H2 sounds like the safe choice.  

You could also try/evaluate the latest 
mapdb: https://github.com/jankotek/MapDB#features 
It very easy to use from clojure but I only used it on trivial stuff 
however, and it's still considered alpha.

On Sunday, May 26, 2013 5:09:51 PM UTC+2, Cedric Greevey wrote:
>
> I may be developing an application which will need a persistent, ACID 
> local database (on the same disk as the application, rather than having to 
> be accessed over the network) containing information about potentially 
> 100,000-1,000,000 (or more) objects.
>
> Much of that information will be of a quasi-boolean character: "is it an X 
> or not?" for various choices of X, but with "yes", "no", "borderline", and 
> "not yet evaluated" as the four possible values. It will be desirable to 
> query for these, for example to get a lazy seq of all objects for which 
> it's a borderline Y or for which it's not yet evaluated whether it's a Z or 
> for which it's either "yes" or "borderline" on whether it's an X or 
> whatever.
>
> I'm not that familiar with the local-DB solutions out there. I'd like a 
> recommendation for one which is a) a good for for Clojure use and b) a good 
> fit for the type of data and queries noted above. The DB must be able to 
> grow larger then available RAM without crashing the JVM and the seqs 
> resulting from queries like the above will also need to be able to get 
> bigger than RAM.
>
> My own research suggests that H2 may be a good choice, but it's a standard 
> SQL/relational DB and I'm not 100% sure that fits well with the type of 
> data and querying noted above. Note though that not all querying will take 
> that form; there'll also be strings, uuids, dates, and other such field 
> types and the need to query on these and to join on some of them; also, to 
> do less-than comparisons on dates.
>
> Also, what is the current best recommendation of clojure library for 
> interfacing to the DB? (Answer might depend on the sort of DB recommended 
> -- standard, object/NoSQL, graph/ontology, etc.)
>
>

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