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Building Containers

Table of contents

  1. 0. install singularity on your local machine
  2. 1. First start off with installing vagrant
  3. 2. once you’ve logged into vagrant, we’re going to build the container
  4. 3. create the singularity container
  5. 4. Build a docker container and convert it to singularity

Containers aid reproducible research, while alleviating the pain of installing programs/packages every time you’re working in a new environment.

Docker and Singularity are platforms that allow you to build and execute containers.

Reasons I had to build a container: I needed pymvpa and nilearn, which had to run on CU’s cluster. This was around 2018, prior to the conda environment feature that is now enabled on Summit and Blanca. Hence, I needed a singularity container, instead of a docker container. However, converting a docker container to singularity is easy, once you have singularity on your local machine.

0. install singularity on your local machine

Please check here.

  • https://singularity.lbl.gov/install-mac
  • https://singularity.lbl.gov/install-linux
  • https://singularity.lbl.gov/install-windows

1. First start off with installing vagrant

  • where I’ve installed it: Documents/singularity-vm
  • change directory into it and run the following lines 
    cd ~/Documents/singularity-vm
vagrant init singularityware/singularity-2.4
vagrant up
vagrant ssh

2. once you’ve logged into vagrant, we’re going to build the container

using singularity…

IMG : name of the container You need to set the initial size of the image (container) 8000, i.e., 8 GB

DEF : has the code that builds the containers

IMG="snaglab_pymvpa2_nilearn.img"
DEF="debian.def"
sudo rm -f $IMG
sudo singularity create -s 8000 $IMG
sudo singularity image.create -s 8000 $IMG
sudo singularity bootstrap $IMG $DEF

3. create the singularity container

copyout the container ( in local directory not virtual machine)

vagrant port `( in the folder where you've installed vagrant)`

from local dir

scp -P 2222 vagrant@127.0.0.1:/home/vagrant/snaglab_pymvpa2.img .
scp -P 2222 vagrant@127.0.0.1:/home/vagrant/debian.def .
scp -P 2222 vagrant@127.0.0.1:/home/vagrant/definition.def .

4. Build a docker container and convert it to singularity

Example: I built FSL based on https://github.com/BIDS-Apps/dockerfile-templates/blob/master/FSL/Dockerfile go to the local directory where dockerfile exists

docker build -t fslnine .
docker tag f6b20d2fbb99 jungheejung/fslnine:latest
docker push jungheejung/fslnine:latest

If your HPC doesn’t allow for docker, but has singularity, here’s how to convert dockers into singularity containers.

docker run --privileged -t --rm \
-v /var/run/docker.sock:/var/run/docker.sock \
-v /Users/h/Documents/singularity-vm:/output \
singularityware/docker2singularity \
jungheejung/fslnine:latest