[Bioclusters] cache limit?

[Justin Powell]

I've got a small blast cluster which includes a Quad Processor Dell
(kernel 2.2.16-22enterprise #1 SMP) and a bunch of Dual Athlons (kernel
2.4.2-2smp #1).  Repeat BLASTS of the same DB on the Athlons run about 7
times faster than the first BLAST, I assume this is due to the memory
mapped dbs being retained in the cache, but this is not the case with the
Dell.  When I use 'free' to look at memory the cache on the Dell never
goes above 850MB whereas that on the Athlons happily goes up to 3.5GB
after identical BLAST jobs.

All systems have 4GB ram.  Are there some obvious parameters which can be
adjusted to alter the behaviour of the cache under Linux (I can't find
obvious references to such on Google) or is there some difference in the
memory management of different versions of the kernel which makes some of
them less useful for this sort of thing?

Justin Powell
jacp1@mole.bio.cam.ac.uk