First off

my @out = `myprog`;
die "error running myprog: $! $?" if $?;
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Will tell you when things go wrong.

Secondly, you're guessing that the problem is memory related. I'd recommend using top or vmstat to check the memory use while running the programs. I'd be very surprised if just useing a couple of modules will take up that much memory. If it does, you might have more luck requireing the modules after running myprog, if you can.