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:[email protected] | 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
