[Performance] Fused sampling with compaction (#5924)

Co-authored-by: Hesham Mostafa <[email protected]>

Author: agrabow

benchmarks/benchmarks/api/bench_fused_sample_neighbors.py

@@ -0,0 +1,39 @@
+import time
+
+import dgl
+import dgl.function as fn
+
+import numpy as np
+import torch
+
+from .. import utils
+
+
+@utils.benchmark("time")
+@utils.parametrize_cpu("graph_name", ["livejournal", "reddit"])
+@utils.parametrize_gpu("graph_name", ["ogbn-arxiv", "reddit"])
+@utils.parametrize("format", ["csr", "csc"])
+@utils.parametrize("seed_nodes_num", [200, 5000, 20000])
+@utils.parametrize("fanout", [5, 20, 40])
+def track_time(graph_name, format, seed_nodes_num, fanout):
+    device = utils.get_bench_device()
+    graph = utils.get_graph(graph_name, format).to(device)
+
+    edge_dir = "in" if format == "csc" else "out"
+    seed_nodes = np.random.randint(0, graph.num_nodes(), seed_nodes_num)
+    seed_nodes = torch.from_numpy(seed_nodes).to(device)
+
+    # dry run
+    for i in range(3):
+        dgl.sampling.sample_neighbors_fused(
+            graph, seed_nodes, fanout, edge_dir=edge_dir
+        )
+
+    # timing
+    with utils.Timer() as t:
+        for i in range(50):
+            dgl.sampling.sample_neighbors_fused(
+                graph, seed_nodes, fanout, edge_dir=edge_dir
+            )
+
+    return t.elapsed_secs / 50

include/dgl/aten/csr.h

@@ -572,6 +572,72 @@ COOMatrix CSRRowWiseSampling(
     CSRMatrix mat, IdArray rows, int64_t num_samples,
     NDArray prob_or_mask = NDArray(), bool replace = true);
 
+/*!
+ * @brief Randomly select a fixed number of non-zero entries along each given
+ * row independently.
+ *
+ * The function performs random choices along each row independently.
+ * The picked indices are returned in the form of a CSR matrix, with
+ * additional IdArray that is an extended version of CSR's index pointers.
+ *
+ * With template parameter set to True rows are also saved as new seed nodes and
+ * mapped
+ *
+ * If replace is false and a row has fewer non-zero values than num_samples,
+ * all the values are picked.
+ *
+ * Examples:
+ *
+ * // csr.num_rows = 4;
+ * // csr.num_cols = 4;
+ * // csr.indptr = [0, 2, 3, 3, 5]
+ * // csr.indices = [0, 1, 1, 2, 3]
+ * // csr.data = [2, 3, 0, 1, 4]
+ * CSRMatrix csr = ...;
+ * IdArray rows = ... ; // [1, 3]
+ * IdArray seed_mapping = [-1, -1, -1, -1];
+ * std::vector<IdType> new_seed_nodes = {};
+ *
+ * std::pair<CSRMatrix, IdArray> sampled = CSRRowWiseSamplingFused<
+ *                                         typename IdType, True>(
+ *                                         csr, rows, seed_mapping,
+ *                                         new_seed_nodes, 2,
+ *                                         FloatArray(), false);
+ * // possible sampled csr matrix:
+ * // sampled.first.num_rows = 2
+ * // sampled.first.num_cols = 3
+ * // sampled.first.indptr = [0, 1, 3]
+ * // sampled.first.indices = [1, 2, 3]
+ * // sampled.first.data = [0, 1, 4]
+ * // sampled.second = [0, 1, 1]
+ * // seed_mapping = [-1, 0, -1, 1];
+ * // new_seed_nodes = {1, 3};
+ *
+ * @tparam IdType Graph's index data type, can be int32_t or int64_t
+ * @tparam map_seed_nodes If set for true we map and copy rows to new_seed_nodes
+ * @param mat Input CSR matrix.
+ * @param rows Rows to sample from.
+ * @param seed_mapping Mapping array used if map_seed_nodes=true. If so each row
+ * from rows will be set to its position e.g. mapping[rows[i]] = i.
+ * @param new_seed_nodes Vector used if map_seed_nodes=true. If so it will
+ * contain rows.
+ * @param rows Rows to sample from.
+ * @param num_samples Number of samples
+ * @param prob_or_mask Unnormalized probability array or mask array.
+ *                     Should be of the same length as the data array.
+ *                     If an empty array is provided, assume uniform.
+ * @param replace True if sample with replacement
+ * @return A CSRMatrix storing the picked row, col and data indices,
+ *         COO version of picked rows
+ * @note The edges of the entire graph must be ordered by their edge types,
+ *       rows must be unique
+ */
+template <typename IdType, bool map_seed_nodes>
+std::pair<CSRMatrix, IdArray> CSRRowWiseSamplingFused(
+    CSRMatrix mat, IdArray rows, IdArray seed_mapping,
+    std::vector<IdType>* new_seed_nodes, int64_t num_samples,
+    NDArray prob_or_mask = NDArray(), bool replace = true);
+
 /**
  * @brief Randomly select a fixed number of non-zero entries for each edge type
  *        along each given row independently.

