Frequently Asked Questions¶

From time to time, various questions on how to use OpenEM are asked by the community of users. This document attempts to consolidate the most asked questions to assist new users of the library.

Training & Data curation¶

OpenEM allows for flexibly deploying parts of the pipeline relevant for a given problem set. With this complexity comes complication in understanding what is required for a given training run. The following flowchart shows the decision tree required for setting up training data.

Training data flowchart

Docker-related¶

What is Docker?¶

Docker is a container management system. It allows us to package OpenEM as a unit effectively equivilant to a light weight Virtual Machine. All system dependencies are taken care of such that OpenEM can work with minimal administriva.

Key terms to understand in our usage of Docker.

Image : A Docker image is the entity downloaded with a docker pull command. It is the filesystem contents of a given container. + To see images you have on your system, use docker images
Container: A Docker container is the running instance of the “Light weight VM”. + To see running containers you have on your system, use docker ps

How do I get files to/from a docker container?¶

It is preferred to get a file from a docker container while it is still running. The commands provided in the tutorial.md file use bind mounts to expose a directory on the host to running container.

In the following example, the folder /mnt/md0 on the host is mounted as /data to the perspective of the docker container.

docker run --rm -ti -v /mnt/md0:/data ubuntu bash

I got an error like “Gtk-WARNING **: 11:14:47.519: cannot open display: “.¶

Because the docker container is running as an isolated environment it doesn’t have access to the windowing environment of the host (X11). For trusted images the easiest way to facilitate this is to use the same syntax as some of the commands in tutorial.md to allow the container instance to use the host X11 network.

Specifically that entails adding -v"$HOME/.Xauthority:/root/.Xauthority:rw" --env=DISPLAY --net=host to the docker invocation.

The following command creates a vanilla ubuntu X11-enabled container: docker run --rm -ti -v"$HOME/.Xauthority:/root/.Xauthority:rw" --env=DISPLAY --net=host ubuntu bash

Important: When using --net host the container isn’t as isolated from the hosts network interface.

Important: The prompt of the container using the --net host will look similar the host prompt. Care should be taken to avoid mistakes.

I wanted to launch tensorboard, but I can’t access the shell in the running¶

container any longer.¶

If the container was launched with --name openem, then the following command launches another bash process in the running container:

docker exec --env=DISPLAY -it openem bash

Substitute openem for what ever you named your container. If you didn’t name your container, then you need to find your running container via docker ps and use:

docker exec --env=DISPLAY -it <hash_of_container> bash