Getting user-space containers with Singularity - works

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Getting user-space containers with Singularity - works

Steffen Möller
Hello,

Many (most) HPC administrators very much detest the idea to grant any
sort of root privileges to their users. This consequently rules out the
installation of our Debian packages and also the employment of Docker
images for the execution of binaries. Ouch! After all, with this
perpetual avalanche of biological data we are often dependent of some
sort of shared infrastructure for storage and/or computation. Also, for
consistency within long-running projects, one cannot just go and update
Debian packages because of a new project starting. Every project comes
with its own set of versioned tools and data. These are prime use cases
for containers - if they would just work as regular users.

To the rescue comes Singularity. It does what you would want to do with
Docker, without extra privileges:

   * deliver a set of tools and/or data readily configured for the task
   * become Linux-distribution agnostic
   * continue working with Docker images of yours or your collaborators

Our pals from neuro.debian.net are already actively using this
technology and kindly nurture backports.d.o with it. I have also seen
Roland in the changelog. Many thanks! With feedback from Yaroslav I
created a quick introduction to get you started at
https://wiki.debian.org/singularity.  It is quite an eye opener. Enjoy!

Best,

Steffen

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Re: Getting user-space containers with Singularity - works

Afif Elghraoui-6
Hi,

Thanks for bringing this up, Steffen.

على الأحد 23 تـمـوز 2017 ‫11:30، كتب Steffen Möller:
[...]
>
> Our pals from neuro.debian.net are already actively using this
> technology and kindly nurture backports.d.o with it.

I think the Neurodebian group only maintains backports in their own
neurodebian repositories. Singularity's development is moving rather
quickly and the freeze kind of made the official Debian backports of
singularity uselessly outdated for those several months. Now, of course,
we can use jessie-backports-sloppy and stretch-backports, but
singularity there is still outdated at the moment.

> I have also seen
> Roland in the changelog. Many thanks! With feedback from Yaroslav I
> created a quick introduction to get you started at
> https://wiki.debian.org/singularity.  It is quite an eye opener. Enjoy!
>

Thanks, Steffen. Our group at the US NIH HPC has also a guide and
tutorial for our users:

https://hpc.nih.gov/apps/singularity.html
https://github.com/NIH-HPC/Singularity-Tutorial

My old colleague who wrote those actually ended up moving on to a job as
a singularity developer.

I think a very successful Debian example would make use of
snapshot.debian.org as a mirror in the definition file in order to be
able to regenerate exactly the same container at any time.

regards
Afif

--
Afif Elghraoui | عفيف الغراوي
http://afif.ghraoui.name