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Singularity_and_Docker.md

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Why Docker

See this link for a quick primer on why docker is a great tool for doing (data) science.

Installing Docker

OSX

Reference

Preflight Notes

  • Docker for Mac requires OS X El Capitan 10.11 or newer macOS
  • VirtualBox prior to version 4.3.30 must NOT be installed (it is incompatible with Docker for Mac). If you have a newer version of VirtualBox installed, it’s fine.

Installation

https://download.docker.com/mac/stable/Docker.dmg

Linux (labtops)

Installation

#!bash

sudo apt install docker
sudo usermod -a -G docker $USER

Now completely log out (when in doubt, reboot)

Using Docker

Docker will automatically download containers for you:

#!bash

docker run -itp 8888:8888 cmelab/mbuild:latest jupyter notebook --notebook-dir=/home/ --ip='*' --port=8888 --no-browser --allow-root

Why Singularity

Singularity has support on difference national super computing clusters and allows us to leverage docker in a secure way.

This isn't meant to be a comprehensive guide but will provide enough information to build a singularity image for plankton. You will need to install docker as a first step. To test, run docker info. If you get an error like this ERROR: Cannot connect to the Docker daemon at unix:///var/run/docker.sock. Is the docker daemon running? you need to start docker. Now cd into the docker folder in plankcton and run

docker build . -f Dockerfile -t cmelab/planckton:demo

To build the image. This will take awhile (40 minutes on a lower end computer)! We are telling docker to use the Dockerfile as the instructions on how to build the image, and we are telling docker to "tag" the image with cmelab/planckton:demo. Tags are a way to stay organized when building docker images. If you want to push this image to a docker image repository (such as docker hub) then use a tag like username/planckton:demo.

Now to create the singularity image we have two options. If the docker image is pushed to a container repository, we can pull the image down like this singularity pull docker://cmelab/planckton:beta. Another option is to use the Singularity.latest file to build an image. This file tells singularity to create an image from a docker image (which could be from a repository or exist locally) You will need to edit the image tag on the from line in this file (in this example, it would need to be changed to From: cmelab/planckton:demo

Notes

singularity pull shub://mikemhenry/cme-lab-images:hoomd