Speed up DBSCAN post-processing #430
Conversation
aprokop
changed the title
|
@dalg24 Added more comments. |
|
PGI failed in the distributed tree, but it has nothing to do with this PR. |
|
retest this please |
| // truncate the permutation array, see comment above | ||
| reallocWithoutInitializing(cluster_indices, num_cluster_indices); | ||
| Kokkos::deep_copy( | ||
| exec_space, cluster_indices, | ||
| Kokkos::subview(permute, std::make_pair(0, num_cluster_indices))); |
There was a problem hiding this comment.
This is a Kokkos::resize()isn't it? Did you chose do it this way because Kokkos initializes the array before copying entries? If so please comment.
If I understand it right, this is something that could be reported to Kokkos.
There was a problem hiding this comment.
Thanks for bringing this to my attention. Now that I look at the complete code, I realize that we no longer use permute in any of the following kernels, and thus don't have to be careful with it anymore. Thus, you are right, it could be done as
Kokkos::resize(permute, num_cluster_indices));
cluster_indices = permute;At this moment, I'm not sure about the complexity of the first line. Is it 1 allocation, 1 initialization of size num_cluster_indices and 1 deep_copy? If yes, that it indeed has an extra initialization cost that we don't need. I think I tried a solution proposed in this comment (Kokkos::resize( Kokkos::view_resize (WithoutInitializing), A, 2*N );) but it did not compile, because there is no view_resize.
There was a problem hiding this comment.
Actually, it seems to have been fixed in kokkos/kokkos#2285. So it almost works with this:
Kokkos::resize(Kokkos::WithoutInitializing, permute, num_cluster_indices);
cluster_indices = permute;except they have different value types:
error: no operator "=" matches these operands
operand types are:
Kokkos::View<int *, Kokkos::Cuda::memory_space> =
Kokkos::View<unsigned int *, Kokkos::Device<Kokkos::CudaSpace::execution_space, Kokkos::CudaSpace::memory_space>>
There was a problem hiding this comment.
Try Kokkos::resize(Kokkos::WithoutInitializing, A, 2*N);
There was a problem hiding this comment.
Anyway I missed that you were copying into another view.
I'm still not sure if this is the best way to do, but it speeds up postproccessing on V100 for halo finding from 0.050 to 0.027. 3% overall time improvement for the win :) The improvements are better on AMD.
A side note:
--verifyoption does not test this. The only way right now to validate this patch is to run with--output-sizes-and-centersand compare the output to master.