Opterons (was Re: [Bioclusters] Any issues porting applications to OS X?)

Chris Dagdigian bioclusters@bioinformatics.org
Fri, 05 Mar 2004 11:39:30 -0500

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?


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.
>>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.
>>>Dr Tim Cutts
>>>Informatics Systems Group
>>>Wellcome Trust Sanger Institute
>>>Hinxton, Cambridge, CB10 1SA, UK
>>>Bioclusters maillist  -  Bioclusters@bioinformatics.org
>>Bioclusters maillist  -  Bioclusters@bioinformatics.org
> ==================
> 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

Chris Dagdigian, <dag@sonsorol.org>
BioTeam  - Independent life science IT & informatics consulting
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