Updates to enable HDBSCAN (#208)

cjnolet · web-flow · commit d5763480b899 · 2021-05-27T15:59:04.000Z
Authors: - Corey J. Nolet (https://github.com/cjnolet) - Divye Gala (https://github.com/divyegala) Approvers: - Dante Gama Dessavre (https://github.com/dantegd) URL: #208
diff --git a/cpp/include/raft/sparse/hierarchy/detail/agglomerative.cuh b/cpp/include/raft/sparse/hierarchy/detail/agglomerative.cuh
@@ -73,9 +73,15 @@ class UnionFind {
 };
 
 /**
- * Standard single-threaded agglomerative labeling on host. This should work
- * well for smaller sizes of m. This is a C++ port of the original reference
- * implementation of HDBSCAN.
+ * Agglomerative labeling on host. This has not been found to be a bottleneck
+ * in the algorithm. A parallel version of this can be done using a parallel
+ * variant of Kruskal's MST algorithm
+ * (ref http://cucis.ece.northwestern.edu/publications/pdf/HenPat12.pdf),
+ * which breaks apart the sorted MST results into overlapping subsets and
+ * independently runs Kruskal's algorithm on each subset, merging them back
+ * together into a single hierarchy when complete. Unfortunately,
+ * this is nontrivial and the speedup wouldn't be useful until this
+ * becomes a bottleneck.
  *
  * @tparam value_idx
  * @tparam value_t
@@ -91,9 +97,8 @@ class UnionFind {
 template <typename value_idx, typename value_t>
 void build_dendrogram_host(const handle_t &handle, const value_idx *rows,
                            const value_idx *cols, const value_t *data,
-                           size_t nnz, value_idx *children,
-                           rmm::device_uvector<value_t> &out_delta,
-                           rmm::device_uvector<value_idx> &out_size) {
+                           size_t nnz, value_idx *children, value_t *out_delta,
+                           value_idx *out_size) {
   auto d_alloc = handle.get_device_allocator();
   auto stream = handle.get_stream();
 
@@ -103,8 +108,6 @@ void build_dendrogram_host(const handle_t &handle, const value_idx *rows,
   std::vector<value_idx> mst_dst_h(n_edges);
   std::vector<value_t> mst_weights_h(n_edges);
 
-  printf("n_edges: %d\n", n_edges);
-
   update_host(mst_src_h.data(), rows, n_edges, stream);
   update_host(mst_dst_h.data(), cols, n_edges, stream);
   update_host(mst_weights_h.data(), data, n_edges, stream);
@@ -113,12 +116,14 @@ void build_dendrogram_host(const handle_t &handle, const value_idx *rows,
 
   std::vector<value_idx> children_h(n_edges * 2);
   std::vector<value_idx> out_size_h(n_edges);
+  std::vector<value_t> out_delta_h(n_edges);
 
   UnionFind<value_idx, value_t> U(nnz + 1);
 
   for (value_idx i = 0; i < nnz; i++) {
     value_idx a = mst_src_h[i];
     value_idx b = mst_dst_h[i];
+    value_t delta = mst_weights_h[i];
 
     value_idx aa = U.find(a);
     value_idx bb = U.find(b);
@@ -127,72 +132,15 @@ void build_dendrogram_host(const handle_t &handle, const value_idx *rows,
 
     children_h[children_idx] = aa;
     children_h[children_idx + 1] = bb;
+    out_delta_h[i] = delta;
     out_size_h[i] = U.size[aa] + U.size[bb];
 
