Can we simulate holes and start robot on a higher level (floor)?

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Of course. You can specify where to spawn your robot (full 3d pose) , and you can use the building editor in gazebo to create buildings with floors, steps, walls, doors, etc. Here is a link to the gazebo tutorial for it: http://gazebosim.org/tutorials?tut=bu...

As far as creating holes in the ground, you'll have to create an sdf that can be loaded into gazebo that represents the terrain you want your robot to move around in. This sdf should be static. Just doing a quick search for "gazebo height map" I found a nice looking tutorial: https://github.com/AS4SR/general_info...