[GraphBolt] Support saving graph and TVT_Sets in `int32` (#7127)

Co-authored-by: Muhammed Fatih BALIN <m.f.balin@gmail.com>

python/dgl/graphbolt/impl/ondisk_dataset.py

 """GraphBolt OnDiskDataset."""
 
+import bisect
 import json
 import os
 import shutil
@@ -40,11 +41,20 @@ from .torch_based_feature_store import TorchBasedFeatureStore
 
 __all__ = ["OnDiskDataset", "preprocess_ondisk_dataset", "BuiltinDataset"]
 
+NAMES_INDICATING_NODE_IDS = [
+    "seed_nodes",
+    "node_pairs",
+    "seeds",
+    "negative_srcs",
+    "negative_dsts",
+]
+
 
 def _graph_data_to_fused_csc_sampling_graph(
     dataset_dir: str,
     graph_data: Dict,
     include_original_edge_id: bool,
+    auto_cast_to_optimal_dtype: bool,
 ) -> FusedCSCSamplingGraph:
     """Convert the raw graph data into FusedCSCSamplingGraph.
 
@@ -56,6 +66,9 @@ def _graph_data_to_fused_csc_sampling_graph(
         The raw data read from yaml file.
     include_original_edge_id : bool
         Whether to include the original edge id in the FusedCSCSamplingGraph.
+    auto_cast_to_optimal_dtype: bool, optional
+        Casts the dtypes of tensors in the dataset into smallest possible dtypes
+        for reduced storage requirements and potentially increased performance.
 
     Returns
     -------
@@ -83,6 +96,14 @@ def _graph_data_to_fused_csc_sampling_graph(
         del coo_tensor
         indptr, indices, edge_ids = sparse_matrix.csc()
         del sparse_matrix
+
+        if auto_cast_to_optimal_dtype:
+            if num_nodes <= torch.iinfo(torch.int32).max:
+                indices = indices.to(torch.int32)
+            if num_edges <= torch.iinfo(torch.int32).max:
+                indptr = indptr.to(torch.int32)
+                edge_ids = edge_ids.to(torch.int32)
+
         node_type_offset = None
         type_per_edge = None
         node_type_to_id = None
@@ -127,6 +148,14 @@ def _graph_data_to_fused_csc_sampling_graph(
         del coo_src_list
         coo_dst = torch.cat(coo_dst_list)
         del coo_dst_list
+        if auto_cast_to_optimal_dtype:
+            dtypes = [torch.uint8, torch.int16, torch.int32, torch.int64]
+            dtype_maxes = [torch.iinfo(dtype).max for dtype in dtypes]
+            dtype_id = bisect.bisect_left(dtype_maxes, len(edge_type_to_id) - 1)
+            etype_dtype = dtypes[dtype_id]
+            coo_etype_list = [
+                tensor.to(etype_dtype) for tensor in coo_etype_list
+            ]
         coo_etype = torch.cat(coo_etype_list)
         del coo_etype_list
 
@@ -137,17 +166,32 @@ def _graph_data_to_fused_csc_sampling_graph(
         del coo_src, coo_dst
         indptr, indices, edge_ids = sparse_matrix.csc()
         del sparse_matrix
-        node_type_offset = torch.tensor(node_type_offset)
+
+        if auto_cast_to_optimal_dtype:
+            if total_num_nodes <= torch.iinfo(torch.int32).max:
+                indices = indices.to(torch.int32)
+            if total_num_edges <= torch.iinfo(torch.int32).max:
+                indptr = indptr.to(torch.int32)
+                edge_ids = edge_ids.to(torch.int32)
+
+        node_type_offset = torch.tensor(node_type_offset, dtype=indices.dtype)
         type_per_edge = torch.index_select(coo_etype, dim=0, index=edge_ids)
         del coo_etype
         node_attributes = {}
         edge_attributes = {}
         if include_original_edge_id:
-            edge_ids -= torch.gather(
-                input=torch.tensor(edge_type_offset),
+            # If uint8 or int16 was chosen above for etypes, we cast to int.
+            temp_etypes = (
+                type_per_edge.int()
+                if type_per_edge.element_size() < 4
+                else type_per_edge
+            )
+            edge_ids -= torch.index_select(
+                torch.tensor(edge_type_offset, dtype=edge_ids.dtype),
                 dim=0,
-                index=type_per_edge,
+                index=temp_etypes,
             )
+            del temp_etypes
             edge_attributes[ORIGINAL_EDGE_ID] = edge_ids
 
