The mod_perl Performance Guide suggests the Gtop module. If you're able to create your data structure in one swoop, you can get a good feel for its size with code similar to:

use GTop;
my $gtop = GTop->new;
my $before = $gtop->proc_mem($$)->rss;

# initialize your data structure here

my $after  = $gtop->proc_mem($$)->rss;
print "diff: ",$after-$before, " bytes\n";
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As the Guide says, you'll need libgtop installed. It's only a workable solution if you're running a free sort of operating system, however.