You'll double the size of file you can load by using this:

my $data; do {local $/; $data = <FILE> };
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Instead of:

my $data = do {local $/; <FILE> };
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And probably, though I haven't tested it recently, faster by doing:

my $size = -s( $filename );
open my $fh, '<', $filename or die $!;
read( $fh, my $data, $size );
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But if you're being limited to a few hundred MB, on a system with many GB available; Corion's right. Either your process is a 32-bit Perl; or it is being subject to a ulimit; or both.