项目文件夹

文件
peizhou001 9699b93136 [API Deprecation]Change DGLHeteroGraph to DGLGraph in DOC (#4840)
* Update from master (#4584)

* [Example][Refactor] Refactor graphsage multigpu and full-graph example (#4430)

* Add refactors for multi-gpu and full-graph example

* Fix format

* Update

* Update

* Update

* [Cleanup] Remove async_transferer (#4505)

* Remove async_transferer

* remove test

* Remove AsyncTransferer

Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>

* [Cleanup] Remove duplicate entries of CUB submodule   (issue# 4395) (#4499)

* remove third_part/cub

* remove from third_party

Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>

* [Bug] Enable turn on/off libxsmm at runtime (#4455)

* enable turn on/off libxsmm at runtime by adding a global config and related API


Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>

* [Feature] Unify the cuda stream used in core library (#4480)

* Use an internal cuda stream for CopyDataFromTo

* small fix white space

* Fix to compile

* Make stream optional in copydata for compile

* fix lint issue

* Update cub functions to use internal stream

* Lint check

* Update CopyTo/CopyFrom/CopyFromTo to use internal stream

* Address comments

* Fix backward CUDA stream

* Avoid overloading CopyFromTo()

* Minor comment update

* Overload copydatafromto in cuda device api

Co-authored-by: xiny <xiny@nvidia.com>

* [Feature] Added exclude_self and output_batch to knn graph construction (Issues #4323 #4316) (#4389)

* * Added "exclude_self" and "output_batch" options to knn_graph and segmented_knn_graph
* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information

* * Changed defaults on new knn_graph and segmented_knn_graph function parameters, for compatibility; pytorch/test_geometry.py was failing

* * Added test to ensure dgl.remove_self_loop function correctly updates batch information

* * Added new knn_graph and segmented_knn_graph parameters to dgl.nn.KNNGraph and dgl.nn.SegmentedKNNGraph

* * Formatting

* * Oops, I missed the one in segmented_knn_graph when I fixed the similar thing in knn_graph

* * Fixed edge case handling when invalid k specified, since it still needs to be handled consistently for tests to pass
* Fixed context of batch info, since it must match the context of the input position data for remove_self_loop to succeed

* * Fixed batch info resulting from knn_graph when output_batch is true, for case of 3D input tensor, representing multiple segments

* * Added testing of new exclude_self and output_batch parameters on knn_graph and segmented_knn_graph, and their wrappers, KNNGraph and SegmentedKNNGraph, into the test_knn_cuda test

* * Added doc comments for new parameters

* * Added correct handling for uncommon case of k or more coincident points when excluding self edges in knn_graph and segmented_knn_graph
* Added test cases for more than k coincident points

* * Updated doc comments for output_batch parameters for clarity

* * Linter formatting fixes

* * Extracted out common function for test_knn_cpu and test_knn_cuda, to add the new test cases to test_knn_cpu

* * Rewording in doc comments

* * Removed output_batch parameter from knn_graph and segmented_knn_graph, in favour of always setting the batch information, except in knn_graph if x is a 2D tensor

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [CI] only known devs are authorized to trigger CI (#4518)

* [CI] only known devs are authorized to trigger CI

* fix if author is null

* add comments

* [Readability] Auto fix setup.py and update-version.py (#4446)

* Auto fix update-version

* Auto fix setup.py

* Auto fix update-version

* Auto fix setup.py

* [Doc] Change random.py to random_partition.py in guide on distributed partition pipeline (#4438)

* Update distributed-preprocessing.rst

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* fix unpinning when tensoradaptor is not available (#4450)

* [Doc] fix print issue in tutorial (#4459)

* [Example][Refactor] Refactor RGCN example (#4327)

* Refactor full graph entity classification

* Refactor rgcn with sampling

* README update

* Update

* Results update

* Respect default setting of self_loop=false in entity.py

* Update

* Update README

* Update for multi-gpu

* Update

* [doc] fix invalid link in user guide (#4468)

* [Example] directional_GSN for ogbg-molpcba (#4405)

* version-1

* version-2

* version-3

* update examples/README

* Update .gitignore

* update performance in README, delete scripts

* 1st approving review

* 2nd approving review

Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Clarify the message name, which is 'm'. (#4462)

Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>

* [Refactor] Auto fix view.py. (#4461)

Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [Example] SEAL for OGBL (#4291)

