[Distributed] Reduce memory consumption in graph partitioning (dmlc#1823

)

* save mem.

* save mem.

* reduce mem

* fix test

* fix lint

* fix test

* fix.

* fix.

* fix.

* fix.

* fix lint.

* fix backend operator.

* fix tensorflow operators.

* fix.

* revert change in mxnet operator.

Co-authored-by: Ubuntu <[email protected]>

include/dgl/graph_interface.h

@@ -428,9 +428,6 @@ struct NegSubgraph: public Subgraph {
 struct HaloSubgraph: public Subgraph {
   /*! \brief Indicate if a node belongs to the partition. */
   IdArray inner_nodes;
-
-  /*! \brief Indicate if an edge belongs to the partition. */
-  IdArray inner_edges;
 };
 
 // Define SubgraphRef

python/dgl/backend/mxnet/tensor.py

@@ -356,7 +356,7 @@ def nonzero_1d(input):
     # TODO: fallback to numpy is unfortunate
     tmp = input.asnumpy()
     tmp = np.nonzero(tmp)[0]
-    return nd.array(tmp, ctx=input.context, dtype=input.dtype)
+    return nd.array(tmp, ctx=input.context, dtype=tmp.dtype)
 
 def sort_1d(input):
     # TODO: this isn't an ideal implementation.

python/dgl/backend/tensorflow/tensor.py

@@ -63,7 +63,8 @@ def initialize_context():
     tf.zeros(1)
 
 def as_scalar(data):
-    return data.numpy().asscalar()
+    data = data.numpy()
+    return data if np.isscalar(data) else data.asscalar()
 
 
 def get_preferred_sparse_format():
@@ -384,7 +385,7 @@ def full_1d(length, fill_value, dtype, ctx):
 
 
 def nonzero_1d(input):
-    nonzero_bool = (input != False)
+    nonzero_bool = tf.cast(input, tf.bool)
     return tf.reshape(tf.where(nonzero_bool), (-1, ))
 
 

python/dgl/distributed/graph_partition_book.py

@@ -101,10 +101,10 @@ def __init__(self, part_id, num_parts, node_map, edge_map, part_graph):
         self._part_id = int(part_id)
         self._num_partitions = int(num_parts)
         self._nid2partid = F.tensor(node_map)
-        assert F.dtype(self._nid2partid) in (F.int32, F.int64), \
+        assert F.dtype(self._nid2partid) == F.int64, \
                 'the node map must be stored in an integer array'
         self._eid2partid = F.tensor(edge_map)
-        assert F.dtype(self._eid2partid) in (F.int32, F.int64), \
+        assert F.dtype(self._eid2partid) == F.int64, \
                 'the edge map must be stored in an integer array'
         # Get meta data of the partition book.
         self._partition_meta_data = []

python/dgl/distributed/partition.py

@@ -254,49 +254,36 @@ def partition_graph(g, graph_name, num_parts, out_path, num_hops=1, part_method=
         Indicate whether to balance the edges.
     '''
     if num_parts == 1:
-        client_parts = {0: g}
+        parts = {0: g}
         node_parts = F.zeros((g.number_of_nodes(),), F.int64, F.cpu())
         g.ndata[NID] = F.arange(0, g.number_of_nodes())
         g.edata[EID] = F.arange(0, g.number_of_edges())
-        g.ndata['inner_node'] = F.ones((g.number_of_nodes(),), F.int64, F.cpu())
-        g.edata['inner_edge'] = F.ones((g.number_of_edges(),), F.int64, F.cpu())
+        g.ndata['inner_node'] = F.ones((g.number_of_nodes(),), F.int8, F.cpu())
+        g.edata['inner_edge'] = F.ones((g.number_of_edges(),), F.int8, F.cpu())
         if reshuffle:
             g.ndata['orig_id'] = F.arange(0, g.number_of_nodes())
             g.edata['orig_id'] = F.arange(0, g.number_of_edges())
     elif part_method == 'metis':
         node_parts = metis_partition_assignment(g, num_parts, balance_ntypes=balance_ntypes,
                                                 balance_edges=balance_edges)
-        client_parts = partition_graph_with_halo(g, node_parts, num_hops, reshuffle=reshuffle)
+        parts = partition_graph_with_halo(g, node_parts, num_hops, reshuffle=reshuffle)
     elif part_method == 'random':
         node_parts = random_choice(num_parts, g.number_of_nodes())
-        client_parts = partition_graph_with_halo(g, node_parts, num_hops, reshuffle=reshuffle)
+        parts = partition_graph_with_halo(g, node_parts, num_hops, reshuffle=reshuffle)
     else:
         raise Exception('Unknown partitioning method: ' + part_method)
 
