I am running a docker image for Juypter and tensorboard. The data seem to get deleted everytime the VM instance is stopped is there away to stop this from happening i could find anything on the web that would allow me to do this?
TL;DR: You are not persisting your data.
Docker containers does not persist data out of the box, you need to explicity tell docker to persist any data created inside the container when the container is deleted.
You can read more at Use volumes page at Docker documentation.
If you want to persist data you need to do the next steps:
Create a local volume inside the VM where you want to persist data. This command should be executed on the GCE instance
mkdir -p /opt/data/jupyterdata
Set the correct ownership of the folder to the user id that the user inside your container uses. For example, let's imagine that your container lspvic/tensorboard-notebook run the application using the user tensorflow with the UID 1500. So you need to set the ownership of your folder to the UID 1500:
chown 1500:1500 /opt/data/jupyterdata -R
Modify your docker run command to mount the local directory as a volume inside the container. For example, lets imagine that inside your container you want to save the files at /var/lib/jupyter (this is an example), you will need to modify the docker run command as follows:
docker run -it --rm -p 8888:8888 \
-v /opt/data/jupyterdata:/var/lib/jupyter:Z \
lspvic/tensorboard-notebook
NOTE: the :Z parameter is needed to avoid SELINUX issues
With this steps now your data saved on folder /var/lib/jupyter inside the container will be saved on /opt/data/jupyterdata inside the VM so no more data loss.
Let's say I have pulled the official mysql:5.6.21 image.
I have deployed this image by creating several docker containers.
These containers have been running for some time until MySQL 5.6.22 is released. The official image of mysql:5.6 gets updated with the new release, but my containers still run 5.6.21.
How do I propagate the changes in the image (i.e. upgrade MySQL distro) to all my existing containers? What is the proper Docker way of doing this?
After evaluating the answers and studying the topic I'd like to summarize.
The Docker way to upgrade containers seems to be the following:
Application containers should not store application data. This way you can replace app container with its newer version at any time by executing something like this:
docker pull mysql
docker stop my-mysql-container
docker rm my-mysql-container
docker run --name=my-mysql-container --restart=always \
-e MYSQL_ROOT_PASSWORD=mypwd -v /my/data/dir:/var/lib/mysql -d mysql
You can store data either on host (in directory mounted as volume) or in special data-only container(s). Read more about it
About volumes (Docker docs)
Tiny Docker Pieces, Loosely Joined (by Tom Offermann)
How to deal with persistent storage (e.g. databases) in Docker (Stack Overflow question)
Upgrading applications (eg. with yum/apt-get upgrade) within containers is considered to be an anti-pattern. Application containers are supposed to be immutable, which shall guarantee reproducible behavior. Some official application images (mysql:5.6 in particular) are not even designed to self-update (apt-get upgrade won't work).
I'd like to thank everybody who gave their answers, so we could see all different approaches.
I don't like mounting volumes as a link to a host directory, so I came up with a pattern for upgrading docker containers with entirely docker managed containers. Creating a new docker container with --volumes-from <container> will give the new container with the updated images shared ownership of docker managed volumes.
docker pull mysql
docker create --volumes-from my_mysql_container [...] --name my_mysql_container_tmp mysql
By not immediately removing the original my_mysql_container yet, you have the ability to revert back to the known working container if the upgraded container doesn't have the right data, or fails a sanity test.
At this point, I'll usually run whatever backup scripts I have for the container to give myself a safety net in case something goes wrong
docker stop my_mysql_container
docker start my_mysql_container_tmp
Now you have the opportunity to make sure the data you expect to be in the new container is there and run a sanity check.
docker rm my_mysql_container
docker rename my_mysql_container_tmp my_mysql_container
The docker volumes will stick around so long as any container is using them, so you can delete the original container safely. Once the original container is removed, the new container can assume the namesake of the original to make everything as pretty as it was to begin.
There are two major advantages to using this pattern for upgrading docker containers. Firstly, it eliminates the need to mount volumes to host directories by allowing volumes to be directly transferred to an upgraded containers. Secondly, you are never in a position where there isn't a working docker container; so if the upgrade fails, you can easily revert to how it was working before by spinning up the original docker container again.