* [Example] SEAL for OGBL

* update index

* update

* fix readme typo

* add seal sampler

* modify set ops

* prefetch

* efficiency test

* update

* optimize

* fix ScatterAdd dtype issue

* update sampler style

* update

Co-authored-by: Quan Gan <coin2028@hotmail.com>

* [CI] use https instead of http (#4488)

* [BugFix] fix crash due to incorrect dtype in dgl.to_block() (#4487)

* [BugFix] fix crash due to incorrect dtype in dgl.to_block()

* fix test failure in TF

* [Feature] Make TensorAdapter Stream Aware (#4472)

* Allocate tensors in DGL's current stream

* make tensoradaptor stream-aware

* replace TAemtpy with cpu allocator

* fix typo

* try fix cpu allocation

* clean header

* redirect AllocDataSpace as well

* resolve comments

* [Build][Doc] Specify the sphinx version (#4465)

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* reformat

* reformat

* Auto fix update-version

* Auto fix setup.py

* reformat

* reformat

Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
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Co-authored-by: Mufei Li <mufeili1996@gmail.com>
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Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>

* Move mock version of dgl_sparse library to DGL main repo (#4524)

* init

* Add api doc for sparse library

* support op btwn matrices with differnt sparsity

* Fixed docstring

* addresses comments

* lint check

* change keyword format to fmt

Co-authored-by: Israt Nisa <nisisrat@amazon.com>

* [DistPart] expose timeout config for process group (#4532)

* [DistPart] expose timeout config for process group

* refine code

* Update tools/distpartitioning/data_proc_pipeline.py

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [Feature] Import PyTorch's CUDA stream management (#4503)

* add set_stream

* add .record_stream for NDArray and HeteroGraph

* refactor dgl stream Python APIs

* test record_stream

* add unit test for record stream

* use pytorch's stream

* fix lint

* fix cpu build

* address comments

* address comments

* add record stream tests for dgl.graph

* record frames and update dataloder

* add docstring

* update frame

* add backend check for record_stream

* remove CUDAThreadEntry::stream

* record stream for newly created formats

* fix bug

* fix cpp test

* fix None c_void_p to c_handle

* [examples]educe memory consumption (#4558)

* [examples]educe memory consumption

* reffine help message

* refine

* [Feature][REVIEW] Enable DGL cugaph nightly CI  (#4525)

* Added cugraph nightly scripts

* Removed nvcr.io//nvidia/pytorch:22.04-py3 reference

Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>

* Revert "[Feature][REVIEW] Enable DGL cugaph nightly CI  (#4525)" (#4563)

This reverts commit ec171c648a.

* [Misc] Add flake8 lint workflow. (#4566)

* Add pyproject.toml for autopep8.

* Add pyproject.toml for autopep8.

* Add flake8 annotation in workflow.

* remove

* add

* clean up

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Misc] Try use official pylint workflow. (#4568)

* polish update_version

* update pylint workflow.

* add

* revert.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [CI] refine stage logic (#4565)

* [CI] refine stage logic

* refine

* refine

* remove (#4570)

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* Add Pylint workflow for flake8. (#4571)

* remove

* Add pylint.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Misc] Update the python version in Pylint workflow for flake8. (#4572)

* remove

* Add pylint.

* Change the python version for pylint.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* Update pylint. (#4574)

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Misc] Use another workflow. (#4575)

* Update pylint.

* Use another workflow.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* Update pylint. (#4576)

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* Update pylint.yml

* Update pylint.yml

* Delete pylint.yml

* [Misc]Add pyproject.toml for autopep8 & black. (#4543)

* Add pyproject.toml for autopep8.

* Add pyproject.toml for autopep8.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* [Feature] Bump DLPack to v0.7 and decouple DLPack from the core library (#4454)

* rename `DLContext` to `DGLContext`

* rename `kDLGPU` to `kDLCUDA`

* replace DLTensor with DGLArray

* fix linting

* Unify DGLType and DLDataType to DGLDataType

* Fix FFI

* rename DLDeviceType to DGLDeviceType

* decouple dlpack from the core library

* fix bug

* fix lint

* fix merge

* fix build

* address comments

* rename dl_converter to dlpack_convert

* remove redundant comments

Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>
Co-authored-by: Israt Nisa <neesha295@gmail.com>
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: peizhou001 <110809584+peizhou001@users.noreply.github.com>
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Co-authored-by: ndickson-nvidia <99772994+ndickson-nvidia@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>
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Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
Co-authored-by: Vibhu Jawa <vibhujawa@gmail.com>

