[Bioclusters] Any issues porting applications to OS X?

Elia Stupka bioclusters@bioinformatics.org
Fri, 5 Mar 2004 17:30:16 +0100

> I'm anxious to try out my first G5 cluster one day, hopefully soon, 
> but the Opteron path makes more applications available to me.

On the G5 side of things so far I don't have as positive comments as in 
my earlier mail. We got 4 2Ghz dual G5s as soon as they were available 
and we really really felt like Apple's guinea pigs (though the price 
was not guinea pig price) as 3 out of 4 had various hardware issues, 
instabilities,etc. Once again, they were very prompt and helpful in 
sorting those issues out, but still for quite a while we weren't really 
productive on those machines.  In a week or so we should be Sun Grid 
Engine'ing them together so we should know how well they behave under 


> 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
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