     U.perform_union(aa, bb);
   }
 
-  out_size.resize(n_edges, stream);
-
-  printf("Finished dendrogram\n");
-
   raft::update_device(children, children_h.data(), n_edges * 2, stream);
-  raft::update_device(out_size.data(), out_size_h.data(), n_edges, stream);
-}
-
-/**
- * Parallel agglomerative labeling. This amounts to a parallel Kruskal's
- * MST algorithm, which breaks apart the sorted MST results into overlapping
- * subsets and independently runs Kruskal's algorithm on each subset,
- * merging them back together into a single hierarchy when complete.
- *
- * This outputs the same format as the reference HDBSCAN, but as 4 separate
- * arrays, rather than a single 2D array.
- *
- * Reference: http://cucis.ece.northwestern.edu/publications/pdf/HenPat12.pdf
- *
- * TODO: Investigate potential for the following end-to-end single-hierarchy batching:
- *    For each of k (independent) batches over the input:
- *    - Sample n elements from X
- *    - Compute mutual reachability graph of batch
- *    - Construct labels from batch
- *
- * The sampled datasets should have some overlap across batches. This will
- * allow for the cluster hierarchies to be merged. Being able to batch
- * will reduce the memory cost so that the full n^2 pairwise distances
- * don't need to be materialized in memory all at once.
- *
- * @tparam value_idx
- * @tparam value_t
- * @param[in] handle the raft handle
- * @param[in] rows src edges of the sorted MST
- * @param[in] cols dst edges of the sorted MST
- * @param[in] nnz the number of edges in the sorted MST
- * @param[out] out_src parents of output
- * @param[out] out_dst children of output
- * @param[out] out_delta distances of output
- * @param[out] out_size cluster sizes of output
- * @param[in] k_folds number of folds for parallelizing label step
- */
-template <typename value_idx, typename value_t>
-void build_dendrogram_device(const handle_t &handle, const value_idx *rows,
-                             const value_idx *cols, const value_t *data,
-                             value_idx nnz, value_idx *children,
-                             value_t *out_delta, value_idx *out_size,
-                             value_idx k_folds) {
-  ASSERT(k_folds < nnz / 2, "k_folds must be < n_edges / 2");
-  /**
-   * divide (sorted) mst coo into overlapping subsets. Easiest way to do this is to
-   * break it into k-folds and iterate through two folds at a time.
-   */
-
-  // 1. Generate ranges for the overlapping subsets
-
-  // 2. Run union-find in parallel for each pair of folds
-
-  // 3. Sort individual label hierarchies
-
-  // 4. Merge label hierarchies together
+  raft::update_device(out_size, out_size_h.data(), n_edges, stream);
+  raft::update_device(out_delta, out_delta_h.data(), n_edges, stream);
 }
 
 template <typename value_idx>
diff --git a/cpp/include/raft/sparse/hierarchy/detail/mst.cuh b/cpp/include/raft/sparse/hierarchy/detail/mst.cuh
@@ -19,6 +19,7 @@
 #include <raft/cudart_utils.h>
 #include <raft/cuda_utils.cuh>
 
+#include <raft/sparse/op/sort.h>
 #include <raft/mr/device/buffer.hpp>
 #include <raft/sparse/mst/mst.cuh>
 #include <raft/sparse/selection/connect_components.cuh>
@@ -35,29 +36,6 @@ namespace raft {
 namespace hierarchy {
 namespace detail {
 
-/**
- * Sorts a COO by its weight
- * @tparam value_idx
- * @tparam value_t
- * @param[inout] rows source edges
- * @param[inout] cols dest edges
- * @param[inout] data edge weights
- * @param[in] nnz number of edges in edge list
- * @param[in] stream cuda stream for which to order cuda operations
- */
-template <typename value_idx, typename value_t>
-void sort_coo_by_data(value_idx *rows, value_idx *cols, value_t *data,
-                      value_idx nnz, cudaStream_t stream) {
-  thrust::device_ptr<value_idx> t_rows = thrust::device_pointer_cast(rows);
-  thrust::device_ptr<value_idx> t_cols = thrust::device_pointer_cast(cols);
-  thrust::device_ptr<value_t> t_data = thrust::device_pointer_cast(data);
-
-  auto first = thrust::make_zip_iterator(thrust::make_tuple(rows, cols));
-
-  thrust::sort_by_key(thrust::cuda::par.on(stream), t_data, t_data + nnz,
-                      first);
-}
-
 template <typename value_idx, typename value_t>
 void merge_msts(raft::Graph_COO<value_idx, value_idx, value_t> &coo1,
                 raft::Graph_COO<value_idx, value_idx, value_t> &coo2,
@@ -95,19 +73,20 @@ void merge_msts(raft::Graph_COO<value_idx, value_idx, value_t> &coo1,
  * @param[inout] color the color labels array returned from the mst invocation
  * @return updated MST edge list
  */
-template <typename value_idx, typename value_t>
+template <typename value_idx, typename value_t, typename red_op>
 void connect_knn_graph(const raft::handle_t &handle, const value_t *X,
                        raft::Graph_COO<value_idx, value_idx, value_t> &msf,
                        size_t m, size_t n, value_idx *color,
+                       red_op reduction_op,
                        raft::distance::DistanceType metric =
                          raft::distance::DistanceType::L2SqrtExpanded) {
   auto d_alloc = handle.get_device_allocator();
   auto stream = handle.get_stream();
 
   raft::sparse::COO<value_t, value_idx> connected_edges(d_alloc, stream);
 
