Singularity is a linux container technology that is well suited to use in shared-user environments such as the clusters we maintain at Yale. It is similar to Docker; You can bring with you a stack of software, libraries, and a Linux operating system that is independent of the host computer you run the container on. This can be very useful if you want to share your software environment with other researchers or yourself across several computers. Because Singularity containers run as the user that started them and mount home directories by default, you can usually see the data you're interested in working on that is stored on a host computer without any extra work.
Below we will outline some common use cases covering the creation and use of containers. There is also excellent documentation available on the full and official user guide for Singularity. We are happy to help, just email us with your questions.
On the Yale clusters, Singularity is not installed on login nodes. You will need to run it from compute nodes.
Get a Container Image
Images are the file(s) you use to run your container. Singularity images are single files that usually end in
.img and are read-only by default, meaning changes you make to the environment inside the container are not persistent.
Use a pre-existing container
If someone has already built a container that suits your needs, you can use it directly. You can either copy the singularity image file directly with
rsync, or globus. You can also use Docker Hub or Singularity Hub images hosted on their respective registries. Container images can take up a lot of disk space (dozens of gigabytes), so you may want to change the default location singularity uses to cache these files. To do this before getting started, you should add something like the example below to to your
# set SINGULARITY_CACHEDIR if you want to pull files (which can get big) somewhere other than $HOME/.singularity # e.g. export SINGULARITY_CACHEDIR=~/project/.singularity
Here are some examples of getting containers already built by someone else with singularity:
# from Docker Hub (https://hub.docker.com/) singularity build ubuntu-18.10.simg docker://ubuntu:18.10 singularity build tensorflow-10.0-py3.simg docker://tensorflow/tensorflow:1.10.0-py3 # from Singularity Hub (https://singularity-hub.org/) singularity build bioconvert-latest.simg shub://biokit/bioconvert:latest
Build Your Own
You can define a container image to be exactly how you want/need it to be, including applications, libraries, and files of your choosing with a recipe file. Singularity recipe files are similar to Docker's
Dockerfile, but use different syntax. To build a container from a recipe file, you need administrative privileges on a Linux machine where Singularity is installed. If you don't have such an environment available, get in touch with us for help getting set up. For full recipes and more documentation please see the singularity site.
Every container recipe must begin with a header that defines what image to start with, or bootstrap from. This can be an official Linux distribution or someone else's container that gets you nearly what you want.
To start from Ubuntu Bionic Beaver (18.04 LTS):
Bootstrap: docker From: ubuntu:18.04
Or an Nvidia developer image
Bootstrap: docker From: nvidia/cuda:9.2-cudnn7-devel-ubuntu18.04
The rest of the sections all begin with
% and the section name. You will see section contents indented by convention, but this is not required.
The labels section allows you to define metadata for your container:
%labels Name Maintainer "YCRC Support Team"
Version v99.9 Architecture x86_64 URL https://research.computing.yale.edu/
You can examine container metadata with the
singularity inspect command.
If you'd like to copy any files from the system you are building on, you do so in the %files section. Each line in the files section is a pair of source and destination paths, where the source is on your host system, and destination is a path in the container.
%files sample_data.tar /opt/sample_data/ example_script.sh /opt/sample_data/
The post section is where you can run updates, installs, etc in your container to customize it.
%post echo "Customizing Ubuntu" apt-get update apt-get -y install software-properties-common build-essential cmake add-apt-repository universe apt-get update apt-get -y libboost-all-dev libgl1-mesa-dev libglu1-mesa-dev cd /tmp git clone https://github.com/gitdudette/myapp && cd myapp # ... etc etc
The environment section allows you to define environment variables for your container. These variables are available when you run the built container, not during its build.
%environment export PATH=/opt/my_app/bin:$PATH export LD_LIBRARY_PATH=/opt/my_app/lib:$LD_LIBRARY_PATH
To finally build your container after saving your recipe file as
my_app.def, for example, you would run
singularity build my_app.simg my_app.def
Use a Container Image
Once you have a container image, you can run it as a part of a batch job, or interactively.
To get a shell in a container so you can interactively work in its environment:
singularity shell --shell /bin/bash containername.simg
In a job script
You can also run applications from your container non-interactively as you would in a batch job. If I wanted to run a script called
my_script.py using my container's python:
singularity exec containername.simg python my_script.py
If you are unsure if you are running inside or outside your container, you can run:
If you get back text, you are in your container.
If you'd like to pass environment variables into your container, you can do so by defining them prefixed with
SINGULARITYENV_ . For Example:
export SINGULARITYENV_BLASTDB=/home/me/db/blast singularity exec my_blast_image.simg env | grep BLAST
BLASTDB=/home/me/db/blast, which means you set the
BLASTDB environment variable in the container properly.
MPI support for Singularity is relatively straight-forward. The only thing to watch is to make sure that you are using the same version of MPI inside your container as you are on the cluster.
You can use gpu-accelerated code inside your container, which will need most everything also installed in your container (e.g. CUDA, cuDNN). In order for your applications to have access to the right drivers on the host machine, use the
--nv flag. For example:
singularity exec --nv tensorflow-10.0-py3.simg python ./my-tf-model.py
Sometimes the maintainer of a docker container you are trying to use installed software into a special user's home directory. If you need access to someone's home directory that exists in the container and not on the host, you should add the
--contain option. Unfortunately, you will also then have to explicitly tell Singularity about the paths that you want to use from inside the container with the
singularity shell --shell /bin/bash --contain --bind /gpfs/ysm/project/be59:/home/be59/project bioconvert-latest.simg