Minikube: docker driver: Persistent Volume data not restored after minikube new start

[dpolivaev]

With minikube versions v1.9.2 up to v1.11.0 data contained in persistent volumes created by persistent volume claim is not restored after minikube is stopped and started again.

To demonstrate it I install mysql helm template from https://github.com/helm/charts/tree/master/stable/mysql
I connect to mysql using CLI client and create a new user testuser and obtain a list of all users to check that the user was created.

After I stop and restart minikube, connec to mysql again and obtain the user list again, the created user is not available. It indicates that all mysql databases are reset to their original state.

Actually, no data is restored after minikube starts again, and all files are recreated.

Minikube v1.8.2 works as expected.

Please see the log below.

Steps to reproduce the issue:
~~~~
dimitry-> minikube start
😄 minikube v1.11.0 on Ubuntu 18.04
✨ Automatically selected the docker driver
👍 Starting control plane node minikube in cluster minikube
🔥 Creating docker container (CPUs=2, Memory=3900MB) ...
🐳 Preparing Kubernetes v1.18.3 on Docker 19.03.2 ...
▪ kubeadm.pod-network-cidr=10.244.0.0/16
🔎 Verifying Kubernetes components...
🌟 Enabled addons: default-storageclass, storage-provisioner
🏄 Done! kubectl is now configured to use "minikube"
dimitry-> helm repo list
NAME URL
stable https://kubernetes-charts.storage.googleapis.com
dimitry-> helm install mysql stable/mysql
NAME: mysql
LAST DEPLOYED: Thu Jun 11 20:09:08 2020
NAMESPACE: default
STATUS: deployed
REVISION: 1
NOTES:
MySQL can be accessed via port 3306 on the following DNS name from within your cluster:
mysql.default.svc.cluster.local

To get your root password run:

MYSQL_ROOT_PASSWORD=$(kubectl get secret --namespace default mysql -o jsonpath="{.data.mysql-root-password}" | base64 --decode; echo)

To connect to your database:

1. Run an Ubuntu pod that you can use as a client:

   kubectl run -i --tty ubuntu --image=ubuntu:16.04 --restart=Never -- bash -il

2. Install the mysql client:

   $ apt-get update && apt-get install mysql-client -y

3. Connect using the mysql cli, then provide your password:
   $ mysql -h mysql -p

To connect to your database directly from outside the K8s cluster:
MYSQL_HOST=127.0.0.1
MYSQL_PORT=3306

# Execute the following command to route the connection:
kubectl port-forward svc/mysql 3306

mysql -h ${MYSQL_HOST} -P${MYSQL_PORT} -u root -p${MYSQL_ROOT_PASSWORD}

dimitry-> kubectl get secret --namespace default mysql -o jsonpath="{.data.mysql-root-password}" | base64 --decode; echo
qA2IHCiKkV
dimitry-> kubectl run -i --tty ubuntu --image=ubuntu:16.04 --restart=Never -- bash -il
If you don't see a command prompt, try pressing enter.
root@ubuntu:/#
root@ubuntu:/# apt-get update && apt-get install mysql-client -y
root@ubuntu:/# mysql -h mysql -p
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 39
Server version: 5.7.30 MySQL Community Server (GPL)

Copyright (c) 2000, 2020, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> CREATE USER 'testuser'@'localhost' IDENTIFIED BY 'test123test!';
Query OK, 0 rows affected (0.00 sec)

mysql> SELECT User,Host FROM mysql.user;
+---------------+-----------+
| User | Host |
+---------------+-----------+
| root | % |
| mysql.session | localhost |
| mysql.sys | localhost |
| root | localhost |
| testuser | localhost |
+---------------+-----------+
5 rows in set (0.00 sec)

mysql> ^DBye
root@ubuntu:/# logout
dimitry-> kubectl delete pod ubuntu
pod "ubuntu" deleted
dimitry-> minikube stop
✋ Stopping "minikube" in docker ...
🛑 Powering off "minikube" via SSH ...
🛑 Node "minikube" stopped.
dimitry-> minikube start
😄 minikube v1.11.0 on Ubuntu 18.04
✨ Using the docker driver based on existing profile
👍 Starting control plane node minikube in cluster minikube
🔄 Restarting existing docker container for "minikube" ...
🐳 Preparing Kubernetes v1.18.3 on Docker 19.03.2 ...
▪ kubeadm.pod-network-cidr=10.244.0.0/16
🔎 Verifying Kubernetes components...
🌟 Enabled addons: default-storageclass, storage-provisioner
🏄 Done! kubectl is now configured to use "minikube"
kubectl run -i --tty ubuntu --image=ubuntu:16.04 --restart=Never -- bash -il
If you don't see a command prompt, try pressing enter.
root@ubuntu:/#
root@ubuntu:/# apt-get update && apt-get install mysql-client -y
root@ubuntu:/# mysql -h mysql -p
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 39
Server version: 5.7.30 MySQL Community Server (GPL)

Copyright (c) 2000, 2020, Oracle and/or its affiliates. All rights reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

mysql> SELECT User,Host FROM mysql.user;
+---------------+-----------+
| User | Host |
+---------------+-----------+
| root | % |
| mysql.session | localhost |
| mysql.sys | localhost |
| root | localhost |
+---------------+-----------+
4 rows in set (0.00 sec)

mysql> ^DBye
root@ubuntu:/# logout
~~~~

[dpolivaev]

The issue may be related to https://github.com/kubernetes/minikube/issues/7828

[medyagh]

@dpolivaev do you mind sharing what addons do u have enabled?

minikube addons list

[medyagh]

@afbjorklund could this be something about storage provisioner?