-  raft::linkage::connect_components<value_idx, value_t>(handle, connected_edges,
-                                                        X, color, m, n);
+  raft::linkage::connect_components<value_idx, value_t>(
+    handle, connected_edges, X, color, m, n, reduction_op);
 
   rmm::device_uvector<value_idx> indptr2(m + 1, stream);
   raft::sparse::convert::sorted_coo_to_csr(connected_edges.rows(),
@@ -147,38 +126,34 @@ void connect_knn_graph(const raft::handle_t &handle, const value_t *X,
  * @param[in] max_iter maximum iterations to run knn graph connection. This
  *  argument is really just a safeguard against the potential for infinite loops.
  */
-template <typename value_idx, typename value_t>
+template <typename value_idx, typename value_t, typename red_op>
 void build_sorted_mst(const raft::handle_t &handle, const value_t *X,
                       const value_idx *indptr, const value_idx *indices,
                       const value_t *pw_dists, size_t m, size_t n,
-                      rmm::device_uvector<value_idx> &mst_src,
-                      rmm::device_uvector<value_idx> &mst_dst,
-                      rmm::device_uvector<value_t> &mst_weight,
-                      const size_t nnz,
+                      value_idx *mst_src, value_idx *mst_dst,
+                      value_t *mst_weight, value_idx *color, size_t nnz,
+                      red_op reduction_op,
                       raft::distance::DistanceType metric =
                         raft::distance::DistanceType::L2SqrtExpanded,
                       int max_iter = 10) {
   auto d_alloc = handle.get_device_allocator();
   auto stream = handle.get_stream();
 
-  rmm::device_uvector<value_idx> color(m, stream);
-
   // We want to have MST initialize colors on first call.
   auto mst_coo = raft::mst::mst<value_idx, value_idx, value_t, double>(
-    handle, indptr, indices, pw_dists, (value_idx)m, nnz, color.data(), stream,
-    false, true);
+    handle, indptr, indices, pw_dists, (value_idx)m, nnz, color, stream, false,
+    true);
 
   int iters = 1;
-  int n_components =
-    linkage::get_n_components(color.data(), m, d_alloc, stream);
+  int n_components = linkage::get_n_components(color, m, d_alloc, stream);
 
   while (n_components > 1 && iters < max_iter) {
-    connect_knn_graph<value_idx, value_t>(handle, X, mst_coo, m, n,
-                                          color.data());
+    connect_knn_graph<value_idx, value_t>(handle, X, mst_coo, m, n, color,
+                                          reduction_op);
 
     iters++;
 
-    n_components = linkage::get_n_components(color.data(), m, d_alloc, stream);
+    n_components = linkage::get_n_components(color, m, d_alloc, stream);
   }
 
   /**
@@ -189,7 +164,7 @@ void build_sorted_mst(const raft::handle_t &handle, const value_t *X,
    * 1. There is a bug in this code somewhere
    * 2. Either the given KNN graph wasn't generated from X or the same metric is not being used
    *    to generate the 1-nn (currently only L2SqrtExpanded is supported).
-   * 3. max_iter was not large enough to connect the graph.
+   * 3. max_iter was not large enough to connect the graph (less likely).
    *
    * Note that a KNN graph generated from 50 random isotropic balls (with significant overlap)
    * was able to be connected in a single iteration.
@@ -201,20 +176,15 @@ void build_sorted_mst(const raft::handle_t &handle, const value_t *X,
                " or increase 'max_iter'",
                max_iter);
 
-  sort_coo_by_data(mst_coo.src.data(), mst_coo.dst.data(),
-                   mst_coo.weights.data(), mst_coo.n_edges, stream);
-
-  // TODO: be nice if we could pass these directly into the MST
-  mst_src.resize(mst_coo.n_edges, stream);
-  mst_dst.resize(mst_coo.n_edges, stream);
-  mst_weight.resize(mst_coo.n_edges, stream);
+  raft::sparse::op::coo_sort_by_weight(mst_coo.src.data(), mst_coo.dst.data(),
+                                       mst_coo.weights.data(), mst_coo.n_edges,
+                                       stream);
 
-  raft::copy_async(mst_src.data(), mst_coo.src.data(), mst_coo.n_edges, stream);
-  raft::copy_async(mst_dst.data(), mst_coo.dst.data(), mst_coo.n_edges, stream);
-  raft::copy_async(mst_weight.data(), mst_coo.weights.data(), mst_coo.n_edges,
-                   stream);
+  raft::copy_async(mst_src, mst_coo.src.data(), mst_coo.n_edges, stream);
+  raft::copy_async(mst_dst, mst_coo.dst.data(), mst_coo.n_edges, stream);
+  raft::copy_async(mst_weight, mst_coo.weights.data(), mst_coo.n_edges, stream);
 }
 
