My job is to collect, process and analyze NetFlow stats for a Tier-1 provider. I accomplish this using cflowd and Perl. As a typical collection for me usually involves in the tens-of-thousands of flows per second, I can emphatically say that in no way is Perl incapable of handling the flow rate you are describing. I too, am using netmatrix aggregation. And, I'm on the cusp of fully automating flow collection from about 25,000 interfaces worldwide!!! Msg me for some more details, if you care to.
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