[dpolivaev]

~~
dimitry-> minikube start
😄 minikube v1.11.0 on Ubuntu 18.04
✨ Automatically selected the docker driver
👍 Starting control plane node minikube in cluster minikube
🔥 Creating docker container (CPUs=2, Memory=3900MB) ...
🐳 Preparing Kubernetes v1.18.3 on Docker 19.03.2 ...
▪ kubeadm.pod-network-cidr=10.244.0.0/16
🔎 Verifying Kubernetes components...
🌟 Enabled addons: default-storageclass, storage-provisioner
🏄 Done! kubectl is now configured to use "minikube"
dimitry-> minikube addons list
|-----------------------------|----------|--------------|
| ADDON NAME | PROFILE | STATUS |
|-----------------------------|----------|--------------|
| ambassador | minikube | disabled |
| dashboard | minikube | disabled |
| default-storageclass | minikube | enabled ✅ |
| efk | minikube | disabled |
| freshpod | minikube | disabled |
| gvisor | minikube | disabled |
| helm-tiller | minikube | disabled |
| ingress | minikube | disabled |
| ingress-dns | minikube | disabled |
| istio | minikube | disabled |
| istio-provisioner | minikube | disabled |
| logviewer | minikube | disabled |
| metallb | minikube | disabled |
| metrics-server | minikube | disabled |
| nvidia-driver-installer | minikube | disabled |
| nvidia-gpu-device-plugin | minikube | disabled |
| olm | minikube | disabled |
| registry | minikube | disabled |
| registry-aliases | minikube | disabled |
| registry-creds | minikube | disabled |
| storage-provisioner | minikube | enabled ✅ |
| storage-provisioner-gluster | minikube | disabled |
|-----------------------------|----------|--------------|
~~

[afbjorklund]

I think it is more related to #8151, and storing the PV on tmpfs ?

[dpolivaev]

Looks you are right. The missing data is placed in directories under /tmp/hostpath-provisioner

[dpolivaev]

https://minikube.sigs.k8s.io/docs/handbook/persistent_volumes/ says them to be persisted

[afbjorklund]

Minikube v1.8.2 works as expected.

Probably because it didn't default to the "docker" driver ? I don't think this has changed in KIC

[afbjorklund]

https://minikube.sigs.k8s.io/docs/handbook/persistent_volumes/ says them to be persisted

Unfortunately that only applies to the VM, it is not valid for the "none" driver or the "docker" driver.

[dpolivaev]

Sorry, I have not got it.
I see the directories if I execute minikube ssh followed by cd /tmp/hostpath-provisioner
Are they not on VM?
I use minikube with VirtualBox as recommended.

[afbjorklund]

An alternative solution is #7511, where the mount point is moved to the (persisted) /var/tmp

[afbjorklund]

I use minikube with VirtualBox as recommended.

Hmm, maybe that is the problem here then:

😄 minikube v1.11.0 on Ubuntu 18.04
✨ Automatically selected the docker driver

You need to add --driver=virtualbox, if so.

But the volumes _should_ be persisted also on the container-based version (KIC) of minikube.
Just that it hasn't been implemented yet. We should also persist all of /data, for manual data.

[dpolivaev]

Anyway my intended use case is running minikube on AWS with --driver=none
Are the data lost in this case too?

[dpolivaev]

Minikube v1.8.2 uses virtualbox driver by default.
It looks like it is the reason why my test worked with v1.8.2

I would appreciate if you tell me what happens with --driver=none.
I expect that the directories do not have to be saved and restored because they are saved on the host machine.

[dpolivaev]

I confirm that using --driver=virtualbox fixes it

[medyagh]

thanks for confriming I will add this bug to v1.13.0 milestone, I am looking for help for this issue, if you are an expert in storage and mounts specailly for docker driver your help is wanted.

[afbjorklund]

I would appreciate if you tell me what happens with --driver=none.
I expect that the directories do not have to be saved and restored because they are saved on the host machine.

You will have to set up the mounts yourself, otherwise the contents will disappear when the host machine is rebooted. You are supposed to provide the bind mounts for the persistent storage:

    /data
    /tmp/hostpath_pv
    /tmp/hostpath-provisioner

To some suitable place on the host, where the contents will be kept.

For instance you could have a special data partition, that you mount.

[Harkishen-Singh]

I didnt get this. Is this behaviour intentional or do we want to persist /data, /tmp/hostpath* even on --driver=none || docker || podman? In short, what do we exactly mean by bug here?

@afbjorklund @medyagh

[afbjorklund]

@Harkishen-Singh : It means that when you are using the "none" driver, it is up to you to set a permanent storage location and then bind mount this to the expected paths. When using the "docker" or "podman" drivers, then minikube _should_ do it.

The bug here is that the persistent storage is kept on tmpfs by default, due to #8151. It is a bug in the kic base image. When using the virtualbox VM, the files _are_ persisted correctly... They are supposed to be stored on the disk image / volume.

[afbjorklund]

This issue is a duplicate of #8151 so it will be solved at the same time.