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You can do some running around or on the grounds of Kumamoto Castle. Perhaps the best place is a flat rectangular court on the grounds between the outside walls and the main castle. The court is grass, and the loop around the outside is about 1 kilometer in length - a number of people walk or jog around it. In the early morning around 6:15 or so, a number of people come to walk and then do "radio calesthenics" as directed by a national radio program. It is the only decent place I found to run in the center of Kumamoto.