Unable to link volume to the rocker/rstudio container on linux - docker

When I execute commands in Ubuntu 18:
cd ~/r-projects
docker run -d -v $PWD:/home/rstudio rocker/rstudio
docker creates rstudio container accessible in localhost:8787. But I can't see the content of the $PWD inside RStudio session. When I save files in RStudio session and then restart the container those files persist, but I can not find them in the host using locate command. It seems that $PWD is not mounted but docker uses another folder to preserve RStudio state.
This is strange behavior. What I really want is to link some folder on the host to the rstudio inside docker container. What am I doing wrong?
Official instructions did not help me.
Please, provide correct command.

I resolved the issue:
docker run -d -p 8787:8787 -e PASSWORD=123 -v $PWD:/home/rstudio rocker/rstudio
The problem was that I executed commands inside kubernetes cluster.

Related

How to print the current directory of the docker image which is running in a centOS7 OS from windows docker desktop [duplicate]

I've noticed with docker that I need to understand what's happening inside a container or what files exist in there. One example is downloading images from the docker index - you don't have a clue what the image contains so it's impossible to start the application.
What would be ideal is to be able to ssh into them or equivalent. Is there a tool to do this, or is my conceptualisation of docker wrong in thinking I should be able to do this.
Here are a couple different methods...
A) Use docker exec (easiest)
Docker version 1.3 or newer supports the command exec that behave similar to nsenter. This command can run new process in already running container (container must have PID 1 process running already). You can run /bin/bash to explore container state:
docker exec -t -i mycontainer /bin/bash
see Docker command line documentation
B) Use Snapshotting
You can evaluate container filesystem this way:
# find ID of your running container:
docker ps
# create image (snapshot) from container filesystem
docker commit 12345678904b5 mysnapshot
# explore this filesystem using bash (for example)
docker run -t -i mysnapshot /bin/bash
This way, you can evaluate filesystem of the running container in the precise time moment. Container is still running, no future changes are included.
You can later delete snapshot using (filesystem of the running container is not affected!):
docker rmi mysnapshot
C) Use ssh
If you need continuous access, you can install sshd to your container and run the sshd daemon:
docker run -d -p 22 mysnapshot /usr/sbin/sshd -D
# you need to find out which port to connect:
docker ps
This way, you can run your app using ssh (connect and execute what you want).
D) Use nsenter
Use nsenter, see Why you don't need to run SSHd in your Docker containers
The short version is: with nsenter, you can get a shell into an
existing container, even if that container doesn’t run SSH or any kind
of special-purpose daemon
UPDATE: EXPLORING!
This command should let you explore a running docker container:
docker exec -it name-of-container bash
The equivalent for this in docker-compose would be:
docker-compose exec web bash
(web is the name-of-service in this case and it has tty by default.)
Once you are inside do:
ls -lsa
or any other bash command like:
cd ..
This command should let you explore a docker image:
docker run --rm -it --entrypoint=/bin/bash name-of-image
once inside do:
ls -lsa
or any other bash command like:
cd ..
The -it stands for interactive... and tty.
This command should let you inspect a running docker container or image:
docker inspect name-of-container-or-image
You might want to do this and find out if there is any bash or sh in there. Look for entrypoint or cmd in the json return.
NOTE: This answer relies on commen tool being present, but if there is no bash shell or common tools like ls present you could first add one in a layer if you have access to the Dockerfile:
example for alpine:
RUN apk add --no-cache bash
Otherwise if you don't have access to the Dockerfile then just copy the files out of a newly created container and look trough them by doing:
docker create <image> # returns container ID the container is never started.
docker cp <container ID>:<source_path> <destination_path>
docker rm <container ID>
cd <destination_path> && ls -lsah
see docker exec documentation
see docker-compose exec documentation
see docker inspect documentation
see docker create documentation
In case your container is stopped or doesn't have a shell (e.g. hello-world mentioned in the installation guide, or non-alpine traefik), this is probably the only possible method of exploring the filesystem.
You may archive your container's filesystem into tar file:
docker export adoring_kowalevski > contents.tar
Or list the files:
docker export adoring_kowalevski | tar t
Do note, that depending on the image, it might take some time and disk space.
Before Container Creation :
If you to explore the structure of the image that is mounted inside the container you can do
sudo docker image save image_name > image.tar
tar -xvf image.tar
This would give you the visibility of all the layers of an image and its configuration which is present in json files.
After container creation :