Just for providing a more general (not mysql specific) answer...
In short
Synchronize with service image registry (https://docs.docker.com/compose/compose-file/#image):
docker-compose pull
Recreate container if docker-compose file or image have changed:
docker-compose up -d
Background
Container image management is one of the reason for using docker-compose
(see https://docs.docker.com/compose/reference/up/)
If there are existing containers for a service, and the service’s configuration or image was changed after the container’s creation, docker-compose up picks up the changes by stopping and recreating the containers (preserving mounted volumes). To prevent Compose from picking up changes, use the --no-recreate flag.
Data management aspect being also covered by docker-compose through mounted external "volumes" (See https://docs.docker.com/compose/compose-file/#volumes) or data container.
This leaves potential backward compatibility and data migration issues untouched, but these are "applicative" issues, not Docker specific, which have to be checked against release notes and tests...
I would like to add that if you want to do this process automatically (download, stop and restart a new container with the same settings as described by #Yaroslav) you can use WatchTower. A program that auto updates your containers when they are changed https://github.com/v2tec/watchtower
Consider for this answers:
The database name is app_schema
The container name is app_db
The root password is root123
How to update MySQL when storing application data inside the container
This is considered a bad practice, because if you lose the container, you will lose the data. Although it is a bad practice, here is a possible way to do it:
1) Do a database dump as SQL:
docker exec app_db sh -c 'exec mysqldump app_schema -uroot -proot123' > database_dump.sql
2) Update the image:
docker pull mysql:5.6
3) Update the container:
docker rm -f app_db
docker run --name app_db --restart unless-stopped \
-e MYSQL_ROOT_PASSWORD=root123 \
-d mysql:5.6
4) Restore the database dump:
docker exec app_db sh -c 'exec mysql -uroot -proot123' < database_dump.sql
How to update MySQL container using an external volume
Using an external volume is a better way of managing data, and it makes easier to update MySQL. Loosing the container will not lose any data. You can use docker-compose to facilitate managing multi-container Docker applications in a single host:
1) Create the docker-compose.yml file in order to manage your applications:
version: '2'
services:
app_db:
image: mysql:5.6
restart: unless-stopped
volumes_from: app_db_data
app_db_data:
volumes: /my/data/dir:/var/lib/mysql
2) Update MySQL (from the same folder as the docker-compose.yml file):
docker-compose pull
docker-compose up -d
Note: the last command above will update the MySQL image, recreate and start the container with the new image.
Similar answer to above
docker images | awk '{print $1}' | grep -v 'none' | grep -iv 'repo' | xargs -n1 docker pull
Here's what it looks like using docker-compose when building a custom Dockerfile.
Build your custom Dockerfile first, appending a next version number to differentiate. Ex: docker build -t imagename:version . This will store your new version locally.
Run docker-compose down
Edit your docker-compose.yml file to reflect the new image name you set at step 1.
Run docker-compose up -d. It will look locally for the image and use your upgraded one.
-EDIT-
My steps above are more verbose than they need to be. I've optimized my workflow by including the build: . parameter to my docker-compose file. The steps looks this now:
Verify that my Dockerfile is what I want it to look like.
Set the version number of my image name in my docker-compose file.
If my image isn't built yet: run docker-compose build
Run docker-compose up -d
I didn't realize at the time, but docker-compose is smart enough to simply update my container to the new image with the one command, instead of having to bring it down first.
If you do not want to use Docker Compose, I can recommend portainer. It has a recreate function that lets you recreate a container while pulling the latest image.
You need to either rebuild all the images and restart all the containers, or somehow yum update the software and restart the database. There is no upgrade path but that you design yourself.
Taking from http://blog.stefanxo.com/2014/08/update-all-docker-images-at-once/
You can update all your existing images using the following command pipeline:
docker images | awk '/^REPOSITORY|\<none\>/ {next} {print $1}' | xargs -n 1 docker pull
Make sure you are using volumes for all the persistent data (configuration, logs, or application data) which you store on the containers related to the state of the processes inside that container. Update your Dockerfile and rebuild the image with the changes you wanted, and restart the containers with your volumes mounted at their appropriate place.
