: slow
capacity:
storage: 10Gi
accessModes:
- ReadWriteOnce
hostPath:
path: "/data/staging/sumatra/mariadb-data"
---
kind: PersistentVolumeClaim
apiVersion: v1
metadata:
name: local-db-pv-claim
labels:
app: supertubes
spec:
storageClassName: slow
accessModes:
- ReadWriteOnce
resources:
requests:
storage: 10Gi
selector:
matchLabels:
type: local
tier: mariadb
---
kind: Deployment
apiVersion: apps/v1
metadata:
name: mariadb-deployment
labels:
app: supertubes
spec:
selector:
matchLabels:
app: supertubes
tier: mariadb
template:
metadata:
labels:
app: supertubes
tier: mariadb
spec:
securityContext:
fsGroup: 1001
containers:
- image: bitnami/mariadb:latest
name: mariadb
env:
- name: MARIADB_ROOT_PASSWORD
value: <db-password>
- name: MARIADB_DATABASE
value: <db-name>
ports:
- containerPort: 3306
name: mariadb
volumeMounts:
- name: mariadb-persistent-storage
mountPath: /bitnami
volumes:
- name: mariadb-persistent-storage
persistentVolumeClaim:
claimName: local-db-pv-claim
The above config will then fail to boot the pod and inspecting the pods logs within minikube dashboard shows the following:
nami INFO Initializing mariadb
mariadb INFO ==> Cleaning data dir...
mariadb INFO ==> Configuring permissions...
mariadb INFO ==> Validating inputs...
mariadb INFO ==> Initializing database...
mariadb INFO ==> Creating 'root' user with unrestricted access...
mariadb INFO ==> Creating database pw_tbs...
mariadb INFO ==> Enabling remote connections...
Error executing 'postInstallation': EACCES: permission denied, mkdir '/bitnami/mariadb'
Looking at the above I believed the issue was to do with Bitnami using user: 1001 to launch their mariadb image:
https://github.com/bitnami/bitnami-docker-mariadb/issues/134
Since reading the above issue I've been playing with securityContext within the containers spec. At present you'll see I have it set to:
deployment.template.spec
securityContext:
fsGroup: 1001
but this isn't working. I've also tried:
securityContext:
privileged: true
but didn't get anywhere with that either.
One other check I made was to remove the volumeMount from deployment.template.spec.containers and see if things worked correctly without it, which they do :)
I then opened a shell into the pod to see what the permissions on /bitnami are:
Reading a bit more on the Bitnami issue posted above it says the user: 1001 is a member of the root group, therefore I'd expect them to have the neccessary permissions... At this stage I'm a little lost as to what is wrong.
If anyone could help me understand how to correctly set up this minikube vm volume within a container that would be amazing!
Edit 15/03/18
Following #Anton Kostenko's suggestions I added a busybox container as an initContainer which ran a chmod on the bitnami directory:
...
spec:
initContainers:
- name: install
image: busybox
imagePullPolicy: Always
command: ["chmod", "-R", "777", "/bitnami"]
volumeMounts:
- name: mariadb-persistent-storage
mountPath: /bitnami
containers:
- image: bitnami/mariadb:latest
name: mariadb
...
however even with setting global rwx permissions (777) the directory couldn't mount as the MariaDB container doesn't allow user 1001 to do so:
nami INFO Initializing mariadb
Error executing 'postInstallation': EPERM: operation not permitted, utime '/bitnami/mariadb/.restored'
Another Edit 15/03/18
Have now tried setting the user:group on my local machine (MacBook) so that when passed to the minikube vm they should already be correct:
Now mariadb-data has rwx permission for eveyone and user: 1001, group: 1001
I then removed the initContainer as I wasn't really sure what that would be adding.
SSHing onto the minikube vm I can see the permissions and user:group have been carried across:
The user & group now being set as docker
Firing up this container results in the same sort of error:
nami INFO Initializing mariadb
Error executing 'postInstallation': EIO: i/o error, utime '/bitnami/mariadb/.restored'
I've tried removing the securityContext, and also adding it as runAsUser: 1001, fsGroup: 1001, however neither made any difference.

Answer 1

Looks like that is an issue in Minikube.
You can try to use the init-container which will fix a permissions before main container will be started, like this:
...........
spec:
initContainers:
- name: "fix-non-root-permissions"
image: "busybox"
imagePullPolicy: "Always"
command: [ "chmod", "-R", "g+rwX", "/bitnami" ]
volumeMounts:
- name: datadir
mountPath: /bitnami
containers:
.........