     # Load the sampling related node/edge features and add them to
@@ -279,6 +323,7 @@ def preprocess_ondisk_dataset(
     dataset_dir: str,
     include_original_edge_id: bool = False,
     force_preprocess: bool = None,
+    auto_cast_to_optimal_dtype: bool = True,
 ) -> str:
     """Preprocess the on-disk dataset. Parse the input config file,
     load the data, and save the data in the format that GraphBolt supports.
@@ -291,6 +336,10 @@ def preprocess_ondisk_dataset(
         Whether to include the original edge id in the FusedCSCSamplingGraph.
     force_preprocess: bool, optional
         Whether to force reload the ondisk dataset.
+    auto_cast_to_optimal_dtype: bool, optional
+        Casts the dtypes of tensors in the dataset into smallest possible dtypes
+        for reduced storage requirements and potentially increased performance.
+        Default is True.
 
     Returns
     -------
@@ -360,6 +409,7 @@ def preprocess_ondisk_dataset(
         dataset_dir,
         input_config["graph"],
         include_original_edge_id,
+        auto_cast_to_optimal_dtype,
     )
 
     # 3. Record value of include_original_edge_id.
@@ -372,6 +422,10 @@ def preprocess_ondisk_dataset(
         processed_dir_prefix, "fused_csc_sampling_graph.pt"
     )
 
+    node_ids_within_int32 = (
+        sampling_graph.indices.dtype == torch.int32
+        and auto_cast_to_optimal_dtype
+    )
     torch.save(
         sampling_graph,
         os.path.join(
@@ -379,6 +433,7 @@ def preprocess_ondisk_dataset(
             output_config["graph_topology"]["path"],
         ),
     )
+    del sampling_graph
     del output_config["graph"]
 
     # 5. Load the node/edge features and do necessary conversion.
@@ -428,11 +483,16 @@ def preprocess_ondisk_dataset(
                             processed_dir_prefix,
                             input_data["path"].replace("pt", "npy"),
                         )
+                        name = (
+                            input_data["name"] if "name" in input_data else None
+                        )
                         copy_or_convert_data(
                             os.path.join(dataset_dir, input_data["path"]),
                             os.path.join(dataset_dir, output_data["path"]),
                             input_data["format"],
                             output_data["format"],
+                            within_int32=node_ids_within_int32
+                            and name in NAMES_INDICATING_NODE_IDS,
                         )
 
     # 7. Save the output_config.
@@ -610,6 +670,10 @@ class OnDiskDataset(Dataset):
         Whether to include the original edge id in the FusedCSCSamplingGraph.
     force_preprocess: bool, optional
         Whether to force reload the ondisk dataset.
+    auto_cast_to_optimal_dtype: bool, optional
+        Casts the dtypes of tensors in the dataset into smallest possible dtypes
+        for reduced storage requirements and potentially increased performance.
+        Default is True.
     """
 
