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The "Circuito de Playas" in Miraflores is one possibility, either on top, by the "Malecon" or by the beaches of Barranco and Chorrillos. This run is best early in the morning. Jog down to the beach of Barranquito through the "Bajada de Armendaris". Then continue towards Chorrillos and back. The city of Cusco is a very different ball-park. The altitude will not allow you to do any meaningful jogging during the first two weeks there. The city of Arequipa is more forgiving because of its lower altitude than Cusco, but some adjustment is needed as well. Both Cusco and Arequipa are much nicer cities than metropolitan Lima.