[REVIEW] Adding SLHC prims.

cpp/CMakeLists.txt

@@ -213,9 +213,9 @@ set(RAFT_INCLUDE_DIRECTORIES
   ${FAISS_INCLUDE_DIRS}
   ${RMM_INCLUDE_DIRS})
 
-if(NOT CUB_IS_PART_OF_CTK)
-  list(APPEND RAFT_INCLUDE_DIRECTORIES ${CUB_DIR}/src/cub)
-endif(NOT CUB_IS_PART_OF_CTK)
+#if(NOT CUB_IS_PART_OF_CTK)
+#  list(APPEND RAFT_INCLUDE_DIRECTORIES ${CUB_DIR}/src/cub)
+#endif(NOT CUB_IS_PART_OF_CTK)
 
 if(DEFINED ENV{CONDA_PREFIX})
   message(STATUS "Using RMM installation from $ENV{CONDA_PREFIX}")
@@ -281,6 +281,7 @@ if(BUILD_RAFT_TESTS)
     test/sparse/add.cu
     test/sparse/convert_coo.cu
     test/sparse/convert_csr.cu
+    test/sparse/connect_components.cu
     test/sparse/csr_row_slice.cu
     test/sparse/csr_to_dense.cu
     test/sparse/csr_transpose.cu
@@ -290,6 +291,8 @@ if(BUILD_RAFT_TESTS)
     test/sparse/distance.cu
     test/sparse/filter.cu
     test/sparse/knn.cu
+    test/sparse/knn_graph.cu
+    test/sparse/linkage.cu
     test/sparse/norm.cu
     test/sparse/row_op.cu
     test/sparse/selection.cu

cpp/cmake/Dependencies.cmake

@@ -22,7 +22,7 @@ include(ExternalProject)
 if(NOT CUB_IS_PART_OF_CTK)
   set(CUB_DIR ${CMAKE_CURRENT_BINARY_DIR}/cub CACHE STRING "Path to cub repo")
   ExternalProject_Add(cub
-    GIT_REPOSITORY    https://github.com/thrust/cub.git
+    GIT_REPOSITORY    https://github.com/NVIDIA/cub.git
     GIT_TAG           1.8.0
     PREFIX            ${CUB_DIR}
     CONFIGURE_COMMAND ""

cpp/include/raft/sparse/hierarchy/common.h

@@ -0,0 +1,48 @@
+/*
+ * Copyright (c) 2021, NVIDIA CORPORATION.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+#pragma once
+
+namespace raft {
+namespace hierarchy {
+
+enum LinkageDistance { PAIRWISE = 0, KNN_GRAPH = 1 };
+
+/**
+ * Simple POCO for consolidating linkage results. This closely
+ * mirrors the trained instance variables populated in
+ * Scikit-learn's AgglomerativeClustering estimator.
+ * @tparam value_idx
+ * @tparam value_t
+ */
+template <typename value_idx, typename value_t>
+struct linkage_output {
+  value_idx m;
+  value_idx n_clusters;
+
+  value_idx n_leaves;
+  value_idx n_connected_components;
+
+  value_idx *labels;  // size: m
+
+  value_idx *children;  // size: (m-1, 2)
+};
+
+struct linkage_output_int_float : public linkage_output<int, float> {};
+struct linkage_output__int64_float : public linkage_output<int64_t, float> {};
+
+};  // namespace hierarchy
+};  // namespace raft