On Sun, Jul 09, 2017 at 10:13:03PM +0200, Stephan Wiesand wrote:
> 
> On Jul 9, 2017, at 18:32 , Bruce Ferrell wrote:
> 
> > On 07/09/2017 05:51 AM, Tru Huynh wrote:
> >> On Sun, Jul 09, 2017 at 12:03:02AM -0700, Bruce Ferrell wrote:
> >>> OK, before the flames start I KNOW it's not normal.
> >>> 
> >>> Has anyone have a method to upgrade glibc beyond 2.12?
> >> I would suggest trying singularity (http://singularity.lbl.gov)
> >> and put your application of choice in a single container
> >> (http://singularity.lbl.gov/quickstart).
> > 
> > Thanks Tru, but looking at this, I'm basically spinning up a Centos/RHEL/SciLin7 "container".
> 
> Singularity is not limited to those OSs. When it comes to using recent versions of system libraries, others may be a better choice.
> 
> >  If I'm going that route, spinning up a VM is a WHOLE lot faster...
> 
> Er, no... creating an image is faster than installing a VM, starting
> it is orders of magnitude faster, and on top you dont' have to
> configure and maintain a full system. In particular, you don't have to
> run systemd even if you choose EL7 or Ubuntu 16.04 as the container
> runtime.

Furthermore, you don't need to do anything to share $HOME between the
singularity container and your host $HOME, nor need to create accounts +
ssh/scp back and forth, of course YMMV.

> 
> > And if I have to go VM to do this, I may as well do a "from scratch" (Gentoo FS etc) in the VM.
> > 
> > I have yet to see a good use case for containers... Unless you need a lot of them.  Most people don't.
> 
> Well yours is a very good use case for a Singularity container. Give
> it a serious try, and I'm pretty sure you won't look back to any
> solution you have in mind now.
> 
if you can build a VM from scratch, you can do it with a singularity or a
docker recipe (or use both).

I just made a quick and dirty calibre3 on a singularity container and
shared it on https://singularity-hub.org.
- install singularity 2.3.1
- singularity run shub://truatpasteurdotfr/singularity-docker-centos7-calibre

recipe at https://github.com/truatpasteurdotfr/singularity-docker-centos7-calibre

Feel free to follow-up on the singularity mailing list or slack.

Cheers

Tru

-- 
Dr Tru Huynh | mailto:[log in to unmask] | tel/fax +33 1 45 68 87 37/19
https://research.pasteur.fr/en/team/structural-bioinformatics/
Institut Pasteur, 25-28 rue du Docteur Roux, 75724 Paris CEDEX 15 France