[Beowulf] cluster os

[Jörg Saßmannshausen]

Hi Jonathan,

the only thing I am compiling from source are the HPC programs we are using 
and also some of the HPC libraries. I want to get the best out of the system 
and hence I decided to do it this way. Also, some HPC programs are simply only 
available as source code. So depending how often there is an upgrade of the 
program and how it is distributed (source or binary) I do the upgrades. 

The libraries I usually do once. In particular I don't upgrade say ATLAS, fftw3 
etc until I upgrade the whole cluster. 

I hope that helps a bit.

All the best from London

Jörg

On Friday 20 May 2016 12:34:37 Jonathan Aquilina wrote:
> Going a bit off track from upgrades here.  In a cluster environment with
> debian do you spend a fair bit of time compiling anything from source?
> 
> On 2016-05-20 12:08, Tim Cutts wrote:
> > In practice, at Sanger we haven't made very heavy use of the ability of
> > Debian to upgrade from release to release.  We use FAI to install the
> > boxes, so frankly it's faster and less hassle to just reinstall them from
> > scratch when the next release comes out.
> > 
> > For some complicated bespoke systems, I have done the manual upgrade, and
> > I've even done that across debian-derived distros.
> > 
> > Officially, you're not supposed to be able to use apt to upgrade a system
> > from Debian to Ubuntu, for example, but I have done it in the past - I
> > worked out a documented procedure for doing a dist-upgrade from Debian
> > Lenny to Ubuntu Lucid, for example.  At one point, you do have to force
> > downgrade packages which are newer in the original os than they are in
> > the target, which led to the following one liner of which I am perversely
> > proud:
> > 
> > aptitude search -F '%p' ~i | xargs -n 1 apt-cache policy | sed -n -e '
> > /^[a-z0-9.-]*:$/{h;d;}
> > /\*\*\*/{
> > n
> > /^  *500 /d
> > /^  *100 /{
> > n
> > /^  *[^ ]/{x;s/:/\/lucid/p;x;}
> > }
> > /^[a-z0-9.-]*:$/{h;d;}
> > }
> > ' | xargs apt-get -y --force-yes install
> > 
> > Gotta love sed for resulting in completely impenetrable commands.  I did
> > try to do it in a more readable way using the python APT bindings, but
> > that was actually much harder.
> > 
> > Tim
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-- 
*************************************************************
Dr. Jörg Saßmannshausen, MRSC
University College London
Department of Chemistry
20 Gordon Street
London
WC1H 0AJ 

email: j.sassmannshausen at ucl.ac.uk
web: http://sassy.formativ.net

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