For this there are already lot of answers above. my preferred way to do
this would be -
docker exec -t -i container /bin/bash
The most upvoted answer is working for me when the container is actually started, but when it isn't possible to run and you for example want to copy files from the container this has saved me before:
docker cp <container-name>:<path/inside/container> <path/on/host/>
Thanks to docker cp (link) you can copy directly from the container as it was any other part of your filesystem.
For example, recovering all files inside a container:
mkdir /tmp/container_temp
docker cp example_container:/ /tmp/container_temp/
Note that you don't need to specify that you want to copy recursively.
The file system of the container is in the data folder of docker, normally in /var/lib/docker. In order to start and inspect a running containers file system do the following:
hash=$(docker run busybox)
cd /var/lib/docker/aufs/mnt/$hash
And now the current working directory is the root of the container.
you can use dive to view the image content interactively with TUI
https://github.com/wagoodman/dive
Try using
docker exec -it <container-name> /bin/bash
There might be possibility that bash is not implemented. for that you can use
docker exec -it <container-name> sh
On Ubuntu 14.04 running Docker 1.3.1, I found the container root filesystem on the host machine in the following directory:
/var/lib/docker/devicemapper/mnt/<container id>/rootfs/
Full Docker version information:
Client version: 1.3.1
Client API version: 1.15
Go version (client): go1.3.3
Git commit (client): 4e9bbfa
OS/Arch (client): linux/amd64
Server version: 1.3.1
Server API version: 1.15
Go version (server): go1.3.3
Git commit (server): 4e9bbfa
In my case no shell was supported in container except sh. So, this worked like a charm
docker exec -it <container-name> sh
I use another dirty trick that is aufs/devicemapper agnostic.
I look at the command that the container is running e.g. docker ps
and if it's an apache or java i just do the following:
sudo -s
cd /proc/$(pgrep java)/root/
and voilá you're inside the container.
Basically you can as root cd into /proc/<PID>/root/ folder as long as that process is run by the container. Beware symlinks will not make sense wile using that mode.
The most voted answer is good except if your container isn't an actual Linux system.
Many containers (especially the go based ones) don't have any standard binary (no /bin/bash or /bin/sh). In that case, you will need to access the actual containers file directly:
Works like a charm:
name=<name>
dockerId=$(docker inspect -f {{.Id}} $name)
mountId=$(cat /var/lib/docker/image/aufs/layerdb/mounts/$dockerId/mount-id)
cd /var/lib/docker/aufs/mnt/$mountId
Note: You need to run it as root.
Only for LINUX
The most simple way that I use was using proc dir, the container must be running in order to inspect the docker container files.
Find out the process id (PID) of the container and store it into some variable
PID=$(docker inspect -f '{{.State.Pid}}' your-container-name-here)
Make sure the container process is running, and use the variable name to get into the container folder
cd /proc/$PID/root
If you want to get through the dir without finding out the PID number, just use this long command
cd /proc/$(docker inspect -f '{{.State.Pid}}' your-container-name-here)/root
Tips:
After you get inside the container, everything you do will affect the actual process of the container, such as stopping the service or changing the port number.
Hope it helps
Note:
This method only works if the container is still running, otherwise, the directory wouldn't exist anymore if the container has stopped or removed
None of the existing answers address the case of a container that exited (and can't be restarted) and/or doesn't have any shell installed (e.g. distroless ones). This one works as long has you have root access to the Docker host.
For a real manual inspection, find out the layer IDs first:
docker inspect my-container | jq '.[0].GraphDriver.Data'
In the output, you should see something like
"MergedDir": "/var/lib/docker/overlay2/03e8df748fab9526594cfdd0b6cf9f4b5160197e98fe580df0d36f19830308d9/merged"
Navigate into this folder (as root) to find the current visible state of the container filesystem.
This will launch a bash session for the image:
docker run --rm -it --entrypoint=/bin/bash
On newer versions of Docker you can run docker exec [container_name] which runs a shell inside your container
So to get a list of all the files in a container just run docker exec [container_name] ls
I wanted to do this, but I was unable to exec into my container as it had stopped and wasn't starting up again due to some error in my code.
What worked for me was to simply copy the contents of the entire container into a new folder like this:
docker cp container_name:/app/ new_dummy_folder
I was then able to explore the contents of this folder as one would do with a normal folder.
For me, this one works well (thanks to the last comments for pointing out the directory /var/lib/docker/):
chroot /var/lib/docker/containers/2465790aa2c4*/root/
Here, 2465790aa2c4 is the short ID of the running container (as displayed by docker ps), followed by a star.
For docker aufs driver:
The script will find the container root dir(Test on docker 1.7.1 and 1.10.3 )
