Fixing RAFT CI & a few small updates for SLHC Python wrapper (#178)

Authors:
  - Corey J. Nolet (@cjnolet)

Approvers:
  - Victor Lafargue (@viclafargue)
  - Alex Fender (@afender)

URL: #178

cpp/cmake/Dependencies.cmake

@@ -23,7 +23,7 @@ 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_TAG           1.8.0
+    GIT_TAG           1.12.0
     PREFIX            ${CUB_DIR}
     CONFIGURE_COMMAND ""
     BUILD_COMMAND     ""

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

@@ -29,7 +29,8 @@ enum LinkageDistance { PAIRWISE = 0, KNN_GRAPH = 1 };
  * @tparam value_t
  */
 template <typename value_idx, typename value_t>
-struct linkage_output {
+class linkage_output {
+ public:
   value_idx m;
   value_idx n_clusters;
 
@@ -41,8 +42,8 @@ struct linkage_output {
   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> {};
+class linkage_output_int_float : public linkage_output<int, float> {};
+class linkage_output__int64_float : public linkage_output<int64_t, float> {};
 
 };  // namespace hierarchy
 };  // namespace raft

cpp/include/raft/sparse/hierarchy/detail/agglomerative.cuh

@@ -103,6 +103,8 @@ 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);
@@ -132,6 +134,8 @@ void build_dendrogram_host(const handle_t &handle, const value_idx *rows,
 
   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);
 }
@@ -319,9 +323,6 @@ void extract_flattened_clusters(const raft::handle_t &handle, value_idx *labels,
   raft::copy_async(label_roots.data(), children + children_cpy_start,
                    child_size, stream);
 
-  //  thrust::device_ptr<value_idx> t_label_roots =
-  //    thrust::device_pointer_cast(label_roots.data());
-  //
   thrust::sort(thrust_policy, label_roots.data(),
                label_roots.data() + (child_size), thrust::greater<value_idx>());
 

cpp/include/raft/sparse/hierarchy/detail/connectivities.cuh

@@ -68,6 +68,8 @@ struct distance_graph_impl<raft::hierarchy::LinkageDistance::KNN_GRAPH,
     raft::sparse::selection::knn_graph(handle, X, m, n, metric, knn_graph_coo,
                                        c);
 
+    CUDA_CHECK(cudaDeviceSynchronize());
+
     indices.resize(knn_graph_coo.nnz, stream);
     data.resize(knn_graph_coo.nnz, stream);
 

cpp/include/raft/sparse/hierarchy/detail/mst.cuh

@@ -100,6 +100,7 @@ raft::Graph_COO<value_idx, value_idx, value_t> connect_knn_graph(
   raft::copy_async(msf.weights.data() + msf.n_edges, connected_edges.vals(),
                    connected_edges.nnz, stream);
 
+  printf("connected components nnz: %d\n", final_nnz);
   raft::sparse::COO<value_t, value_idx> final_coo(d_alloc, stream);
   raft::sparse::linalg::symmetrize(handle, msf.src.data(), msf.dst.data(),
                                    msf.weights.data(), m, n, final_nnz,
@@ -162,16 +163,25 @@ void build_sorted_mst(const raft::handle_t &handle, const value_t *X,
     handle, indptr, indices, pw_dists, (value_idx)m, nnz, color.data(), stream,
     false);
 
-  if (linkage::get_n_components(color.data(), m, stream) > 1) {
+  int iters = 1;
+  int n_components = linkage::get_n_components(color.data(), m, stream);
+  while (n_components > 1 && iters < 100) {
+    printf("Found %d components. Going to try connecting graph\n",
+           n_components);
     mst_coo = connect_knn_graph<value_idx, value_t>(handle, X, mst_coo, m, n,
                                                     color.data());
 
-    printf("Edges: %d\n", mst_coo.n_edges);
+    iters++;
 
-    RAFT_EXPECTS(
-      mst_coo.n_edges == m - 1,
-      "MST was not able to connect knn graph in a single iteration.");
+    n_components = linkage::get_n_components(color.data(), m, stream);
+    //
+    //    printf("Connecting knn graph!\n");
+    //
+    //    RAFT_EXPECTS(
+    //      mst_coo.n_edges == m - 1,
+    //      "MST was not able to connect knn graph in a single iteration.");
   }
+  printf("Found %d components.\n", n_components);
 
   sort_coo_by_data(mst_coo.src.data(), mst_coo.dst.data(),
                    mst_coo.weights.data(), mst_coo.n_edges, stream);

cpp/include/raft/sparse/mst/detail/mst_solver_inl.cuh

@@ -190,8 +190,6 @@ MST_solver<vertex_t, edge_t, weight_t>::solve() {
   mst_result.dst.resize(mst_result.n_edges, stream);
   mst_result.weights.resize(mst_result.n_edges, stream);
 
-  // raft::print_device_vector("Colors before sending: ", color_index, 7, std::cout);
-
   return mst_result;
 }
 

cpp/include/raft/sparse/op/sort.h

@@ -71,6 +71,8 @@ void coo_sort(int m, int n, int nnz, int *rows, int *cols, T *vals,
 
   CUSPARSE_CHECK(cusparseCreateIdentityPermutation(handle, nnz, d_P.data()));
 
+  printf("nnz: %d\n", nnz);
+
   CUSPARSE_CHECK(cusparseXcoosortByRow(handle, m, n, nnz, rows, cols,
                                        d_P.data(), pBuffer.data()));