Right. But you've still not made a compelling argument that the "smart encoding of the data" and "clever search strategy" couldn't be done with/in SQL. I'm quite sure you could probably get a magnitude or two of improvement by diving down outside of SQL -- but there's a big difference between using the schema you have, and setting up a dedicated system.
I was perhaps not clear, but I was wondering if it's not often the case with real-world data, that you could create a new, tailored schema in SQL, and do the analysis on one system -- especially if you allow for something like advanced stored procedures (perhaps in C) and alternate storage engines.
I suppose one could argue when something stops being SQL, and start becomming SQL-like. But the initial statement was that "For some problems SQL would already be way too much overhead.". The implication being (as I understood it, at least) -- that you not only have to change how the date is stored and queried, but that SQL databases are unsuitable to that that task -- and that by going away from your dbs, you can suddenly do something that you couldn't do on a system with X resources.
I'm not saying that's wrong -- I'm just asking if a) that's what you mean, and b) if you can quantify this overhead a bit more. Are using bitfields or whatnot with postgres going to be a 20% overhead, or a 20000% overhead in your scenario? Because if it's 20%, that sounds like it can be "upgraded away".