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BOSTON—On an uncomfortably hot day for distance running, Geoffrey Kirui of Kenya outlasted American Galen Rupp to take the 121st running of the Boston Marathon.

Rupp, who was running his first big-city marathon after taking the bronze medal in the event in the Rio Olympics, stayed with Kirui until the final stages, but couldn’t cover Kirui’s move to the lead in the final two miles. Rupp’s result—he finished just 21 seconds behind Kirui’s winning time of 2:09:37—was especially impressive, given that he had a cortisone…