* [Deprecation] Dataset Attributes (#4546)

* Update

* CI

* CI

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* [Example] Bug Fix (#4665)

* Update

* CI

* CI

* Update

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* Update

* Update (#4724)

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* change DGLHeteroGraph to DGLGraph in DOC

* revert c change

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>
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Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
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2022-11-10 08:38:47 +08:00

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.. _guide_cn-minibatch-custom-gnn-module:
6.5 为小批次训练实现定制化的GNN模块
-------------------------------------------------------------
:ref:`(English Version) <guide-minibatch-custom-gnn-module>`
如果用户熟悉如何定制用于更新整个同构图或异构图的GNN模块(参见
:ref:`guide_cn-nn`),那么在块上计算的代码也是类似的,区别只在于节点被划分为输入节点和输出节点。
以下面的自定义图卷积模块代码为例。注意,该代码并不一定是最高效的实现,
此处只是将其作为自定义GNN模块的一个示例。
.. code:: python
class CustomGraphConv(nn.Module):
def __init__(self, in_feats, out_feats):
super().__init__()
self.W = nn.Linear(in_feats * 2, out_feats)
def forward(self, g, h):
with g.local_scope():
g.ndata['h'] = h
g.update_all(fn.copy_u('h', 'm'), fn.mean('m', 'h_neigh'))
return self.W(torch.cat([g.ndata['h'], g.ndata['h_neigh']], 1))
如果用户已有一个用于整个图的自定义消息传递模块,并且想将其用于块,则只需要按照如下的方法重写forward函数。
注意,以下代码在注释里保留了整图实现的语句,用户可以将用于块的语句和原先用于整图的语句进行比较。
.. code:: python
class CustomGraphConv(nn.Module):
def __init__(self, in_feats, out_feats):
super().__init__()
self.W = nn.Linear(in_feats * 2, out_feats)
# h现在是输入和输出节点的特征张量对,而不是一个单独的特征张量
# def forward(self, g, h):
def forward(self, block, h):
# with g.local_scope():
with block.local_scope():
# g.ndata['h'] = h
h_src = h
h_dst = h[:block.number_of_dst_nodes()]
block.srcdata['h'] = h_src
block.dstdata['h'] = h_dst
# g.update_all(fn.copy_u('h', 'm'), fn.mean('m', 'h_neigh'))
block.update_all(fn.copy_u('h', 'm'), fn.mean('m', 'h_neigh'))
# return self.W(torch.cat([g.ndata['h'], g.ndata['h_neigh']], 1))
return self.W(torch.cat(
[block.dstdata['h'], block.dstdata['h_neigh']], 1))
通常,需要对用于整图的GNN模块进行如下调整以将其用于块作为输入的情况:
- 切片取输入特征的前几行,得到输出节点的特征。切片行数可以通过
:meth:`block.number_of_dst_nodes <dgl.DGLGraph.number_of_dst_nodes>` 获得。
- 如果原图只包含一种节点类型,对输入节点特征,将 :attr:`g.ndata <dgl.DGLGraph.ndata>` 替换为
:attr:`block.srcdata <dgl.DGLGraph.srcdata>`;对于输出节点特征,将
:attr:`g.ndata <dgl.DGLGraph.ndata>` 替换为
:attr:`block.dstdata <dgl.DGLGraph.dstdata>`
- 如果原图包含多种节点类型,对于输入节点特征,将
:attr:`g.nodes <dgl.DGLGraph.nodes>` 替换为
:attr:`block.srcnodes <dgl.DGLGraph.srcnodes>`;对于输出节点特征,将
:attr:`g.nodes <dgl.DGLGraph.nodes>` 替换为
:attr:`block.dstnodes <dgl.DGLGraph.dstnodes>`
- 对于输入节点数量,将 :meth:`g.number_of_nodes <dgl.DGLGraph.number_of_nodes>` 替换为
:meth:`block.number_of_src_nodes <dgl.DGLGraph.number_of_src_nodes>`
对于输出节点数量,将 :meth:`g.number_of_nodes <dgl.DGLGraph.number_of_nodes>` 替换为