if [ -z "$1" ] ; then
echo 'docker-find-root $container_id_or_name '
exit 1
fi
CID=$(docker inspect --format {{.Id}} $1)
if [ -n "$CID" ] ; then
if [ -f /var/lib/docker/image/aufs/layerdb/mounts/$CID/mount-id ] ; then
F1=$(cat /var/lib/docker/image/aufs/layerdb/mounts/$CID/mount-id)
d1=/var/lib/docker/aufs/mnt/$F1
fi
if [ ! -d "$d1" ] ; then
d1=/var/lib/docker/aufs/diff/$CID
fi
echo $d1
fi
This answer will help those (like myself) who want to explore the docker volume filesystem even if the container isn't running.
List running docker containers:
docker ps
=> CONTAINER ID "4c721f1985bd"
Look at the docker volume mount points on your local physical machine (https://docs.docker.com/engine/tutorials/dockervolumes/):
docker inspect -f {{.Mounts}} 4c721f1985bd
=> [{ /tmp/container-garren /tmp true rprivate}]
This tells me that the local physical machine directory /tmp/container-garren is mapped to the /tmp docker volume destination.
Knowing the local physical machine directory (/tmp/container-garren) means I can explore the filesystem whether or not the docker container is running. This was critical to helping me figure out that there was some residual data that shouldn't have persisted even after the container was not running.
If you are using Docker v19.03, you follow the below steps.
# find ID of your running container:
docker ps
# create image (snapshot) from container filesystem
docker commit 12345678904b5 mysnapshot
# explore this filesystem
docker run -t -i mysnapshot /bin/sh
For an already running container, you can do:
dockerId=$(docker inspect -f {{.Id}} [docker_id_or_name])
cd /var/lib/docker/btrfs/subvolumes/$dockerId
You need to be root in order to cd into that dir. If you are not root, try 'sudo su' before running the command.
Edit: Following v1.3, see Jiri's answer - it is better.
another trick is to use the atomic tool to do something like:
mkdir -p /path/to/mnt && atomic mount IMAGE /path/to/mnt
The Docker image will be mounted to /path/to/mnt for you to inspect it.
My preferred way to understand what is going on inside container is:
expose -p 8000
docker run -it -p 8000:8000 image
Start server inside it
python -m SimpleHTTPServer
If you are using the AUFS storage driver, you can use my docker-layer script to find any container's filesystem root (mnt) and readwrite layer :
# docker-layer musing_wiles
rw layer : /var/lib/docker/aufs/diff/c83338693ff190945b2374dea210974b7213bc0916163cc30e16f6ccf1e4b03f
mnt : /var/lib/docker/aufs/mnt/c83338693ff190945b2374dea210974b7213bc0916163cc30e16f6ccf1e4b03f
Edit 2018-03-28 :
docker-layer has been replaced by docker-backup
The docker exec command to run a command in a running container can help in multiple cases.
Usage: docker exec [OPTIONS] CONTAINER COMMAND [ARG...]
Run a command in a running container
Options:
-d, --detach Detached mode: run command in the background
--detach-keys string Override the key sequence for detaching a
container
-e, --env list Set environment variables
-i, --interactive Keep STDIN open even if not attached
--privileged Give extended privileges to the command
-t, --tty Allocate a pseudo-TTY
-u, --user string Username or UID (format:
[:])
-w, --workdir string Working directory inside the container
For example :
1) Accessing in bash to the running container filesystem :
docker exec -it containerId bash
2) Accessing in bash to the running container filesystem as root to be able to have required rights :
docker exec -it -u root containerId bash
This is particularly useful to be able to do some processing as root in a container.
3) Accessing in bash to the running container filesystem with a specific working directory :
docker exec -it -w /var/lib containerId bash
Often times I only need to explore the docker filesystem because my build won't run, so docker run -it <container_name> bash is impractical. I also do not want to waste time and memory copying filesystems, so docker cp <container_name>:<path> <target_path> is impractical too.
While possibly unorthodox, I recommend re-building with ls as the final command in the Dockerfile:
CMD [ "ls", "-R" ]
I've found the easiest, all-in-one solution to View, Edit, Copy files with a GUI app inside almost any running container.
mc editing files in docker
inside the container install mc and ssh: docker exec -it <container> /bin/bash, then with prompt install mc and ssh packages
in same exec-bash console, run mc
press ESC then 9 then ENTER to open menu and select "Shell link..."
using "Shell link..." open SCP-based filesystem access to any host with ssh server running (including the one running docker) by it's IP address
do your job in graphical UI
this method overcomes all issues with permissions, snap isolation etc., allows to copy directly to any machine and is the most pleasant to use for me
I had an unknown container, that was doing some production workload and did not want to run any command.
So, I used docker diff.
This will list all files that the container had changed and therefore good suited to explore the container file system.
To get only a folder you can just use grep:
docker diff <container> | grep /var/log
It will not show files from the docker image. Depending on your use case this can help or not.
Late to the party, but in 2022 we have VS Code

