Github user NathanHowell commented on the pull request:

    https://github.com/apache/spark/pull/8246#issuecomment-139339009
  
    @jkbradley yeah, I figured out as much. a lot of the internals also assume 
dense feature space, which isn't very common with a large number of features.
    
    i tried it with `useNodeIdCache` on and off and it didn't make much of a 
difference. checkpointing was also enabled... the dataset fits in memory though 
(8TB was allocated to RDD storage), i don't know how much that changes things.
    
    the lower levels of the trees (near the roots) look similar but i haven't 
done a thorough comparison of the two.


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