     def __init__(
@@ -617,12 +681,16 @@ class OnDiskDataset(Dataset):
         path: str,
         include_original_edge_id: bool = False,
         force_preprocess: bool = None,
+        auto_cast_to_optimal_dtype: bool = True,
     ) -> None:
         # Always call the preprocess function first. If already preprocessed,
         # the function will return the original path directly.
         self._dataset_dir = path
         yaml_path = preprocess_ondisk_dataset(
-            path, include_original_edge_id, force_preprocess
+            path,
+            include_original_edge_id,
+            force_preprocess,
+            auto_cast_to_optimal_dtype,
         )
         with open(yaml_path) as f:
             self._yaml_data = yaml.load(f, Loader=yaml.loader.SafeLoader)
@@ -824,7 +892,7 @@ class OnDiskDataset(Dataset):
     def _init_all_nodes_set(self, graph) -> Union[ItemSet, ItemSetDict]:
         if graph is None:
             dgl_warning(
-                "`all_node_set` is returned as None, since graph is None."
+                "`all_nodes_set` is returned as None, since graph is None."
             )
             return None
         num_nodes = graph.num_nodes

python/dgl/graphbolt/internal/utils.py

@@ -85,6 +85,17 @@ def get_npy_dim(npy_path):
         return len(shape)
 
 
+def _to_int32(data):
+    if isinstance(data, torch.Tensor):
+        return data.to(torch.int32)
+    elif isinstance(data, np.ndarray):
+        return data.astype(np.int32)
+    else:
+        raise TypeError(
+            "Unsupported input type. Please provide a torch tensor or numpy array."
+        )
+
+
 def copy_or_convert_data(
     input_path,
     output_path,
@@ -92,24 +103,27 @@ def copy_or_convert_data(
     output_format="numpy",
     in_memory=True,
     is_feature=False,
+    within_int32=False,
 ):
     """Copy or convert the data from input_path to output_path."""
     assert (
         output_format == "numpy"
     ), "The output format of the data should be numpy."
     os.makedirs(os.path.dirname(output_path), exist_ok=True)
-    # If the original format is numpy, just copy the file.
+    # We read the data always in case we need to cast its type.
+    data = read_data(input_path, input_format, in_memory)
+    if within_int32:
+        data = _to_int32(data)
     if input_format == "numpy":
         # If dim of the data is 1, reshape it to n * 1 and save it to output_path.
         if is_feature and get_npy_dim(input_path) == 1:
-            data = read_data(input_path, input_format, in_memory)
             data = data.reshape(-1, 1)
-            save_data(data, output_path, output_format)
-        else:
+        # If the data does not need to be modified, just copy the file.
+        elif not within_int32:
             shutil.copyfile(input_path, output_path)
+            return
     else:
-        # If the original format is not numpy, convert it to numpy.
-        data = read_data(input_path, input_format, in_memory)
+        # If dim of the data is 1, reshape it to n * 1 and save it to output_path.
         if is_feature and data.dim() == 1:
             data = data.reshape(-1, 1)
     save_data(data, output_path, output_format)

tests/python/pytorch/graphbolt/impl/test_ondisk_dataset.py

@@ -1151,7 +1151,11 @@ def test_OnDiskDataset_preprocess_homogeneous(edge_fmt):
         num_samples = 100
         fanout = 1
         subgraph = fused_csc_sampling_graph.sample_neighbors(
-            torch.arange(num_samples),
+            torch.arange(
+                0,
+                num_samples,
+                dtype=fused_csc_sampling_graph.indices.dtype,
+            ),
             torch.tensor([fanout]),
         )
         assert len(subgraph.sampled_csc.indices) <= num_samples
@@ -1191,7 +1195,10 @@ def test_OnDiskDataset_preprocess_homogeneous(edge_fmt):
         fused_csc_sampling_graph = None
 
 
-def test_OnDiskDataset_preprocess_homogeneous_hardcode(edge_fmt="numpy"):
+@pytest.mark.parametrize("auto_cast", [False, True])
+def test_OnDiskDataset_preprocess_homogeneous_hardcode(
+    auto_cast, edge_fmt="numpy"
+):
     """Test preprocess of OnDiskDataset."""
     with tempfile.TemporaryDirectory() as test_dir:
         """Original graph in COO:
@@ -1312,6 +1319,7 @@ def test_OnDiskDataset_preprocess_homogeneous_hardcode(edge_fmt="numpy"):
         output_file = gb.ondisk_dataset.preprocess_ondisk_dataset(
             test_dir,
             include_original_edge_id=True,
+            auto_cast_to_optimal_dtype=auto_cast,
         )
 
         with open(output_file, "rb") as f:
@@ -1351,16 +1359,31 @@ def test_OnDiskDataset_preprocess_homogeneous_hardcode(edge_fmt="numpy"):
             torch.tensor([7, 8, 0, 9, 1, 2, 3, 4, 5, 6]),
         )
 
