I would run them vertically if they are mounted only from the top & bottom, and horizontally if they are going to be mounted from the side.
The reason I say this is if the wind load is hitting them while they are mounted on the side a vertical flute is likely to give and bend. Whereas the horizontal flute will give resistance.
If they are mounted from the top and bottom you want the flutes vertical to both provide resistance against the wind and to allow water to drain.