Make sure trove use the 3-d thread index when we update local version of trove

[hummingtree]

trafficstars

Currently trove uses 1-d thread index, i.e. it uses threadIdx.x instead of (threadIdx.z * blockDim.y + threadIdx.y) * blockDim.x + threadIdx.x. We should make sure 3-d thread index is used when we update local version of trove.

[hummingtree]

@weinbe2 @maddyscientist