> We have 2 gigs of RAM per Node. For our testing purposes we are > willing to > add as much RAM as necessary, up to 8 is permitted on the Xserves. > The IBM > actually has 8 gigs in it. I'd be willing to tweak the kernel, or > anything > else necessary to have memory allocation work a little more > effectively for > BLAST if possible. We've even considered simply dedicating a machine > or two > to performing at its best with BLAST. It might be wise to look into some of the specialized accelerators available on the market. If BLAST is really the primary and only use for a certain set of resources, it's possible to achieve two or three orders of magnitude of speedup by using specialized hardware. Of course, it all depends on how the problem is stated and what the users need. I know very few researchers for whom BLAST is the rate limiting step. It's a mature, popular, free piece of software, which makes for a great benchmark, but my suspicion is that even if the time requirement for BLAST were reduced to zero, it wouldn't appreciably change the way in which life scientists do their work. Naturally, many of the exceptions are on this list. :) -Chris Dwan The BioTeam