In case the problem is memory-consumption + thrashing, it may be worthwhile to batch-process your rows with a LIMIT-clause to your SQL-statement (and repeated execution, of course). Just get n rows at a time and process those, before going on with the next batch. I guess n should be 1000 or 2500 or so (try and err ;)

Or use fetchrow_arrayref() and get your row processing out of the way immediately.

(Btw, have you found out anything yet about where the bottleneck is?)