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 lfreeman@altair.com (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. . . _______________________________________________ . Bioclusters maillist - Bioclusters@bioinformatics.org . https://bioinformatics.org/mailman/listinfo/bioclusters