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I had this problem recently what I found was that in the run configuration you need to direct the eclipse to the binary. Check if you have the path to the binary and verify the binary is present in the place. it will be something like this

/home/username/catkin_ws/devel/lib/package_name/executable_name

I also recommend you to follow this answer

http://answers.ros.org/question/52013/catkin-and-eclipse/