:meth:`block.number_of_dst_nodes <dgl.DGLGraph.number_of_dst_nodes>`
异构图上的模型定制
~~~~~~~~~~~~~~~~~~~~
为异构图修改GNN模块的方法是类似的。例如,以下面用于全图的GNN模块为例:
.. code:: python
class CustomHeteroGraphConv(nn.Module):
def __init__(self, g, in_feats, out_feats):
super().__init__()
self.Ws = nn.ModuleDict()
for etype in g.canonical_etypes:
utype, _, vtype = etype
self.Ws[etype] = nn.Linear(in_feats[utype], out_feats[vtype])
for ntype in g.ntypes:
self.Vs[ntype] = nn.Linear(in_feats[ntype], out_feats[ntype])
def forward(self, g, h):
with g.local_scope():
for ntype in g.ntypes:
g.nodes[ntype].data['h_dst'] = self.Vs[ntype](h[ntype])
g.nodes[ntype].data['h_src'] = h[ntype]
for etype in g.canonical_etypes:
utype, _, vtype = etype
g.update_all(
fn.copy_u('h_src', 'm'), fn.mean('m', 'h_neigh'),
etype=etype)
g.nodes[vtype].data['h_dst'] = g.nodes[vtype].data['h_dst'] + \
self.Ws[etype](g.nodes[vtype].data['h_neigh'])
return {ntype: g.nodes[ntype].data['h_dst'] for ntype in g.ntypes}
对于 ``CustomHeteroGraphConv``,原则是将 ``g.nodes`` 替换为 ``g.srcnodes``
``g.dstnodes`` (根据需要输入还是输出节点的特征来选择)。
.. code:: python
class CustomHeteroGraphConv(nn.Module):
def __init__(self, g, in_feats, out_feats):
super().__init__()
self.Ws = nn.ModuleDict()
for etype in g.canonical_etypes:
utype, _, vtype = etype
self.Ws[etype] = nn.Linear(in_feats[utype], out_feats[vtype])
for ntype in g.ntypes:
self.Vs[ntype] = nn.Linear(in_feats[ntype], out_feats[ntype])
def forward(self, g, h):
with g.local_scope():
for ntype in g.ntypes:
h_src, h_dst = h[ntype]
g.dstnodes[ntype].data['h_dst'] = self.Vs[ntype](h[ntype])
g.srcnodes[ntype].data['h_src'] = h[ntype]
for etype in g.canonical_etypes:
utype, _, vtype = etype
g.update_all(
fn.copy_u('h_src', 'm'), fn.mean('m', 'h_neigh'),
etype=etype)
g.dstnodes[vtype].data['h_dst'] = \
g.dstnodes[vtype].data['h_dst'] + \
self.Ws[etype](g.dstnodes[vtype].data['h_neigh'])
return {ntype: g.dstnodes[ntype].data['h_dst']
for ntype in g.ntypes}
实现能够处理同构图、二分图和块的模块
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DGL中所有的消息传递模块(参见 :ref:`apinn`)都能够处理同构图、
单向二分图(包含两种节点类型和一种边类型)和包含一种边类型的块。
本质上,内置的DGL神经网络模块的输入图及特征必须满足下列情况之一:
- 如果输入特征是一个张量对,则输入图必须是一个单向二分图
- 如果输入特征是一个单独的张量且输入图是一个块,则DGL会自动将输入节点特征前一部分设为输出节点的特征。
- 如果输入特征是一个单独的张量且输入图不是块,则输入图必须是同构图。
例如,下面的代码是 :class:`dgl.nn.pytorch.SAGEConv` 的简化版(DGL同样支持它在MXNet和TensorFlow后端里的实现)。
代码里移除了归一化,且只考虑平均聚合函数的情况。
.. code:: python
import dgl.function as fn
class SAGEConv(nn.Module):
def __init__(self, in_feats, out_feats):
super().__init__()
self.W = nn.Linear(in_feats * 2, out_feats)
def forward(self, g, h):
if isinstance(h, tuple):
h_src, h_dst = h
elif g.is_block:
h_src = h
h_dst = h[:g.number_of_dst_nodes()]
else:
h_src = h_dst = h
g.srcdata['h'] = h_src
g.dstdata['h'] = h_dst
g.update_all(fn.copy_u('h', 'm'), fn.sum('m', 'h_neigh'))
return F.relu(
self.W(torch.cat([g.dstdata['h'], g.dstdata['h_neigh']], 1)))
:ref:`guide_cn-nn` 提供了对 :class:`dgl.nn.pytorch.SAGEConv` 代码的详细解读,
其适用于单向二分图、同构图和块。