>From ozgun:
>
> Inlining replies.
>
>> 1. What's the environment; Solaris, GNU/Linux, *nix, Windows?
>
> Linux.
>
>> 2. What hard information do you have on the resources being used? Have
>> you been able to profile it? Pareto's Law applies surprisingly often.
>
> Tons. In fact, we have more information than we'd like. Since we
> profile and optimize on a regular basis, our workset doesn't exhibit
> Pareto's Law.
>
>> 3. What sort of application is it? Is it CPU or I/O intensive?
>
> CPU intensive. In fact, there is no disk I/O. We're planning to take
> the disks out at some point because they cost too much.
>
Are you doing DNA sequencing?
It looks as though you've done all the obvious things. If you haven't
already done them, my only questions remain: are the boxes maxed-out with
memory, and are the algorithms optimal? (Checking that might be difficult
if you've got a "death by a thousand cuts" type of workload.)
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