 };  // namespace detail
 };  // namespace hierarchy
-};  // namespace raft
+};  // namespace raft
diff --git a/cpp/include/raft/sparse/hierarchy/single_linkage.hpp b/cpp/include/raft/sparse/hierarchy/single_linkage.hpp
@@ -70,16 +70,19 @@ void single_linkage(const raft::handle_t &handle, const value_t *X, size_t m,
   detail::get_distance_graph<value_idx, value_t, dist_type>(
     handle, X, m, n, metric, indptr, indices, pw_dists, c);
 
-  rmm::device_uvector<value_idx> mst_rows(EMPTY, stream);
-  rmm::device_uvector<value_idx> mst_cols(EMPTY, stream);
-  rmm::device_uvector<value_t> mst_data(EMPTY, stream);
+  rmm::device_uvector<value_idx> mst_rows(m - 1, stream);
+  rmm::device_uvector<value_idx> mst_cols(m - 1, stream);
+  rmm::device_uvector<value_t> mst_data(m - 1, stream);
 
   /**
    * 2. Construct MST, sorted by weights
    */
+  rmm::device_uvector<value_idx> color(m, stream);
+  raft::linkage::FixConnectivitiesRedOp<value_idx, value_t> op(color.data(), m);
   detail::build_sorted_mst<value_idx, value_t>(
-    handle, X, indptr.data(), indices.data(), pw_dists.data(), m, n, mst_rows,
-    mst_cols, mst_data, indices.size(), metric);
+    handle, X, indptr.data(), indices.data(), pw_dists.data(), m, n,
+    mst_rows.data(), mst_cols.data(), mst_data.data(), color.data(),
+    indices.size(), op, metric);
 
   pw_dists.release();
 
@@ -93,7 +96,7 @@ void single_linkage(const raft::handle_t &handle, const value_t *X, size_t m,
   // Create dendrogram
   detail::build_dendrogram_host<value_idx, value_t>(
     handle, mst_rows.data(), mst_cols.data(), mst_data.data(), n_edges,
-    out->children, out_delta, out_size);
+    out->children, out_delta.data(), out_size.data());
   detail::extract_flattened_clusters(handle, out->labels, out->children,
                                      n_clusters, m);
 
diff --git a/cpp/include/raft/sparse/op/reduce.cuh b/cpp/include/raft/sparse/op/reduce.cuh
@@ -136,8 +136,8 @@ void max_duplicates(const raft::handle_t &handle,
 
   compute_duplicates_mask(diff.data(), rows, cols, nnz, stream);
 
-  thrust::exclusive_scan(exec_policy, diff.data(), diff.data() + diff.size(),
-                         diff.data());
+  thrust::exclusive_scan(thrust::cuda::par.on(stream), diff.data(),
+                         diff.data() + diff.size(), diff.data());
 
   // compute final size
   value_idx size = 0;
diff --git a/cpp/include/raft/sparse/op/sort.h b/cpp/include/raft/sparse/op/sort.h
@@ -92,6 +92,29 @@ void coo_sort(COO<T> *const in,
   coo_sort<T>(in->n_rows, in->n_cols, in->nnz, in->rows(), in->cols(),
               in->vals(), d_alloc, stream);
 }
+
+/**
+ * Sorts a COO by its weight
+ * @tparam value_idx
+ * @tparam value_t
+ * @param[inout] rows source edges
+ * @param[inout] cols dest edges
+ * @param[inout] data edge weights
+ * @param[in] nnz number of edges in edge list
+ * @param[in] stream cuda stream for which to order cuda operations
+ */
+template <typename value_idx, typename value_t>
+void coo_sort_by_weight(value_idx *rows, value_idx *cols, value_t *data,
+                        value_idx nnz, cudaStream_t stream) {
+  thrust::device_ptr<value_idx> t_rows = thrust::device_pointer_cast(rows);
+  thrust::device_ptr<value_idx> t_cols = thrust::device_pointer_cast(cols);
+  thrust::device_ptr<value_t> t_data = thrust::device_pointer_cast(data);
+
+  auto first = thrust::make_zip_iterator(thrust::make_tuple(rows, cols));
+
+  thrust::sort_by_key(thrust::cuda::par.on(stream), t_data, t_data + nnz,
+                      first);
+}
 };  // namespace op
 };  // end NAMESPACE sparse
 };  // end NAMESPACE raft
diff --git a/cpp/include/raft/sparse/selection/connect_components.cuh b/cpp/include/raft/sparse/selection/connect_components.cuh
diff --git a/cpp/test/sparse/connect_components.cu b/cpp/test/sparse/connect_components.cu
