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Singularity

Note: Singularity was originally a project out of Lawrence Berkeley National Laboratory. It has now been spun off into a distinct offering under a new corporate entity under the name Sylabs Inc. This guide pertains to the open source community edition, SingularityCE.

Link to section 'What is Singularity?' of 'Singularity' What is Singularity?

Singularity is a new feature of the Community Clusters allowing the portability and reproducibility of operating system and application environments through the use of Linux containers. It gives users complete control over their environment.

Singularity is like Docker but tuned explicitly for HPC clusters. More information is available from the project’s website.

Link to section 'Features' of 'Singularity' Features

  • Run the latest applications on an Ubuntu or Centos userland
  • Gain access to the latest developer tools
  • Launch MPI programs easily
  • Much more

Singularity’s user guide is available at: sylabs.io/guides/3.8/user-guide

Link to section 'Example' of 'Singularity' Example

Here is an example using an Ubuntu 16.04 image on Hammer:

singularity exec /depot/itap/singularity/ubuntu1604.img cat /etc/lsb-release
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=16.04
DISTRIB_CODENAME=xenial
DISTRIB_DESCRIPTION="Ubuntu 16.04 LTS"

Here is another example using a Centos 7 image:

singularity exec /depot/itap/singularity/centos7.img cat /etc/redhat-release
CentOS Linux release 7.2.1511 (Core) 

Link to section 'Purdue Cluster Specific Notes' of 'Singularity' Purdue Cluster Specific Notes

All service providers will integrate Singularity slightly differently depending on site. The largest customization will be which default files are inserted into your images so that routine services will work.

Services we configure for your images include DNS settings and account information. File systems we overlay into your images are your home directory, scratch, Data Depot, and application file systems.

Here is a list of paths:

  • /etc/resolv.conf
  • /etc/hosts
  • /home/$USER
  • /apps
  • /scratch
  • /depot

This means that within the container environment these paths will be present and the same as outside the container. The /apps, /scratch, and /depot directories will need to exist inside your container to work properly.

Link to section 'Creating Singularity Images' of 'Singularity' Creating Singularity Images

Due to how singularity containers work, you must have root privileges to build an image. Once you have a singularity container image built on your own system, you can copy the image file up to the cluster (you do not need root privileges to run the container).

You can find information and documentation for how to install and use singularity on your system:

We have version 3.8.0-1.el7 on the cluster. You will most likely not be able to run any container built with any singularity past that version. So be sure to follow the installation guide for version 3.8 on your system.

singularity --version
singularity version 3.8.0-1.el7

Everything you need on how to build a container is available from their user-guide. Below are merely some quick tips for getting your own containers built for Hammer.

You can use a Definition File to both build your container and share its specification with collaborators (for the sake of reproducibility). Here is a simplistic example of such a file:

# FILENAME: Buildfile

Bootstrap: docker
From: ubuntu:18.04

%post
    apt-get update && apt-get upgrade -y
    mkdir /apps /depot /scratch

To build the image itself:

sudo singularity build ubuntu-18.04.sif Buildfile

The challenge with this approach however is that it must start from scratch if you decide to change something. In order to create a container image iteratively and interactively, you can use the --sandbox option.

sudo singularity build --sandbox ubuntu-18.04 docker://ubuntu:18.04

This will not create a flat image file but a directory tree (i.e., a folder), the contents of which are the container's filesystem. In order to get a shell inside the container that allows you to modify it, user the --writable option.

sudo singularity shell --writable ubuntu-18.04
Singularity: Invoking an interactive shell within container...

Singularity ubuntu-18.04.sandbox:~>

You can then proceed to install any libraries, software, etc. within the container. Then to create the final image file, exit the shell and call the build command once more on the sandbox.

sudo singularity build ubuntu-18.04.sif ubuntu-18.04

Finally, copy the new image to Hammer and run it.

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