Understanding a Docker .Sh file

The .sh file I am working with is:
docker run -d --rm -it --gpus '"device=0,1,2,3"' --ipc=host -v $HOME/Folder:/Folder tr_xl_container nohup python /Path/file.py -p/Path/ |& tee $HOME/Path/log.txt
I am confused about the -v and everything after that. Specifically, the -v $HOME/Folder:/Folder tr_xl_container section and -p/Path/. If someone would be able to help breakdown what those commands mean or point me to a reference that does, that would be very much appreciated. I checked Docker documentation and Linux command line documentation and did not come up with anything too helpful.
A docker run command is split up in 3 parts:
docker options
the image to run
a command for the container
In your case -d --rm -it --gpus '"device=0,1,2,3"' --ipc=host -v $HOME/Folder:/Folder are docker options.
tr_xl_container is the image name.
nohup python /Path/file.py -p/Path/ is the command sent to the container.
The last part, |& tee $HOME/Path/log.txt isn't run in the container, but takes the output from the docker run command and saves it in $HOME/Path/log.txt.
As for -v $HOME/Folder:/Folder, it's a volume mapping or more precisely, a bind mount. It creates a directory in the container with the path /Folder that is linked to the directory $Home/Folder on the host machine. That makes files in the host directory visible inside the container and if the container does anything with files in the /Folder directory, those changes will be visible in the host directory.
The command after the image name is for the container and it's up to the container what to do with it. From looking at it, it looks like it runs a Python program stored in /Path/file.py in the image. But to be sure, you'll need to know what the image does.

(dockerfile) for flag -v: bad mode specified

I have problems with the introduction of these instructions https://github.com/notabenoid/notabenoid-dockerfile
Out my error command
docker run -v `pwd`:/srv/example.com -p 127.0.0.1:8080:80 --name notabenoid notabenoid
I managed to turn the site, but my goal is to change a few files and pictures
How to edit files to container ?
use docker execto modify some files in a container, see the doc
https://docs.docker.com/engine/reference/commandline/exec/
check also the docs for docker run
https://docs.docker.com/engine/reference/commandline/run/
and the examples with -v
If You only need to change some files use docker cp.
docker run -p 127.0.0.1:8080:80 --name notabenoid notabenoid
docker cp notabenoid:/srv/example.com/file_to_change .
edit file
docker cp file_to_change notabenoid:/srv/example.com/file_to_change
where /srv/example.com/file_to_change is a path to file in container.
edit
Let's Your new logo is /home/Hellioob/new_logo.gif.
docker cp /home/Hellioob/new_logo.gif notabenoid:/notabenoid/site/www/i/logo.gif

