[Sampler] improve random shuffle performance in sampler (dmlc#228)

* fix.

* make it generic.

* add the API.

* fix.

* remove mxnet.

examples/mxnet/sse/sse_batch.py

@@ -158,13 +158,12 @@ def copy_to_gpu(subg, ctx):
         subg.ndata[key] = frame[key].as_in_context(ctx)
 
 class CachedSubgraph(object):
-    def __init__(self, subg, seeds, subg_seeds):
+    def __init__(self, subg, seeds):
         # We can't cache the input subgraph because it contains node frames
         # and data frames.
         self.subg = dgl.DGLSubGraph(subg._parent, subg._parent_nid, subg._parent_eid,
                                 subg._graph)
         self.seeds = seeds
-        self.subg_seeds = subg_seeds
 
 class CachedSubgraphLoader(object):
     def __init__(self, loader, shuffle):
@@ -184,14 +183,13 @@ def __iter__(self):
     def __next__(self):
         if len(self._subgraphs) > 0:
             s = self._subgraphs.pop(0)
-            subg, seeds, subg_seeds = s.subg, s.seeds, s.subg_seeds
+            subg, seeds = s.subg, s.seeds
         elif self._gen_subgraph:
             subg, seeds = self._loader.__next__()
-            subg_seeds = subg.map_to_subgraph_nid(seeds)
         else:
             raise StopIteration
-        self._cached.append(CachedSubgraph(subg, seeds, subg_seeds))
-        return subg, seeds, subg_seeds
+        self._cached.append(CachedSubgraph(subg, seeds))
+        return subg, seeds
 
 def main(args, data):
     if isinstance(data.features, mx.nd.NDArray):
@@ -266,15 +264,16 @@ def main(args, data):
     sampler = dgl.contrib.sampling.NeighborSampler(g, args.batch_size, neigh_expand,
             neighbor_type='in', num_workers=args.num_parallel_subgraphs, seed_nodes=train_vs,
             shuffle=True)
-    sampler = CachedSubgraphLoader(sampler, shuffle=True)
+    if args.cache_subgraph:
+        sampler = CachedSubgraphLoader(sampler, shuffle=True)
     for epoch in range(args.n_epochs):
         t0 = time.time()
         train_loss = 0
         i = 0
         num_batches = len(train_vs) / args.batch_size
         start1 = time.time()
-        sampler.restart()
-        for subg, seeds, subg_seeds in sampler:
+        for subg, seeds in sampler:
+            subg_seeds = subg.map_to_subgraph_nid(seeds)
             subg.copy_from_parent()
 
             losses = []
@@ -308,6 +307,14 @@ def main(args, data):
             if i > num_batches / 3:
                 break
 
+        if args.cache_subgraph:
+            sampler.restart()
+        else:
+            sampler = dgl.contrib.sampling.NeighborSampler(g, args.batch_size, neigh_expand,
+                                                           neighbor_type='in',
+                                                           num_workers=args.num_parallel_subgraphs,
+                                                           seed_nodes=train_vs, shuffle=True)
+
         # prediction.
         logits = model_infer(g, eval_vs)
         eval_loss = mx.nd.softmax_cross_entropy(logits, eval_labels)
@@ -381,11 +388,13 @@ def __init__(self, csr, num_feats):
     parser.add_argument("--use-spmv", action="store_true",
             help="use SpMV for faster speed.")
     parser.add_argument("--dgl", action="store_true")
+    parser.add_argument("--cache-subgraph", default=False, action="store_false")
     parser.add_argument("--num-parallel-subgraphs", type=int, default=1,
             help="the number of subgraphs to construct in parallel.")
     parser.add_argument("--neigh-expand", type=int, default=16,
             help="the number of neighbors to sample.")
     args = parser.parse_args()
+    print("cache: " + str(args.cache_subgraph))
 
     # load and preprocess dataset
     if args.graph_file != '':

python/dgl/backend/backend.py

@@ -681,6 +681,23 @@ def arange(start, stop):
     """
     pass
 
+def rand_shuffle(arr):
+    """Random shuffle the data in the first dimension of the array.
+
+    The shuffled data is stored in a new array.
+
+    Parameters
+    ----------
+    arr : Tensor
+        The data tensor
+
+    Returns
+    -------
+    Tensor
+        The result tensor
+    """
+    pass
+
 def zerocopy_to_dlpack(input):
     """Create a dlpack tensor that shares the input memory.
 

python/dgl/backend/mxnet/tensor.py

@@ -179,6 +179,9 @@ def sort_1d(input):
 def arange(start, stop):
     return nd.arange(start, stop, dtype=np.int64)
 
+def rand_shuffle(arr):
+    return mx.nd.random.shuffle(arr)
+
 def zerocopy_to_dlpack(arr):
     return arr.to_dlpack_for_read()
 

python/dgl/backend/numpy/tensor.py

@@ -128,6 +128,11 @@ def sort_1d(input):
 def arange(start, stop):
     return np.arange(start, stop, dtype=np.int64)
 
+def rand_shuffle(arr):
+    copy = np.copy(arr)
+    np.random.shuffle(copy)
+    return copy
+
 # zerocopy_to_dlpack not enabled
 
 # zerocopy_from_dlpack not enabled

python/dgl/backend/pytorch/tensor.py

@@ -136,6 +136,10 @@ def sort_1d(input):
 def arange(start, stop):
     return th.arange(start, stop, dtype=th.int64)
 
+def rand_shuffle(arr):
+    idx = th.randperm(len(arr))
+    return arr[idx]
+
 def zerocopy_to_dlpack(input):
     return dlpack.to_dlpack(input.contiguous())
 

python/dgl/contrib/sampling/sampler.py

@@ -4,6 +4,7 @@
 
 from ... import utils
 from ...subgraph import DGLSubGraph
+from ... import backend as F
 
 __all__ = ['NeighborSampler']
 
@@ -22,11 +23,11 @@ def __init__(self, g, batch_size, expand_factor, num_hops=1,
             assert self._node_prob.shape[0] == g.number_of_nodes(), \
                     "We need to know the sampling probability of every node"
         if seed_nodes is None:
-            self._seed_nodes = np.arange(0, g.number_of_nodes(), dtype=np.int64)
+            self._seed_nodes = F.arange(0, g.number_of_nodes())
         else:
             self._seed_nodes = seed_nodes
         if shuffle:
-            np.random.shuffle(self._seed_nodes)
+            self._seed_nodes = F.rand_shuffle(self._seed_nodes)
         self._num_workers = num_workers
         if max_subgraph_size is None:
             # This size is set temporarily.