     # Let's calculate edge assignment.
-    # TODO(zhengda) we should replace int64 with int16. int16 should be sufficient.
-    start = time.time()
     if not reshuffle:
+        start = time.time()
+        # We only optimize for reshuffled case. So it's fine to use int64 here.
         edge_parts = np.zeros((g.number_of_edges(),), dtype=np.int64) - 1
-    num_edges = 0
-    num_nodes = 0
-    lnodes_list = []      # The node ids of each partition
-    ledges_list = []      # The edge Ids of each partition
-    for part_id in range(num_parts):
-        part = client_parts[part_id]
-        # To get the edges in the input graph, we should use original node Ids.
-        data_name = 'orig_id' if reshuffle else NID
-        local_nodes = F.boolean_mask(part.ndata[data_name], part.ndata['inner_node'])
-        local_edges = g.in_edges(local_nodes, form='eid')
-        if not reshuffle:
+        for part_id in parts:
+            part = parts[part_id]
+            # To get the edges in the input graph, we should use original node Ids.
+            local_edges = F.boolean_mask(part.edata[EID], part.edata['inner_edge'])
             edge_parts[F.asnumpy(local_edges)] = part_id
-        num_edges += len(local_edges)
-        num_nodes += len(local_nodes)
-        lnodes_list.append(local_nodes)
-        ledges_list.append(local_edges)
-    assert num_edges == g.number_of_edges()
-    assert num_nodes == g.number_of_nodes()
-    print('Calculate edge assignment: {:.3f} seconds'.format(time.time() - start))
+        print('Calculate edge assignment: {:.3f} seconds'.format(time.time() - start))
 
     os.makedirs(out_path, mode=0o775, exist_ok=True)
     tot_num_inner_edges = 0
@@ -314,8 +301,14 @@ def partition_graph(g, graph_name, num_parts, out_path, num_hops=1, part_method=
         # With reshuffling, we can ensure that all nodes and edges are reshuffled
         # and are in contiguous Id space.
         if num_parts > 1:
-            node_map_val = np.cumsum([len(lnodes) for lnodes in lnodes_list]).tolist()
-            edge_map_val = np.cumsum([len(ledges) for ledges in ledges_list]).tolist()
+            node_map_val = [F.as_scalar(F.sum(F.astype(parts[i].ndata['inner_node'], F.int64),
+                                              0)) for i in parts]
+            node_map_val = np.cumsum(node_map_val).tolist()
+            assert node_map_val[-1] == g.number_of_nodes()
+            edge_map_val = [F.as_scalar(F.sum(F.astype(parts[i].edata['inner_edge'], F.int64),
+                                              0)) for i in parts]
+            edge_map_val = np.cumsum(edge_map_val).tolist()
+            assert edge_map_val[-1] == g.number_of_edges()
         else:
             node_map_val = [g.number_of_nodes()]
             edge_map_val = [g.number_of_edges()]
@@ -330,14 +323,17 @@ def partition_graph(g, graph_name, num_parts, out_path, num_hops=1, part_method=
                      'node_map': node_map_val,
                      'edge_map': edge_map_val}
     for part_id in range(num_parts):
-        part = client_parts[part_id]
+        part = parts[part_id]
 
         # Get the node/edge features of each partition.
         node_feats = {}
         edge_feats = {}
         if num_parts > 1:
-            local_nodes = lnodes_list[part_id]
-            local_edges = ledges_list[part_id]
+            # To get the edges in the input graph, we should use original node Ids.
+            ndata_name = 'orig_id' if reshuffle else NID
+            edata_name = 'orig_id' if reshuffle else EID
+            local_nodes = F.boolean_mask(part.ndata[ndata_name], part.ndata['inner_node'])
+            local_edges = F.boolean_mask(part.edata[edata_name], part.edata['inner_edge'])
             print('part {} has {} nodes and {} edges.'.format(
                 part_id, part.number_of_nodes(), part.number_of_edges()))
             print('{} nodes and {} edges are inside the partition'.format(

python/dgl/graph_index.py

@@ -566,8 +566,7 @@ def node_halo_subgraph(self, v, num_hops):
         v_array = v.todgltensor()
         subg = _CAPI_DGLGetSubgraphWithHalo(self, v_array, num_hops)
         inner_nodes = _CAPI_GetHaloSubgraphInnerNodes(subg)
-        inner_edges = _CAPI_GetHaloSubgraphInnerEdges(subg)
-        return subg, inner_nodes, inner_edges
+        return subg, inner_nodes
 
     def node_subgraphs(self, vs_arr):
         """Return the induced node subgraphs.
@@ -1297,7 +1296,4 @@ def create_graph_index(graph_data, readonly):
 def _get_halo_subgraph_inner_node(halo_subg):
     return _CAPI_GetHaloSubgraphInnerNodes(halo_subg)
 