+        expected_dtype = torch.int32 if auto_cast else torch.int64
+        assert fused_csc_sampling_graph.csc_indptr.dtype == expected_dtype
+        assert fused_csc_sampling_graph.indices.dtype == expected_dtype
+        assert (
+            fused_csc_sampling_graph.edge_attributes[gb.ORIGINAL_EDGE_ID].dtype
+            == expected_dtype
+        )
+
         num_samples = 5
         fanout = 1
         subgraph = fused_csc_sampling_graph.sample_neighbors(
-            torch.arange(num_samples),
+            torch.arange(
+                0,
+                num_samples,
+                dtype=fused_csc_sampling_graph.indices.dtype,
+            ),
             torch.tensor([fanout]),
         )
         assert len(subgraph.sampled_csc.indices) <= num_samples
 
 
-def test_OnDiskDataset_preprocess_heterogeneous_hardcode(edge_fmt="numpy"):
+@pytest.mark.parametrize("auto_cast", [False, True])
+def test_OnDiskDataset_preprocess_heterogeneous_hardcode(
+    auto_cast, edge_fmt="numpy"
+):
     """Test preprocess of OnDiskDataset."""
     with tempfile.TemporaryDirectory() as test_dir:
         """Original graph in COO:
@@ -1507,6 +1530,7 @@ def test_OnDiskDataset_preprocess_heterogeneous_hardcode(edge_fmt="numpy"):
         output_file = gb.ondisk_dataset.preprocess_ondisk_dataset(
             test_dir,
             include_original_edge_id=True,
+            auto_cast_to_optimal_dtype=auto_cast,
         )
 
         with open(output_file, "rb") as f:
@@ -1548,6 +1572,18 @@ def test_OnDiskDataset_preprocess_heterogeneous_hardcode(edge_fmt="numpy"):
             fused_csc_sampling_graph.edge_attributes[gb.ORIGINAL_EDGE_ID],
             torch.tensor([0, 1, 0, 2, 0, 1, 2, 0, 1, 2]),
         )
+        expected_dtype = torch.int32 if auto_cast else torch.int64
+        assert fused_csc_sampling_graph.csc_indptr.dtype == expected_dtype
+        assert fused_csc_sampling_graph.indices.dtype == expected_dtype
+        assert (
+            fused_csc_sampling_graph.edge_attributes[gb.ORIGINAL_EDGE_ID].dtype
+            == expected_dtype
+        )
+        assert fused_csc_sampling_graph.node_type_offset.dtype == expected_dtype
+        expected_etype_dtype = torch.uint8 if auto_cast else torch.int64
+        assert (
+            fused_csc_sampling_graph.type_per_edge.dtype == expected_etype_dtype
+        )
 
 
 def test_OnDiskDataset_preprocess_path():
@@ -2622,9 +2658,12 @@ def test_BuiltinDataset():
             _ = gb.BuiltinDataset(name=dataset_name, root=test_dir).load()
 
