[Bioclusters] Debian cluster

Matthew Laird bioclusters@bioinformatics.org
Thu, 18 Sep 2003 22:28:57 -0700 (PDT)

The one comment I would like to offer is out of courtesy to the Debian 
community I hope you will have a local mirror or the package archive or 
subset you are using.

On my personal machines I'm a Debian boy all the way just for the apt-get 
reason.  But if you're planning to build a 50+ machine cluster using 
Debian then run an apt-get upgrade on all of them when a patch comes 
out... that could add noticable strain to the mirrors over time as well as 
your institution's connection.

I know on campus we have a Redhat mirror just for on campus use.  I also 
have scripts to keep the subset I use on our cluster current and the 
machines patched.

This is definitely an avenue you might want to investgate for the courtesy 
reason plus it's just faster to install from a local mirror.

Another advantage I've learned about having a local mirror, especially 
with Debian, is you can freeze the packages at any point you want so you 
can always recreate the exact same configuration with no risk of package 
upgrades conflicting with something.  That is one beef I had with Debian a 
few years ago, mysterious package upgrades that sometimes broke other 
packages, but I guess that's what you get when using the unstable release. 

Anyhow, just wanted to pass along those lessons I've learned.  Good luck, 
and let me know how Debian works out as the basis for a cluster.  I might 
rebuild mine from RH9 to Debian if you have great successes. :)

On Fri, 19 Sep 2003, Nox wrote:

> We have begun to investigate FAI and Debian for our clustering 
> solutions.
> I have always been partial to Debian, its my OS of choice,
> has been for yrs.
> So when I discovered the clustering tools, I was excited.
> (FAI, Fully Automated Install)
> Does anyone have experience with this?
> Pitfalls, things to watch for,
> success stories etc.
> from my perspective:
> Debian offers ease of use
> Updates are a snap (apt-get) --Including security
> Ability to be a very minimalist system
> Quick access to Biotech tools (bioperl as an example)
> We currently use debian as our Halted Firewall as well.
> Thanks in advance
> Nox
> GenMicro Systems
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Matthew Laird
SysAdmin/Web Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University