Tried a bunch of things from here, but this worked out for me eventually.
IF you have AutoRemove: On on the Containers you can't STOP and EDIT the contianers, or a Service is running that can't be stopped even momentarily,
You must:
PULL latest image --> docker pull [image:latest]
Verify if the correct image is pulled, you can see the UNUSED tag in the Portainer Images section
UPDATE the service using Portainer or CLI and make sure you use LATEST VERSION of the image, Portainer will give you the option to do same.
THis would not only UPDATE the Container with Latest Image, but also keep the Service Running.
This is something I've also been struggling with for my own images. I have a server environment from which I create a Docker image. When I update the server, I'd like all users who are running containers based on my Docker image to be able to upgrade to the latest server.
Ideally, I'd prefer to generate a new version of the Docker image and have all containers based on a previous version of that image automagically update to the new image "in place." But this mechanism doesn't seem to exist.
So the next best design I've been able to come up with so far is to provide a way to have the container update itself--similar to how a desktop application checks for updates and then upgrades itself. In my case, this will probably mean crafting a script that involves Git pulls from a well-known tag.
The image/container doesn't actually change, but the "internals" of that container change. You could imagine doing the same with apt-get, yum, or whatever is appropriate for you environment. Along with this, I'd update the myserver:latest image in the registry so any new containers would be based on the latest image.
I'd be interested in hearing whether there is any prior art that addresses this scenario.
Update
This is mainly to query the container not to update as building images is the way to be done
I had the same issue so I created docker-run, a very simple command-line tool that runs inside a docker container to update packages in other running containers.
It uses docker-py to communicate with running docker containers and update packages or run any arbitrary single command
Examples:
docker run --rm -v /var/run/docker.sock:/tmp/docker.sock itech/docker-run exec
by default this will run date command in all running containers and return results but you can issue any command e.g. docker-run exec "uname -a"
To update packages (currently only using apt-get):
docker run --rm -v /var/run/docker.sock:/tmp/docker.sock itech/docker-run update
You can create and alias and use it as a regular command line
e.g.
alias docker-run='docker run --rm -v /var/run/docker.sock:/tmp/docker.sock itech/docker-run'
I'm working on a project using NodeRed deployed with docker and I would like to save the state of my deployment, including flows, settings and new added modules so that I can save the image and load it on another host replicating exactly the same NodeRed instance.
I created the container using:
docker run -itd --name my-nodered node-red
After implementing the flows and installing some custom modules, with the container running I used this command:
docker commit my-nodered my-project-nodered/my-nodered:version1
docker save my-project-nodered/my-nodered:version1 > tar-archive.tar.gz
And on another machine I'd imported the image using:
docker load < tar-archive.tar.gz
And run it using:
docker run -itd my-project-nodered/my-nodered:version1
And I obtain a vanilla NodeRed docker container with a default /data directory and just the files on the data directory maintained.
What am I missing? It could be possibile that my /data directory is overwrittenm as well as my settings.js file in the home directory? And in this case, which is the best practice to achieve my target?
Thank you a lot in advance
commit will not work, as you can see that there is volume defined in the Dockerfile.
# User configuration directory volume
VOLUME ["/data"]
That makes it impossible to create a derived image with any different content in that directory tree. (This is the same reason you can't create a mysql or postgresql image with prepopulated data.)
docker commit doesn't consider volumes at all, so you'll get an unchanged image with nothing preloaded in it.
You can see the offical documentation
Managing User Data
Once you have Node-RED running with Docker, we need to ensure any
added nodes or flows are not lost if the container is destroyed. This
user data can be persisted by mounting a data directory to a volume
outside the container. This can either be done using a bind mount or a
named data volume.
