Yes, it is also not clear to me whether sorting the hash keys is necessary, but if it is necessary, you might consider sorting the keys before entering the nested loops and storing them into an array (and walking through the arrays containing the sorted keys rather than the hash keys). I do not know whether it will really reduce memory usage sufficiently, but it will certainly reduce considerably the run time. The hash keys used in the most inner loops might be sorted millions or possibly even billions of times, this is a huge waste of CPU power, as your program is likely to spend most of its running time sorting again and again the same data. Now, to restate, this will certainly also save some memory, but I have no idea whether this will be enough to solve your memory problem.

One additional point: how many elements do you have in each of your hashes?