How long does it take the perl program to run out of memory? If there's a delay and then that message, it could be the perl script has some bizarre bug that really is chewing up memory. In that case, you can run the perl script under Devel::NYTProf to see which routines are the hottest, and narrow in on the problem.

If the script runs out of memory immediately with no hot code paths, then possibly there is some insanely large allocation that immediately fails?