It is not really an error per-say, it is just a warning. It looks like the markers that are coming from the octomap server have not initialized the quaternions (where each field is probably 0). So instead, rviz is just assuming they have a zero rotation (a quaternion of [0,0,0,1]), which is probably a fair assumption.

Each Marker message used in the MarkerArray that you are subscribing to has a pose associated with it.

Looking at the octomap server code publishing the message, they do not set the pose at all. However, the position is set from setting the point in the message it seems.

Funny enough, a pose does get initialized but is never really used anywhere... I would assume someone forget to set the pose for the visualization messages.

I would assume the "Uninitialized quaternion, assuming identity." warning has nothing to do with your octomap performance issues, which it looks like it was a tf issue based on your edit.

You need to initialized quaternion of marker

add four line under marker = Marker()

marker.pose.orientation.x = 0.0
marker.pose.orientation.y = 0.0
marker.pose.orientation.z = 0.0
marker.pose.orientation.w = 1.0

or

from geometry_msgs.msg import Quaternion

# your code

marker = Marker()
marker.pose.orientation = Quaternion(0.0, 0.0, 0.0, 1.0)