[Bioclusters] Re: Opterons

Fri, 05 Mar 2004 11:53:38 -0500

I have built some e325 based clusters.  Used ROCKS 3.1 x86_64 edition. 
Works nicely.  

On Fri, 2004-03-05 at 11:39, Chris Dagdigian wrote:
> The opteron mention brings up another question I wanted to ask this list--
> 
> What Linux distributions are people using for Opteron based machines?
> 
> I have a pair of IBM e325 opteron servers in the lab/office and 
> initially have been using Suse 9.0 on them mainly because I know that 
> IBM and Suse are tight and I figured that it would be the safe choice 
> since I'm still slightly worried about the somewhat new support for
> 
> Suse 9 on Opteron has been great so far. I'm going to start 
> experimenting with Tao Linux (www.taolinux.org) which is a 'generic' 
> form of RH Enterprise Linux built from source rpm files next.
> 
> After Tao I want to try Fedora, Fedora-legacy and the actual Redhat 
> branded AS or ES products. Anything else I should try? any 
> recommendations from people using opterons in production settings?
> 
> -Chris
> 
> 
> 
> 
> Arnie Miles wrote:
> 
> > Has anyone considered Opterons?  Our preliminary investigations indicate
> > that the Opterons have a considerably better bang/buck ratio then
> > anything else out there right now, particularly Xeon, even in 32 bit
> > configuration.  We're getting dual processor Opterons in the under $3k
> > price range.
> > 
> > I'm anxious to try out my first G5 cluster one day, hopefully soon, but
> > the Opteron path makes more applications available to me.
> > 
> > Arnie Miles
> > Advanced Research Computing
> > Georgetown University
> > 
> > On Fri, 2004-03-05 at 10:53, Michael Chute wrote:
> > 
> >>For my two cents I would have to disagree with the Xeon approach.  A 
> >>cluster of Xserves is probley going to give you more speed and storage 
> >>for the buck than a Xeon machine.  We have  a small cluster of Xserves 
> >>running osX server and we find that it is very fast, and the new g5 
> >>slusters are even faster.  Another alternative that has been done in 
> >>the past is to actually run Linux on Xserves.  I don't know the details 
> >>of this but I do know that this has been done.  If you look at the 
> >>bioteam software as well there are over 200 bioinformatics tools 
> >>included with the package and they all have a gui interface which is 
> >>very nice for the average user.  As far as management features you 
> >>can't beat osx server.  Everything is so easy to do you don't need a 
> >>bunch of IT people to do it for you.  I am a microbiologist and I admin 
> >>our cluster.  I think the "most tools for bioinformatics under linux" 
> >>is not exactly true.  I don't think you will find much trouble finding 
> >>an osx port for most of the tools.  FYI there is going to be a webcast 
> >>about the Xserve cluster for use in bioinformatics next thursday, you 
> >>might want to watch, you might get some of your questions answered.
> >>
> >>http://education.apple.com/webcast/workgroupcluster/
> >>
> >>Mike
> >>
> >>Michael D. Chute
> >>BSL-3 Lab Manager
> >>Naval Medical Research Center
> >>Biological Defense Research Directorate
> >>Suite 1N29
> >>503 Robert Grant Ave
> >>Silver Spring, MD 20910
> >>Voice: 301-319-7529
> >>Fax: 301-319-7513
> >>On Mar 5, 2004, at 10:41 AM, Tim Cutts wrote:
> >>
> >>
> >>>On 5 Mar 2004, at 15:32, Christopher Porter wrote:
> >>>
> >>>
> >>>>We're in the market for a cluster; most of our options are 
> >>>>Xeon/Linux, but one is a cluster of XServe G5s running OS X. We're 
> >>>>going to run some benchmarks to see how the performance compares, but 
> >>>>some in of our group have expressed concern that 'the vast majority 
> >>>>bioinformatics software is developed on Linux', and 'there may be a 
> >>>>long time lag before new software is available on OS X'.
> >>>
> >>>Most stuff compiles quite cleanly.  You could get bitten though with 
> >>>anything that builds shared libraries.  OS X dylib bundles are *very* 
> >>>different from normal UNIX shared objects.  Have a look at the 
> >>>O'Reilly book "MacOS X for Unix Geeks" which is very small, but covers 
> >>>some of this stuff.
> >>>
> >>>There are various other gotchas as well, but I don't know about them 
> >>>in detail.
> >>>
> >>>
> >>>>I have never had problems getting software I need to run on OS X, but 
> >>>>I wondered if anyone can provide me with examples of applications 
> >>>>that won't run on OS X, or are Linux only (only binaries released & 
> >>>>no source available).
> >>>
> >>>I suspect you'll get much more bang-per-buck with Xeon machines.  
> >>>You'll also probably get better management features, although how 
> >>>crucial that is rather depends on how large a cluster you want to get.
> >>>
> >>>Personally, although I love Macs, and have one as my day-to-day 
> >>>machine, I'm currently happier with Linux for the larger scale stuff.
> >>>
> >>>Tim
> >>>
> >>>-- 
> >>>Dr Tim Cutts
> >>>Informatics Systems Group
> >>>Wellcome Trust Sanger Institute
> >>>Hinxton, Cambridge, CB10 1SA, UK
> >>>
> >>>_______________________________________________
> >>>Bioclusters maillist  -  Bioclusters@bioinformatics.org
> >>>https://bioinformatics.org/mailman/listinfo/bioclusters
> >>
> >>_______________________________________________
> >>Bioclusters maillist  -  Bioclusters@bioinformatics.org
> >>https://bioinformatics.org/mailman/listinfo/bioclusters
> > 
> > ==================
> > Arnie Miles
> > Systems Administrator, Advanced Research Computing (ARC)
> > Adjunct Assistant Professor, Computer Science Dept.
> > Georgetown University
> > 401 Reiss Science
> > 37th and O Streets NW,
> > Washington, DC  20057
> > 202-687-9379
> > 
> > http://www.georgetown.edu/users/adm35/   (Personal)
> > http://www.clusters.arc.georgetown.edu/  (GUPPI Initiative)
> > http://www.georgetown.edu/research/arc/  (Division)
> > ==================
> > 
> > 
> > 
> > 
> > 
> > _______________________________________________
> > Bioclusters maillist  -  Bioclusters@bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/bioclusters