What is the maximum limit of nodes in the most recent version of NS-3? I have found in some (older) sources saying that the maximum limit of 6000 nodes. Is this still the case? If so, what is the main reason not allowing to increase this limit?
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There is no limit such as the 6000 that you cite. The practical limit is based on how much memory you have in your simulation server. Even then, the limit can be extended by the use of distributed (parallel) simulation if the simulation scenario allows it. The largest ns-3 simulations on a supercomputer approached a network size of one billion nodes (see https://dl.acm.org/doi/abs/10.1145/2756509.2756525).