include/dgl/sampling/neighbor.h

@@ -9,6 +9,7 @@
 #include <dgl/array.h>
 #include <dgl/base_heterograph.h>
 
+#include <tuple>
 #include <vector>
 
 namespace dgl {
@@ -47,6 +48,55 @@ HeteroSubgraph SampleNeighbors(
     const std::vector<FloatArray>& probability,
     const std::vector<IdArray>& exclude_edges, bool replace = true);
 
+/**
+ * @brief Sample from the neighbors of the given nodes and convert a graph into
+ * a bipartite-structured graph for message passing.
+ *
+ * Specifically, we create one node type \c ntype_l on the "left" side and
+ * another node type \c ntype_r on the "right" side for each node type \c ntype.
+ * The nodes of type \c ntype_r would contain the nodes designated by the
+ * caller, and node type \c ntype_l would contain the nodes that has an edge
+ * connecting to one of the designated nodes.
+ *
+ * The nodes of \c ntype_l would also contain the nodes in node type \c ntype_r.
+ * When sampling with replacement, the sampled subgraph could have parallel
+ * edges.
+ *
+ * For sampling without replace, if fanout > the number of neighbors, all the
+ * neighbors will be sampled.
+ *
+ * Non-deterministic algorithm, requires nodes parameter to store unique Node
+ * IDs.
+ *
+ * @tparam IdType Graph's index data type, can be int32_t or int64_t
+ * @param hg The input graph.
+ * @param nodes Node IDs of each type. The vector length must be equal to the
+ * number of node types. Empty array is allowed.
+ * @param mapping External parameter that should be set to a vector of IdArrays
+ *                filled with -1, required for mapping of nodes in returned
+ *                graph
+ * @param fanouts Number of sampled neighbors for each edge type. The vector
+ * length should be equal to the number of edge types, or one if they all have
+ * the same fanout.
+ * @param dir Edge direction.
+ * @param probability A vector of 1D float arrays, indicating the transition
+ * probability of each edge by edge type.  An empty float array assumes uniform
+ * transition.
+ * @param exclude_edges Edges IDs of each type which will be excluded during
+ * sampling. The vector length must be equal to the number of edges types. Empty
+ * array is allowed.
+ * @param replace If true, sample with replacement.
+ * @return Sampled neighborhoods as a graph. The return graph has the same
+ * schema as the original one.
+ */
+template <typename IdType>
+std::tuple<HeteroGraphPtr, std::vector<IdArray>, std::vector<IdArray>>
+SampleNeighborsFused(
+    const HeteroGraphPtr hg, const std::vector<IdArray>& nodes,
+    const std::vector<IdArray>& mapping, const std::vector<int64_t>& fanouts,
+    EdgeDir dir, const std::vector<NDArray>& prob_or_mask,
+    const std::vector<IdArray>& exclude_edges, bool replace = true);
+
 /**
  * Select the neighbors with k-largest weights on the connecting edges for each
  * given node.

python/dgl/dataloading/neighbor_sampler.py

@@ -1,5 +1,7 @@
 """Data loading components for neighbor sampling"""
+from .. import backend as F
 from ..base import EID, NID
+from ..heterograph import DGLGraph
 from ..transforms import to_block
 from .base import BlockSampler
 
@@ -54,6 +56,9 @@ class NeighborSampler(BlockSampler):
     output_device : device, optional
         The device of the output subgraphs or MFGs.  Default is the same as the
         minibatch of seed nodes.
+    fused : bool, default True
+        If True and device is CPU fused sample neighbors is invoked. This version
+        requires seed_nodes to be unique
 
     Examples
     --------
@@ -120,6 +125,7 @@ def __init__(
         prefetch_labels=None,
         prefetch_edge_feats=None,
         output_device=None,
+        fused=True,
     ):
         super().__init__(
             prefetch_node_feats=prefetch_node_feats,
@@ -137,10 +143,43 @@ def __init__(
             )
         self.prob = prob or mask
         self.replace = replace
+        self.fused = fused
+        self.mapping = {}
+        self.g = None
 
     def sample_blocks(self, g, seed_nodes, exclude_eids=None):
         output_nodes = seed_nodes
         blocks = []
+
+        if self.fused:
+            cpu = F.device_type(g.device) == "cpu"
+            if isinstance(seed_nodes, dict):
+                for ntype in list(seed_nodes.keys()):
+                    if not cpu:
+                        break
+                    cpu = (
+                        cpu and F.device_type(seed_nodes[ntype].device) == "cpu"
+                    )
+            else:
+                cpu = cpu and F.device_type(seed_nodes.device) == "cpu"
+            if cpu and isinstance(g, DGLGraph) and F.backend_name == "pytorch":
+                if self.g != g:
+                    self.mapping = {}
+                    self.g = g
+                for fanout in reversed(self.fanouts):
+                    block = g.sample_neighbors_fused(
+                        seed_nodes,
+                        fanout,
+                        edge_dir=self.edge_dir,
+                        prob=self.prob,
+                        replace=self.replace,
+                        exclude_edges=exclude_eids,
+                        mapping=self.mapping,
+                    )
+                    seed_nodes = block.srcdata[NID]
+                    blocks.insert(0, block)
+                return seed_nodes, output_nodes, blocks
+
         for fanout in reversed(self.fanouts):
             frontier = g.sample_neighbors(
                 seed_nodes,