On your laptop:
docker pull ubuntu
What is that doing? It's going to https://hub.docker.com/_/ubuntu and pulling down the image with the "latest" tag
docker run ubuntu
Uhh, nothing happened. Not quite - it loaded up the entire OS, but you didn't tell it to do anything!
docker run ubuntu echo "hello world"
What's cool is that didn't run on MacOS, that ran in Linux, and we can prove it:
docker run ubuntu uname -a
But what if we want to do more than one thing at a time? Run docker interactively! (bash is the most common shell that we generally work on)
docker run -it ubuntu /bin/bash
There is one major difference between running docker on the cluster and on your laptop:
whoami
We can't get root access in docker images on the cluster. To oversimplify a complicated topic, that's to prevent people from accessing data they shouldn't be able to.
Here though, we have root, so let's install some software.
python3
fails - it's not installed!
apt-get update
apt-get install python3
Now it should work:
python3
>>> print("Hello World!")
Now, exit out python and your container
<CTRL-D to quit python >
exit
Let's pop back into our container using the above docker run command, then try running python again:
python3
Wait! where'd it go? Let's chat about persistence
Create a folder
mkdir ubuntu-python
cd ubuntu-python
Create a new text file named "Dockerfile" with the following contents:
# start from base ubuntu
FROM ubuntu:latest
MAINTAINER Chris Miller <c.a.miller@wustl.edu>
RUN apt-get -y update
RUN apt-get -y install python3
Save that file in the directory And build a docker image from that Dockerfile
cd ..
docker build -t chrisamiller/ubuntu-python ubuntu-python/
Let's run it:
docker run -it chrisamiller/ubuntu-python
and verify that python is installed
python3
Great, so now let's run a python script on our data. First let's find our data by listing our home directory:
ls -l /Users/cmiller #replace with your path
Wait a minute - there's nothing there... That's because Docker processes are isolated from the rest of your computer. By default, nothing can get in or out. But we probably need to run it on some data, and probably want to save those results when we're done!
In order to do so, we need to mount paths as volumes within the docker container. Let's say I have a directory
at ~/workshop. I'd like to be able to view that within my docker container. No problem, we'll use the volumes option
to mount it, creating a virtual "tunnel" through the docker container's isolation. This uses the -v flag and a colon
separated list of source (local path) and destination (container path)
docker run -v /Users/cmiller/workshop:/data -it chrisamiller/ubuntu-python
So we mounted it at the root in a data folder. Let's check to see if our expected data is there:
ls -l /data/