[Bioclusters] Any issues porting applications to OS X?

Michael Chute bioclusters@bioinformatics.org
Fri, 5 Mar 2004 10:53:53 -0500

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.
> Tim
> -- 
> Dr Tim Cutts
> Informatics Systems Group
> Wellcome Trust Sanger Institute
> Hinxton, Cambridge, CB10 1SA, UK
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