Develop Reference

how to mount a local volume for my docker?

i am newbie to the Linux and docker. I am using the below command to run the docker:
sudo nvidia-docker run --gpus all -p 8888:8888 -it -v /home/pyman/PEYMAN:??????? 21bbc6c8f7ed
where; /home/pyman/PEYMAN is my local directory
and 21bbc6c8f7ed is the image ID.
after running this command, the workspace root changes to root#0ce2ee24bac0:/workspace#
then I type jupyter notebook and run it, and it provides two links which only the second link opens the jupyter notebook in the browser.
http://hostname:8888/?token=xxxxxxxxxxx
http://127.0.0.1:8888/?token=xxxxxxxxxxx
but I dont know what is my container_dir in the first command to put in ?????, and how to get the directory. is the container_dir the same directory that jupyter is?

The container_dir is the path inside the container, where you'd like to see your mounted files. The directory inside container does not even have to exist, yon can pick almost any place to mount your files. If you work with jupyter, it makes sense to add your files to the working directory:
docker run -v /home/pyman/PEYMAN:/workspace/myfiles
Once inside the container you will find /home/pyman/PEYMAN in /workspace/myfiles.

Is there a way to modify files inside docker via PyCharm?

I want to modify files inside docker container with PyCharm. Is there possibility of doing such thing?

What you want to obtain is called Bind Mounting and it can be obtained adding -v parameter to your run command, here's an example with an nginx image:
docker run --name=nginx -d -v ~/nginxlogs:/var/log/nginx -p 5000:80 nginx
The specific parameter obtaining this result is -v.
-v ~/nginxlogs:/var/log/nginx sets up a bindmount volume that links the /var/log/nginx directory from inside the Nginx container to the ~/nginxlogs directory on the host machine.
Docker uses a : to split the host’s path from the container path, and the host path always comes first.
In other words the files that you edit on your local filesystem will be synced to the Docker folder immediately.
Source

Yes. There are multiple ways to do this, and you will need to have PyCharm installed inside the container.
Following set of instructions should work -
docker ps - This will show you details of running containers
docker exec -it *<name of container>* /bin/bash
At this point you will oh shell inside the container. If PyCharm is not installed, you will need to install. Following should work -
sudo apt-get install pycharm-community
Good to go!
Note: The installation is not persistence across Docker image builds. You should add the installation step of PyCharm on DockerFile if you need to access it regularly.

How can I make Docker container shared files with host appeared in the container?

I'm trying to create a container to run a program. I'm using a pre-configured image and now I need to run the program. However, it's a machine learning program and I need a dataset from my computer to run.
The file is too large to be copied to the container. It would be best if the program running in the container searched the dataset in a local directory of my computer, but I don't know how I can do this.
Well, I have made the shared folder from my machine appeared using docker run -it -v ~/Volumes/Data/Studies/PhD\Work/gitlab/J2/ydk-py:/ydk-py ydkdev/ydk-py in the container, but all files in folder ydk-py are not shown. This is the safe, usually-desired behavior. But for development and instance setup, it would be immensely useful to have access to an existing file structure.

docker run with -v will automatically mount sub-directories. In your case you are using relative path, which you need to use absolute path as per this documentation.
So change your command from
docker run -it -v ~/Volumes/Data/Studies/PhD\Work/gitlab/J2/ydk-py:/ydk-py ydkdev/ydk-py
to
docker run -it -v /home/<what ever user>/Volumes/Data/Studies/PhD\Work/gitlab/J2/ydk-py:/ydk-py ydkdev/ydk-py
it will work.
Make sure you have enough permissions on directory that you are trying to mount.

Setting up graph-tool on Docker Toolbox for WIndows

I followed the graph-tool docker installation instructions here. I've set up Docker Toolbox (can't use Docker for Windows, not on Pro), and I've gotten jupyter running with the Docker image.
However, I need to access a notebook in my C: drive. For the sake of this post let's say the notebook is in C:\Users\Gab\Desktop. I've successfully moved into that location, but when I run the command docker run -p 8888:8888 -p 6006:6006 -it -u user -w /home/user tiagopeixoto/graph-tool bash, it opens a bash in /home/user, not in the directory I cd'd into previously.
From what I understand, the -w /home/user is what tells it where to open, but I'm not sure how to tell it to open in the Desktop folder.
How can I set things up properly so that I can run the command jupyter notebook --ip 0.0.0.0, and still be able to access the notebook I need?
Thanks!

Here's the deal with Docker. When you execute the docker run command, what happens is that an entirely new subsystem is created which is separate from your host Operating System ( this is known as a Docker container ). This subsystem runs the tiagopeixoto/graph-tool image in it so hence the graph-tool ( and hence jupyter-notebook ) and the entrypoint /home/user is present inside this system instead of the host OS you use to run the Docker container ( in your case its Windows ). Unfortunately for you the notebook that you wish to view using jupyter-notebook isn't present inside the container and is located elsewhere ( Windows to be exact ).
What you can do in this case is mount a folder of the host Operating System to the container such that this folder contains the notebook you wish to view :-
Open a new command prompt, and type in this command as follows :- docker run -p 8888:8888 -p 6006:6006 -v /c/Users/Gab/Desktop:/mnt/temp/ -it -u user -w /home/user tiagopeixoto/graph-tool bash
The main difference to note here is the -v switch which mounts the C:\Users\Gab\Desktop volume from the host system to the Docker container in /mnt/temp/. Once that is done try viewing the notebook present in /mnt/temp in jupyter-notebook.
According to this post there exists an issue related to mounting a volume in Windows, so please check this out as well :- docker toolbox mount file on windows

Saving changes in docker project

I just started a django project with docker, I used the cookiecutter-django template that is discussed in the book Two scoops of django.
I am trying to set it all up in OSX, but I am having some trouble with the following part from the documentation:
Saving changes
If you are using OS X or Windows, you need to create a
/data partition inside the virtual machine that runs the docker deamon
in order make all changes persistent. If you don’t do that your /data
directory will get wiped out on every reboot. To create a persistent
folder, log into the virtual machine by running:
$ docker-machine ssh dev1
$ sudo su
$ echo 'ln -sfn /mnt/sda1/data /data' >>
/var/lib/boot2docker/bootlocal.sh
However, if I execute these commands, and try to start my docker project, I get the following error:
ERROR: Cannot start container 182a38022fbdf65f7a64f1ca5475a3414084d11c91f1cb48bffc6f76491baf4a: mkdir /data: file exists
I'm quite stuck at this point, do you guys have an idea what I could do to get this up and running?

So in the end this was fixed by making the directory in the local machine. I did that with the following code when adding the line to the bootlocal.sh file:
$ mkdir /mnt/sda1/data