[Bioclusters] Any issues porting applications to OS X?

Lorraine Freeman bioclusters@bioinformatics.org
Fri, 5 Mar 2004 14:09:39 -0500

Has anyone benchmarked BLAST on Altix? It seems that it might be easier to
administer and run bioinformatics applications on a single big machine. I
don't know how the Altix compares in terms of cost.

       Lorraine Freeman
       (408) 761-1279 

. -----Original Message-----
. From: Chris Dagdigian [mailto:dag@sonsorol.org]
. Sent: Friday, March 05, 2004 8:21 AM
. To: bioclusters@bioinformatics.org; biodarwin@bioinformatics.org
. Subject: Re: [Bioclusters] Any issues porting applications to OS X?
. For apps where source code is available OS X has been generally very
. easy to deal with.
. There are, however, commercial apps that are released binary only for
. Linux (and usually only certain flavors of Linux). Two companies who
. sell Linux products into the informatics, chemistry or molecular
. modeling spaces are Schrodinger and Accelrys but I'm sure people can
. come up with more concrete example.
. My personal feeling right now (probably at odds with my partners maybe
. :) is that Linux on X86 or X86_64 is a better generic or
. widest-possible-utility computing platform.
. The decision to go with an alternative (UltraSparc, G5, whatever...)
. should be based on actual benchmarks or local documented need.
. Apple OS X clusters make sense for two distinct groups IMHO:
. 1. People who have real benchmarks that show G5/darwin as being the
. best/fastest platform for the apps that they most care about. There are
. a number of these as the G5 platform is really really slick.
. 2. People who like OS X, have lots of inhouse experience and prefer for
. operational overhead to manage their cluster(s) using the same
. technology and tools they already use inhouse.
. Yellowdog Linux on G5 is a strange one. Probably best for people who
. have a known set of apps that run really fast on G5 and don't want or
. like Panther. I would not recommend this approach for people wanting a
. general purpose platform -- stick with Panther on the G5 unless you have
. a very specific reason not to.
. Linux vs Apple cluster managability is a red herring -- both are easy to
. do. Apple's OS X server OS ships with a number of tools that make
. managment pretty easy. Linux has the same capabilities through the base
. OS itself or via open source tools.
. We generally have various bits of Apple kit floating through our
. office/lab at any given time. The G5 Xserves have been shipped back
. sadly but we still have dual-G5 towers running Panther.
. On a case by case basis we may be able give SSH login access to a G5
. system to people who are investigating porting or benchmarking issues.
. Feel free to drop me a line privately if this would be of assistance.
. -Chris
. bioteam
. 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'.
. >
. > 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).
. >
. > This is only one of the criteria we're judging on, and the performance
. > comparison will be interesting. Any insights on this issue would be
. > extremely useful, though.
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