-def _get_halo_subgraph_inner_edge(halo_subg):
-    return _CAPI_GetHaloSubgraphInnerEdges(halo_subg)
-
 _init_api("dgl.graph_index")

python/dgl/transform.py

@@ -962,35 +962,46 @@ def partition_graph_with_halo(g, node_part, extra_cached_hops, reshuffle=False):
         # that all edges in a partition are in the contiguous Id space.
         orig_eids = _CAPI_DGLReassignEdges(g._graph, True)
         orig_eids = utils.toindex(orig_eids)
-        g.edata['orig_id'] = orig_eids.tousertensor()
+        orig_eids = orig_eids.tousertensor()
+        orig_nids = g.ndata['orig_id']
         print('Reshuffle nodes and edges: {:.3f} seconds'.format(time.time() - start))
 
     start = time.time()
     subgs = _CAPI_DGLPartitionWithHalo(g._graph, node_part.todgltensor(), extra_cached_hops)
+    # g is no longer needed. Free memory.
+    g = None
     print('Split the graph: {:.3f} seconds'.format(time.time() - start))
     subg_dict = {}
     node_part = node_part.tousertensor()
     start = time.time()
+
+    # This creaets a subgraph from subgraphs returned from the CAPI above.
+    def create_subgraph(subg, induced_nodes, induced_edges):
+        subg1 = DGLGraph(graph_data=subg.graph, readonly=True)
+        subg1.ndata[NID] = induced_nodes.tousertensor()
+        subg1.edata[EID] = induced_edges.tousertensor()
+        return subg1
+
     for i, subg in enumerate(subgs):
         inner_node = _get_halo_subgraph_inner_node(subg)
-        subg = g._create_subgraph(subg, subg.induced_nodes, subg.induced_edges)
+        subg = create_subgraph(subg, subg.induced_nodes, subg.induced_edges)
         inner_node = F.zerocopy_from_dlpack(inner_node.to_dlpack())
         subg.ndata['inner_node'] = inner_node
-        subg.ndata['part_id'] = F.gather_row(node_part, subg.parent_nid)
+        subg.ndata['part_id'] = F.gather_row(node_part, subg.ndata[NID])
         if reshuffle:
-            subg.ndata['orig_id'] = F.gather_row(g.ndata['orig_id'], subg.ndata[NID])
-            subg.edata['orig_id'] = F.gather_row(g.edata['orig_id'], subg.edata[EID])
+            subg.ndata['orig_id'] = F.gather_row(orig_nids, subg.ndata[NID])
+            subg.edata['orig_id'] = F.gather_row(orig_eids, subg.edata[EID])
 
         if extra_cached_hops >= 1:
-            inner_edge = F.zeros((subg.number_of_edges(),), F.int64, F.cpu())
+            inner_edge = F.zeros((subg.number_of_edges(),), F.int8, F.cpu())
             inner_nids = F.nonzero_1d(subg.ndata['inner_node'])
             # TODO(zhengda) we need to fix utils.toindex() to avoid the dtype cast below.
             inner_nids = F.astype(inner_nids, F.int64)
             inner_eids = subg.in_edges(inner_nids, form='eid')
             inner_edge = F.scatter_row(inner_edge, inner_eids,
                                        F.ones((len(inner_eids),), F.dtype(inner_edge), F.cpu()))
         else:
-            inner_edge = F.ones((subg.number_of_edges(),), F.int64, F.cpu())
+            inner_edge = F.ones((subg.number_of_edges(),), F.int8, F.cpu())
         subg.edata['inner_edge'] = inner_edge
         subg_dict[i] = subg
     print('Construct subgraphs: {:.3f} seconds'.format(time.time() - start))

src/graph/graph_op.cc

@@ -416,7 +416,6 @@ HaloSubgraph GraphOp::GetSubgraphWithHalo(GraphPtr g, IdArray nodes, int num_hop
   auto orig_nodes = all_nodes;
 
   std::vector<dgl_id_t> edge_src, edge_dst, edge_eid;
-  std::vector<int> inner_edges;
 
