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i have worked with both product. it depending on what you require. say if you need to add some config or do some change in existing setup then you can use GNS3 and test it before commit.
on the other hand scope of Opent is very broad ( Opnet has many module and associate license). you can use it in large scale planing ( ex: WImax for city, Wifi for large campus) or simulate application traffic which you can not do in GNS3. but Opnet has it limitation too (ex: you can not configure all the features of BGP in Opnet where as in GNS3 it is possible due to real IOS)
it is case by case approach
Opnet the most suitable but, beware,it is a very complex piece of software and setting up even a modest network can take some time and dedication. Opnet is usually used to model existing networks and does this by representing devices as state machines. It builds the model by importing the device configs, either manually or via an automated process. If you do not have an existing network then you would have to generate the configs by hand, then debug them. Once you have a network model you can then run traffic demands against it and deploy applications and users on it.
GNS3 or Dynnmips allows you to simulate the network using virtual routers running actual IOS software. This gives you a very accurate network model but there is no way to simulate large numbers of hosts within the model. You are also limited to a small number of older routers and some basic switches so newer hardware cannot be catered for.If you have the time, and the enthusiasm, you could build the network infrastructure using GNS3 then import the resulting configs into Opnet, add your users and traffic flows and get your results that way.
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