Docker logging to container

I'm fresh user of Docker. The fist problem with which I'm faced is logging into container.
I'm found solutions to execute container bash commands by
docker exec -it ID bash
But, this is solution only for install/ remove packages. What to use if I want to edit nginx config in docker container ?
One of solutions can be loggin to container via ssh connection, but maybe Docker have something own for this ?, I mean easilly access without install OpenSSH ?
as you said,
docker exec -it container_id bash
and then use your favorite editor to edit any nginx config file. vi or nano is usually installed, but you may need to install emacs or vim, if this is your favorite editor
if you have just a few characters to modify,
docker exec container_id sed ...
might do the job. If you want to SSH into your container, you will need to install SSH and deal with the SSH keys, I am not sure this is what you need.
You're going about it the wrong way. You should rarely need to log into a container to edit files.
Instead, mount the nginx.conf with -v from the host. That way you can edit the file with your normal editor. Once you've got the config working the way you want it, you can then build a new image with it baked in.
In general, you have to get into the mindset of containers being ephemeral. You don't patch them; you throw them away and replace them with a fixed version.
How: Docker logging to container
Yes, you can. You can login the running container.
Exist docker exec or docker attach is not good enough. Looking to start a shell inside a Docker container? The solution is: jpetazzo/nsenter with two commands: nsenter and docker-enter.
If you are in Linux environment, then run below command:
docker run --rm -v /usr/local/bin:/target jpetazzo/nsenter
docker ps
# replace <container_name_or_ID> with real container name or ID.
PID=$(docker inspect --format {{.State.Pid}} <container_name_or_ID>)
nsenter --target $PID --mount --uts --ipc --net --pid
Then you are in that running container, you can run any linux commands now.
I prefer the other command docker-enter. Without login the container, you can directly run linux commands in container with docker-enter command. Second, I can't memory multiple options of nsenter command and no need to find out the container's PID.
docker-enter 0e8c248982c5 ls /opt
If you are mac or windows user, run docket with toolbox:
docker-machine ssh default
docker run --rm -v /usr/local/bin:/target jpetazzo/nsenter
PID=$(docker inspect --format {{.State.Pid}} 0e8c248982c5)
sudo nsenter --target $PID --mount --uts --ipc --net --pid
If you are mac or windows user, run docket with boot2docker:
boot2docker ssh
docker run --rm -v /usr/local/bin:/target jpetazzo/nsenter
PID=$(docker inspect --format {{.State.Pid}} 0e8c248982c5)
sudo nsenter --target $PID --mount --uts --ipc --net --pid
Note: The command docker run --rm -v /usr/local/bin:/target jpetazzo/nsenter only need run one time.
How: edit nginx config
For your second question, you can think about ONBUILD in Docker.
ONBUILD COPY nginx.conf /etc/nginx/nginx.conf
With this solution, you can:
edit nginx.conf in local, you can use any exist editor .
needn't build your image every time after you change nginx configuration.
every time, after you change nginx.conf file in local, you need stop, remove and re-run the containe, new nginx.conf file will be deployed into contrainer when docker run command.
You can refer the detail on how to use ONBUILD here: docker build

mount a host volume to a container created through Dockerfile

New to docker, and as per the documentation about Dockerfile, due to portability, it is not allowed to specify a host volume mapping. That is fine, but is there a way to map a host volume (I am in MAC, so say, my home dir /Users/bsr to /data of ubuntu image) to a linux container. The documentation of docker volume is talking only about docker run, but not sure how to add a volume after creating it.
http://docs.docker.com/userguide/dockervolumes/
On Linux you can simply mount a directory of your host system to a docker container by passing
-v /path/to/host/directory:/path/to/container/directory
to the docker run command.
You can also see it here in the documentation: https://docs.docker.com/userguide/dockervolumes/#mount-a-host-directory-as-a-data-volume
If you are using boot2docker things are more complicated. The problem ist that boot2docker runs a little linux vm to start docker. So if you mount the volume as described above you will mount the directory of the little linux vm.
A workaround for this is described in the README of the boot2docker GitHub page using a samba share:
https://github.com/boot2docker/boot2docker#folder-sharing
the following worked, with the help of #sciutand.
git clone https://github.com/boot2docker/boot2docker.git
cd boot2docker/
docker build -t my-boot2docker-img .
docker run --rm my-boot2docker-img > boot2docker.iso
boot2docker stop
mv ~/.boot2docker/boot2docker.iso ~/.boot2docker/boot2docker.iso.backup
mv boot2docker.iso ~/.boot2docker/boot2docker.iso
VBoxManage sharedfolder add boot2docker-vm -name /Users -hostpath /Users
boot2docker up
docker run -d -P --name web ubuntu

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