   // When we deal with in-edges, we need to do two things:
   // * find the edges inside the partition and the edges between partitions.
@@ -436,7 +435,6 @@ HaloSubgraph GraphOp::GetSubgraphWithHalo(GraphPtr g, IdArray nodes, int num_hop
       edge_src.push_back(src_data[i]);
       edge_dst.push_back(dst_data[i]);
       edge_eid.push_back(eid_data[i]);
-      inner_edges.push_back(it1 != orig_nodes.end());
     }
     // We need to expand only if the node hasn't been seen before.
     auto it = all_nodes.find(src_data[i]);
@@ -463,7 +461,6 @@ HaloSubgraph GraphOp::GetSubgraphWithHalo(GraphPtr g, IdArray nodes, int num_hop
       edge_src.push_back(src_data[i]);
       edge_dst.push_back(dst_data[i]);
       edge_eid.push_back(eid_data[i]);
-      inner_edges.push_back(false);
       // If we haven't seen this node.
       auto it = all_nodes.find(src_data[i]);
       if (it == all_nodes.end()) {
@@ -502,8 +499,8 @@ HaloSubgraph GraphOp::GetSubgraphWithHalo(GraphPtr g, IdArray nodes, int num_hop
   halo_subg.graph = subg;
   halo_subg.induced_vertices = aten::VecToIdArray(old_node_ids);
   halo_subg.induced_edges = aten::VecToIdArray(edge_eid);
+  // TODO(zhengda) we need to switch to 8 bytes afterwards.
   halo_subg.inner_nodes = aten::VecToIdArray<int>(inner_nodes, 32);
-  halo_subg.inner_edges = aten::VecToIdArray<int>(inner_edges, 32);
   return halo_subg;
 }
 
@@ -603,14 +600,6 @@ DGL_REGISTER_GLOBAL("graph_index._CAPI_GetHaloSubgraphInnerNodes")
   *rv = gptr->inner_nodes;
 });
 
-DGL_REGISTER_GLOBAL("graph_index._CAPI_GetHaloSubgraphInnerEdges")
-.set_body([] (DGLArgs args, DGLRetValue* rv) {
-  SubgraphRef g = args[0];
-  auto gptr = std::dynamic_pointer_cast<HaloSubgraph>(g.sptr());
-  CHECK(gptr) << "The input graph has to be immutable graph";
-  *rv = gptr->inner_edges;
-});
-
 DGL_REGISTER_GLOBAL("graph_index._CAPI_DGLDisjointUnion")
 .set_body([] (DGLArgs args, DGLRetValue* rv) {
     List<GraphRef> graphs = args[0];

tests/compute/test_transform.py

@@ -466,13 +466,13 @@ def test_partition_with_halo():
         for i in range(nf.num_layers):
             layer_nids1 = F.asnumpy(nf.layer_parent_nid(i))
             layer_nids2 = lnf.layer_parent_nid(i)
-            layer_nids2 = F.asnumpy(F.gather_row(subg.parent_nid, layer_nids2))
+            layer_nids2 = F.asnumpy(F.gather_row(subg.ndata[dgl.NID], layer_nids2))
             assert np.all(np.sort(layer_nids1) == np.sort(layer_nids2))
 
         for i in range(nf.num_blocks):
             block_eids1 = F.asnumpy(nf.block_parent_eid(i))
             block_eids2 = lnf.block_parent_eid(i)
-            block_eids2 = F.asnumpy(F.gather_row(subg.parent_eid, block_eids2))
+            block_eids2 = F.asnumpy(F.gather_row(subg.edata[dgl.EID], block_eids2))
             assert np.all(np.sort(block_eids1) == np.sort(block_eids2))
 
     subgs = dgl.transform.partition_graph_with_halo(g, node_part, 2, reshuffle=True)

tests/graph_index/test_subgraph.py

@@ -98,7 +98,7 @@ def create_large_graph_index(num_nodes):
 def test_node_subgraph_with_halo():
     gi = create_large_graph_index(1000)
     nodes = np.random.choice(gi.number_of_nodes(), 100, replace=False)
-    halo_subg, inner_node, inner_edge = gi.node_halo_subgraph(toindex(nodes), 2)
+    halo_subg, inner_node = gi.node_halo_subgraph(toindex(nodes), 2)
 
     # Check if edges in the subgraph are in the original graph.
     for s, d, e in zip(*halo_subg.graph.edges()):
@@ -111,12 +111,6 @@ def test_node_subgraph_with_halo():
     inner_node_ids = halo_subg.induced_nodes.tonumpy()[inner_node_ids]
     assert np.all(np.sort(inner_node_ids) == np.sort(nodes))
 
-    # Check if the inner edge labels are correct.
-    inner_edge = inner_edge.asnumpy()
-    inner_edge_ids = halo_subg.induced_edges.tonumpy()[inner_edge > 0]
-    subg = gi.node_subgraph(toindex(nodes))
-    assert np.all(np.sort(subg.induced_edges.tonumpy()) == np.sort(inner_edge_ids))
-
 if __name__ == '__main__':
     test_node_subgraph()
     test_node_subgraph_with_halo()