"""Torch-based feature store for GraphBolt."""
import copy
import textwrap
from typing import Dict, List
import numpy as np
import torch
from ..base import index_select
from ..feature_store import Feature
from .basic_feature_store import BasicFeatureStore
from .ondisk_metadata import OnDiskFeatureData
__all__ = ["TorchBasedFeature", "TorchBasedFeatureStore"]
[docs]class TorchBasedFeature(Feature):
r"""A wrapper of pytorch based feature.
Initialize a torch based feature store by a torch feature.
Note that the feature can be either in memory or on disk.
Parameters
----------
torch_feature : torch.Tensor
The torch feature.
Note that the dimension of the tensor should be greater than 1.
Examples
--------
>>> import torch
>>> from dgl import graphbolt as gb
1. The feature is in memory.
>>> torch_feat = torch.arange(10).reshape(2, -1)
>>> feature = gb.TorchBasedFeature(torch_feat)
>>> feature.read()
tensor([[0, 1, 2, 3, 4],
[5, 6, 7, 8, 9]])
>>> feature.read(torch.tensor([0]))
tensor([[0, 1, 2, 3, 4]])
>>> feature.update(torch.tensor([[1 for _ in range(5)]]),
... torch.tensor([1]))
>>> feature.read(torch.tensor([0, 1]))
tensor([[0, 1, 2, 3, 4],
[1, 1, 1, 1, 1]])
>>> feature.size()
torch.Size([5])
2. The feature is on disk.
>>> import numpy as np
>>> arr = np.array([[1, 2], [3, 4]])
>>> np.save("/tmp/arr.npy", arr)
>>> torch_feat = torch.from_numpy(np.load("/tmp/arr.npy", mmap_mode="r+"))
>>> feature = gb.TorchBasedFeature(torch_feat)
>>> feature.read()
tensor([[1, 2],
[3, 4]])
>>> feature.read(torch.tensor([0]))
tensor([[1, 2]])
3. Pinned CPU feature.
>>> torch_feat = torch.arange(10).reshape(2, -1).pin_memory()
>>> feature = gb.TorchBasedFeature(torch_feat)
>>> feature.read().device
device(type='cuda', index=0)
>>> feature.read(torch.tensor([0]).cuda()).device
device(type='cuda', index=0)
"""
def __init__(self, torch_feature: torch.Tensor, metadata: Dict = None):
super().__init__()
self._is_inplace_pinned = set()
assert isinstance(torch_feature, torch.Tensor), (
f"torch_feature in TorchBasedFeature must be torch.Tensor, "
f"but got {type(torch_feature)}."
)
assert torch_feature.dim() > 1, (
f"dimension of torch_feature in TorchBasedFeature must be greater "
f"than 1, but got {torch_feature.dim()} dimension."
)
# Make sure the tensor is contiguous.
self._tensor = torch_feature.contiguous()
self._metadata = metadata
def __del__(self):
# torch.Tensor.pin_memory() is not an inplace operation. To make it
# truly in-place, we need to use cudaHostRegister. Then, we need to use
# cudaHostUnregister to unpin the tensor in the destructor.
# https://github.com/pytorch/pytorch/issues/32167#issuecomment-753551842
for tensor in self._is_inplace_pinned:
assert self._inplace_unpinner(tensor.data_ptr()) == 0
[docs] def read(self, ids: torch.Tensor = None):
"""Read the feature by index.
If the feature is on pinned CPU memory and `ids` is on GPU or pinned CPU
memory, it will be read by GPU and the returned tensor will be on GPU.
Otherwise, the returned tensor will be on CPU.
Parameters
----------
ids : torch.Tensor, optional
The index of the feature. If specified, only the specified indices
of the feature are read. If None, the entire feature is returned.
Returns
-------
torch.Tensor
The read feature.
"""
if ids is None:
if self._tensor.is_pinned():
return self._tensor.cuda()
return self._tensor
return index_select(self._tensor, ids)
[docs] def size(self):
"""Get the size of the feature.
Returns
-------
torch.Size
The size of the feature.
"""
return self._tensor.size()[1:]
[docs] def update(self, value: torch.Tensor, ids: torch.Tensor = None):
"""Update the feature store.
Parameters
----------
value : torch.Tensor
The updated value of the feature.
ids : torch.Tensor, optional
The indices of the feature to update. If specified, only the
specified indices of the feature will be updated. For the feature,
the `ids[i]` row is updated to `value[i]`. So the indices and value
must have the same length. If None, the entire feature will be
updated.
"""
if ids is None:
self._tensor = value
else:
assert ids.shape[0] == value.shape[0], (
f"ids and value must have the same length, "
f"but got {ids.shape[0]} and {value.shape[0]}."
)
assert self.size() == value.size()[1:], (
f"The size of the feature is {self.size()}, "
f"while the size of the value is {value.size()[1:]}."
)
if self._tensor.is_pinned() and value.is_cuda and ids.is_cuda:
raise NotImplementedError(
"Update the feature on pinned CPU memory by GPU is not "
"supported yet."