 
+@pytest.mark.parametrize("auto_cast", [True, False])
 @pytest.mark.parametrize("include_original_edge_id", [True, False])
 @pytest.mark.parametrize("edge_fmt", ["csv", "numpy"])
-def test_OnDiskDataset_homogeneous(include_original_edge_id, edge_fmt):
+def test_OnDiskDataset_homogeneous(
+    auto_cast, include_original_edge_id, edge_fmt
+):
     """Preprocess and instantiate OnDiskDataset for homogeneous graph."""
     with tempfile.TemporaryDirectory() as test_dir:
         # All metadata fields are specified.
@@ -2647,7 +2686,9 @@ def test_OnDiskDataset_homogeneous(include_original_edge_id, edge_fmt):
             f.write(yaml_content)
 
         dataset = gb.OnDiskDataset(
-            test_dir, include_original_edge_id=include_original_edge_id
+            test_dir,
+            include_original_edge_id=include_original_edge_id,
+            auto_cast_to_optimal_dtype=auto_cast,
         ).load()
 
         assert dataset.dataset_name == dataset_name
@@ -2673,6 +2714,10 @@ def test_OnDiskDataset_homogeneous(include_original_edge_id, edge_fmt):
         assert isinstance(tasks[0].train_set, gb.ItemSet)
         assert isinstance(tasks[0].validation_set, gb.ItemSet)
         assert isinstance(tasks[0].test_set, gb.ItemSet)
+        assert tasks[0].train_set._items[0].dtype == graph.indices.dtype
+        assert tasks[0].validation_set._items[0].dtype == graph.indices.dtype
+        assert tasks[0].test_set._items[0].dtype == graph.indices.dtype
+        assert dataset.all_nodes_set._items.dtype == graph.indices.dtype
         assert tasks[0].metadata["num_classes"] == num_classes
         assert tasks[0].metadata["name"] == "link_prediction"
 
@@ -2683,6 +2728,7 @@ def test_OnDiskDataset_homogeneous(include_original_edge_id, edge_fmt):
             tasks[0].train_set,
             tasks[0].validation_set,
             tasks[0].test_set,
+            dataset.all_nodes_set,
         ]:
             datapipe = gb.ItemSampler(itemset, batch_size=10)
             datapipe = datapipe.sample_neighbor(graph, [-1])
@@ -2698,9 +2744,12 @@ def test_OnDiskDataset_homogeneous(include_original_edge_id, edge_fmt):
         dataset = None
 
 
+@pytest.mark.parametrize("auto_cast", [True, False])
 @pytest.mark.parametrize("include_original_edge_id", [True, False])
 @pytest.mark.parametrize("edge_fmt", ["csv", "numpy"])
-def test_OnDiskDataset_heterogeneous(include_original_edge_id, edge_fmt):
+def test_OnDiskDataset_heterogeneous(
+    auto_cast, include_original_edge_id, edge_fmt
+):
     """Preprocess and instantiate OnDiskDataset for heterogeneous graph."""
     with tempfile.TemporaryDirectory() as test_dir:
         dataset_name = "OnDiskDataset_hetero"
@@ -2723,7 +2772,9 @@ def test_OnDiskDataset_heterogeneous(include_original_edge_id, edge_fmt):
         )
 
         dataset = gb.OnDiskDataset(
-            test_dir, include_original_edge_id=include_original_edge_id
+            test_dir,
+            include_original_edge_id=include_original_edge_id,
+            auto_cast_to_optimal_dtype=auto_cast,
         ).load()
 
         assert dataset.dataset_name == dataset_name
@@ -2736,6 +2787,8 @@ def test_OnDiskDataset_heterogeneous(include_original_edge_id, edge_fmt):
         assert graph.total_num_edges == sum(
             num_edge for num_edge in num_edges.values()
         )
+        expected_dtype = torch.int32 if auto_cast else torch.int64
+        assert graph.indices.dtype == expected_dtype
         assert (
             graph.node_attributes is not None
             and "feat" in graph.node_attributes
@@ -2763,6 +2816,7 @@ def test_OnDiskDataset_heterogeneous(include_original_edge_id, edge_fmt):
             tasks[0].train_set,
             tasks[0].validation_set,
             tasks[0].test_set,
+            dataset.all_nodes_set,
         ]:
             datapipe = gb.ItemSampler(itemset, batch_size=10)
             datapipe = datapipe.sample_neighbor(graph, [-1])