[Bioclusters] Any issues porting applications to OS X?

Arnie Miles bioclusters@bioinformatics.org
05 Mar 2004 11:22:16 -0500

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
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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

http://www.georgetown.edu/users/adm35/   (Personal)
http://www.clusters.arc.georgetown.edu/  (GUPPI Initiative)
http://www.georgetown.edu/research/arc/  (Division)