)
self._tensor[ids] = value
[docs] def pin_memory_(self):
"""In-place operation to copy the feature to pinned memory. Returns the
same object modified in-place."""
# torch.Tensor.pin_memory() is not an inplace operation. To make it
# truly in-place, we need to use cudaHostRegister. Then, we need to use
# cudaHostUnregister to unpin the tensor in the destructor.
# https://github.com/pytorch/pytorch/issues/32167#issuecomment-753551842
x = self._tensor
if not x.is_pinned() and x.device.type == "cpu":
assert (
x.is_contiguous()
), "Tensor pinning is only supported for contiguous tensors."
cudart = torch.cuda.cudart()
assert (
cudart.cudaHostRegister(
x.data_ptr(), x.numel() * x.element_size(), 0
)
== 0
)
self._is_inplace_pinned.add(x)
self._inplace_unpinner = cudart.cudaHostUnregister
return self
[docs] def is_pinned(self):
"""Returns True if the stored feature is pinned."""
return self._tensor.is_pinned()
[docs] def to(self, device): # pylint: disable=invalid-name
"""Copy `TorchBasedFeature` to the specified device."""
# copy.copy is a shallow copy so it does not copy tensor memory.
self2 = copy.copy(self)
if device == "pinned":
self2._tensor = self2._tensor.pin_memory()
else:
self2._tensor = self2._tensor.to(device)
return self2
def __repr__(self) -> str:
ret = (
"{Classname}(\n"
" feature={feature},\n"
" metadata={metadata},\n"
")"
)
feature_str = textwrap.indent(
str(self._tensor), " " * len(" feature=")
).strip()
metadata_str = textwrap.indent(
str(self.metadata()), " " * len(" metadata=")
).strip()
return ret.format(
Classname=self.__class__.__name__,
feature=feature_str,
metadata=metadata_str,
)
[docs]class TorchBasedFeatureStore(BasicFeatureStore):
r"""A store to manage multiple pytorch based feature for access.
The feature stores are described by the `feat_data`. The `feat_data` is a
list of `OnDiskFeatureData`.
For a feature store, its format must be either "pt" or "npy" for Pytorch or
Numpy formats. If the format is "pt", the feature store must be loaded in
memory. If the format is "npy", the feature store can be loaded in memory or
on disk.
Parameters
----------
feat_data : List[OnDiskFeatureData]
The description of the feature stores.
Examples
--------
>>> import torch
>>> import numpy as np
>>> from dgl import graphbolt as gb
>>> edge_label = torch.tensor([[1], [2], [3]])
>>> node_feat = torch.tensor([[1, 2, 3], [4, 5, 6]])
>>> torch.save(edge_label, "/tmp/edge_label.pt")
>>> np.save("/tmp/node_feat.npy", node_feat.numpy())
>>> feat_data = [
... gb.OnDiskFeatureData(domain="edge", type="author:writes:paper",
... name="label", format="torch", path="/tmp/edge_label.pt",
... in_memory=True),
... gb.OnDiskFeatureData(domain="node", type="paper", name="feat",
... format="numpy", path="/tmp/node_feat.npy", in_memory=False),
... ]
>>> feature_sotre = gb.TorchBasedFeatureStore(feat_data)
"""
def __init__(self, feat_data: List[OnDiskFeatureData]):
features = {}
for spec in feat_data:
key = (spec.domain, spec.type, spec.name)
metadata = spec.extra_fields
if spec.format == "torch":
assert spec.in_memory, (
f"Pytorch tensor can only be loaded in memory, "
f"but the feature {key} is loaded on disk."
)
features[key] = TorchBasedFeature(
torch.load(spec.path), metadata=metadata
)
elif spec.format == "numpy":
mmap_mode = "r+" if not spec.in_memory else None
features[key] = TorchBasedFeature(
torch.as_tensor(np.load(spec.path, mmap_mode=mmap_mode)),
metadata=metadata,
)
else:
raise ValueError(f"Unknown feature format {spec.format}")
super().__init__(features)
[docs] def pin_memory_(self):
"""In-place operation to copy the feature store to pinned memory.
Returns the same object modified in-place."""
for feature in self._features.values():
feature.pin_memory_()
return self
[docs] def is_pinned(self):
"""Returns True if all the stored features are pinned."""
return all(feature.is_pinned() for feature in self._features.values())
[docs] def to(self, device): # pylint: disable=invalid-name
"""Copy `TorchBasedFeatureStore` to the specified device."""
# copy.copy is a shallow copy so it does not copy tensor memory.
self2 = copy.copy(self)
self2._features = {k: v.to(device) for k, v in self2._features.items()}
return self2
def __repr__(self) -> str:
ret = "{Classname}(\n" + " {features}\n" + ")"
features_str = textwrap.indent(str(self._features), " ").strip()
return ret.format(
Classname=self.__class__.__name__, features=features_str
)