you go up to them then push them
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To move boulders in Pokemon Gold you need a Pokemon with the HM move Strength. Selecting the Pokemon in the menu outside of battle should let you use it if you have beaten the Olivine City Gym.
Your Pokemon are supposed to learn strength and move the boulders to the wholes.
First, you have to get the HM strength, then teach it to and a Pokemon and you can move boulders.
Strength
Use the HM move Strength.