Node-RED uses the /data directory inside the container to store user
configuration data.
nodered-user-data-in-docker
one way is to restore the your config file on another machine, for example backup-config then
docker run -it -p 1880:1880 -v $PWD/backup-config/:/data --name mynodered nodered/node-red-docker
or if you want to full for some repo then you can try
docker run -it --rm -v "$PWD/$(wget https://raw.githubusercontent.com/openenergymonitor/oem_node-red/master/flows_emonpi.json)":/data/ nodered/node-red-docker
Assuming that I have a MongoDb or Sql Server container with a lotta data, and all of a sudden (which is very probable) I need to change the port! Maybe due to a sudden security issue! And I need to stop the container and start it up again running on a different port. Why doesn't docker allow me to do that, if I run the image again a new container will be created with no data inside and that causes a lot of mess.
Is there a proper built-in solution? By proper I mean a solution that does not require me to back up databases, move them to out the container volume and restore them again. Something logical such as a command that can allow me to change the forwarded port, for example -p 1433:1234 to 27017:1234.
BLUF: Start your MongoDB container with a volume mapped in to keep the data persistant using this format: docker run --name some-mongo -v /my/own/datadir:/data/db -d mongo
While I agree, it would be great if Docker had the ability to switch port numbers in a running container. As others said, each container is a process, and I do not know a way of changing a port on a running process.
You do not need to import your data if you have set up your volumes properly. I do this all the time for MySQL databases. The MyQSL image is just the database engine separate from the database if you map in your volumes correctly. That's how Docker is designed.
In looking at the section "Where to store data", it gives an example of mounting a volume to a folder on the host to keep your data. This should allow you to start a new container using the same data without having to re-import. But I'm not as familiar with MongoDB which is a NoSQL.
https://hub.docker.com/_/mongo/#!
You may need backup your database using this dump command:
docker exec some-mongo sh -c 'exec mongodump -d <database_name> --archive' > /some/path/on/your/host/all-collections.archive
Start a new container with the volume mapped and restore the data.
docker run --name some-mongo -v /my/own/datadir:/data/db -v /some/path/on/your/host/all-collections.archive:/data/db/collections.archive -d mongo
You'll need to restore that backup.
docker exec some-mongo sh -c 'exec mongorestore --db <database_name> --archive=/data/db/collections.archive
From that point on you should be able to simply stop and start a new container with the volumes mapped in. Your data should remain persistent. You should not need to dump and restore any more (well, obviously for normal backup purposes).
Container is the instantiation of a image.
The port number is the instantiation state of a container, so it can only be changed while creating a container.
You can change the port mapping by directly editing the hostconfig.json file at /var/lib/docker/containers/[hash_of_the_container]/hostconfig.json
You can determine the [hash_of_the_container] via the docker inspect command and the value of the "Id" field is the hash.
1) stop the container
2) change the file
3) restart your docker engine (to flush/clear config caches)
4) start the container
Reference: How do I assign a port mapping to an existing Docker container?
I'm running the official solr 6.6 container used in a docker-compose environment without any relevant volumes.
If i modify a running solr container the data survives a restart.
I dont see any volumes mounted and it works for a plain solr container:
docker run --name solr_test -d -p 8983:8983 -t library/solr:6.6
docker exec -it solr_test /bin/bash -c 'echo woot > /opt/solr/server/solr/testfile'
docker stop solr_test
docker start solr_test
docker exec -it solr_test cat /opt/solr/server/solr/testfile
Above example prints 'woot'. I thought that a container doesnt persist any data? Also the documentation mentions that the solr cores are persisted in the container.
All i found, regarding container persistence is that i need to add volumes on my own like mentioned here.
So i'm confused: do containers store the data changed within the container or not? And how does the solr container achive this behaviour? The only option i see is that i misunderstood peristence in case of docker or the build of the container can set some kind of option to achieve this which i dont know about and didnt see in the solr Dockerfile.
This is expected behaviour.
The data you create inside a container persist as long as you don't delete the container.
But think containers in some way of throw away mentality. Normally you would want to be able to remove the container with docker rm and spawn a new instance including your modified config files. That's why you would need an e.g. named volume here, which survives a container life cycle on your host.
The Dockerfile, because you mention it in your question, actually only defines the image. When you call docker run you create a container from it. Exactly as defined in the image. A fresh instance without any modifications.
When you call docker commit on your container you snapshot it (including the changes you made to the files) and create a new image out of it. They achieve the data persistence this way.
The documentation you referring to explains this in detail.