singularity_talk/singularity_slides.html at main · UTS-eResearch/singularity_talk · GitHub

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<!doctype html>
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<meta charset="utf-8">
<title>A Quick Singularity Overview</title>
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# A Quick Singularity Overview

<[email protected]>
October 2018

<small>These slides are available as a PDF. &#8239; Email me. </small>
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## What is Singularity?

Singularity is a "container" technology. Containers can be used to package
applications and data.

- Need to run an application that is not on the cluster? Install the app in a singularity.
- Need to share your hard to install code? Put it in a singularity container, send that to your collaborator.
- Need to run a different operating system? Just "replace" the operating system
  on your host with one from within a singularity.

https://www.sylabs.io/singularity/
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## How does this Help Science?

- Encourages reproducibility.
- Helps portability.
- Can more easily share your own work.
- Can more easily use other people’s work.
- Can provide a way to archive complex software/workflows.
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## Docker

- Docker is the most well known container platform.
- Aimed at Software Developers
- Docker is designed for the enterprise, not HPC.
- No reasonable support for MPI.
- Docker containers usually run as root.
<aside class="notes">
Message Passing Interface
</aside>
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## Singularity

- Aimed at Scientists.
- Build-in support for MPI (OpenMPI, MPICH, IntelMPI).
- Maintains user credentials: inside user = outside user.
- Singularity can import and run Docker containers.
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## Singularity is Safe for Sys Admins :-)

If you want to be root inside of the container,
you must first be root outside of the container.
*Hence you have to build the container outside of the HPC.*

Then copy the container over to the HPC.
*Now run the container as a normal user.*

HPC Sys Admins will be happy with this!
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## Run a Different Operating System!

You can run a different operating system by "replacing" the
operating system on your host. You can run:
- Fedora, CentOS, RedHat
- Debian, Ubuntu
- Scientific Linux
- Bio-Linux

and many more ...
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Example Singularity Definition File
<pre>
# Singularity definition for a Centos 7 base image.
BootStrap: yum
OSVersion: 7
MirrorURL: http://mirror.centos.org/centos-7/x86_64/

%labels
    Maintainer Mike Lake
    Version 1.0

%help
    This is a Centos 7 Singularity container for
    running fortune and cowsay.

# Applications
%runscript
    echo "Hello from inside the singularity of Centos 7."
    fortune | cowsay
</pre>
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This is how we build the Centos 7 image on our own *local* computer:

    $ sudo singularity build centos7.img centos7.def

Now we copy the image to the HPC cluster:

    $ scp centos7.img [email protected]:/shared/homes/xxxx/

This is how we run the Centos 7 image on the HPC:

    $ singularity run centos7.img
    Hello from inside the singularity of Centos 7.
</textarea></section>


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## Singularity Hub

Singularity Hub is a registry for scientific linux containers.

2385 containers across 1249 collections.
From 1,500 GB sized images to small 22 MB images.

https://www.singularity-hub.org
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## Singularity Hub

Singularity Hub is also a cloud build service for users.

The user pushes to Github, a builder is deployed, and the image is available to the user.
This allows a user to build and run an image from a resource
where they don’t have root access simply by using Github as a middleman.
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## Main References

Singularity Home Page:
https://www.sylabs.io/singularity/

Documentation: https://www.sylabs.io/docs/

FAQ: https://www.sylabs.io/singularity/faq/

Container Registry: https://singularity-hub.org
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## Other References

High-Performance Computing at the NIH: https://hpc.nih.gov/apps/singularity.html

A tutorial at Github, "Creating and running software containers with Singularity":
https://github.com/NIH-HPC/Singularity-Tutorial

PDF presentation at the HPC Developer Conference:
https://wilsonweb.fnal.gov/slides/hpc-containers-singularity-introductory.pdf
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These slides are available as a PDF

Email me at [email protected]
</textarea></section>

</div>
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https://en.wikipedia.org/wiki/Fortune_(Unix)
https://en.wikipedia.org/wiki/Cowsay
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