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I'm not sure if this would fit your needs, but you could possibly make your CUDA specific code a custom external library, which you then link to from catkin. That would make it more straightforward to figure out how to cross compile as you could use nvcc directly and you wouldn't need to search for ROS-specific instructions for cross compiling. Obviously this adds another layer to the process, so it probably depends on whether your code lends itself to being a library.