[Bioclusters] Xserve G5 memory

Michael Maibaum bioclusters@bioinformatics.org
Mon, 11 Oct 2004 12:26:20 +0100

On 5 Oct 2004, at 21:19, Juan Carlos Perin wrote:

> Well, for these benchmarks we focused on the larger NT database.  This 
> is
> the only database that really shows significant lag time in search 
> runs due
> to its large size, but I have confirmed that the database is not 
> overflowing
> into swap space.  This wasn't initially assumed because we have plenty 
> of
> memory, but I verified it anyway.
> OSX can be 'kernel tuned' through 'sysctl' but it doesn't seem obvious 
> how
> to do this to allow retention of a flatfile database for this type of 
> an
> application.

Frankly, I'd be amazed if this was anything other than a addressable 
RAM size issue. I'd presume that the 8-way IBM machine has lots of RAM 
and the XServes probably have less. Thus, the large DB isn't being 
cached as well by the XServes due to memory pressure. How much RAM does 
the IBM/Xeon machine(s) have compared to the XServe. Also, OS X is 
generally 'larger' in terms of memory use than Linux.


Dr Michael Maibaum
Department of Biochemistry and Molecular Biology, UCL
email: maibaum@biochemistry.ucl.ac.uk