There are also pragmas to control page size and in-memory caching. You will want to play with those, as well. If SQLite is in the middle of a transaction and you load it up with commands, it will create a journal file in /tmp/ to start pages that don't fit in the in-memory page cache (or something like that). As such, the pragmas can hugely affect performance. You will likely find that tuning the engine for particular roles -- bulk loading, queries, random updates -- will likely be useful.
See the SQLite documentation for more information.
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