If you cannot see Agile menu in the top navigation bar, that usually means that either your GreenHopper plugin is disabled (or not installed at all) or you haven't provided the license key (evaluation or production one).
To check the former, log in as JIRA administrator, go to Administration | Plugins and see if GreenHopper is on the plugin list and it's "green" (i.e. enabled) with all modules enabled.
To check the license key, as JIRA admin go to Administration and then to GreenHopper License section. There make sure that your license key is entered there and it's valid.
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