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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* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information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

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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: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>
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Co-authored-by: Quan Gan <coin2028@hotmail.com>
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* [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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2022-11-10 08:38:47 +08:00

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.. _guide_ko-minibatch-custom-gnn-module:
6.5 미니-배치 학습을 위한 커스텀 GNN 모듈 구현하기
----------------------------------------
:ref:`(English Version) <guide-minibatch-custom-gnn-module>`
Homogeneous 그래프나 heterogeneous 그래프를 대상으로 전체 그래프를 업데이트하는 커스텀 GNN 모듈을 만드는 것에 익숙하다면, MFG에 대한 연산을 구현하는 코드도 비슷하다는 것을 알 수 있다. 차이점은 노드들이 입력 노드와 출력 노드로 나뉜다는 것 뿐이다.
커스텀 graph convolution 모듈을 예로 들자. 이 코드는 단지 커스텀 GNN 모듈이 어떻게 동작하는지 보여주기 위함이지, 가장 효율적인 구현이 아님을 주의하자.
.. 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))
전체 그래프에 대한 커스텀 메시지 전달 NN 모듈이 있고, 이를 MFG에서 작동하도록 만들고 싶다면, 다음과 같이 forward 함수를 다시 작성하는 것만이 필요하다. 전체 그래프에 대한 구현은 주석 처리를 했으니, 새로운 코드들과 비교해 보자.
.. 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 is now a pair of feature tensors for input and output nodes, instead of
# a single feature tensor.
# 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))
일반적으로, 직접 구현한 NN 모듈이 MFG에서 동작하게 만들기 위해서는 다음과 같은 것을 해야한다.
- 첫 몇 행들(row)을 잘라서 입력 피쳐들로부터 출력 노드의 피처를 얻는다. 행의 개수는 :meth:`block.number_of_dst_nodes <dgl.DGLGraph.number_of_dst_nodes>` 로 얻는다.
- 원본 그래프가 한 하나의 노드 타입을 갖는 경우, :attr:`g.ndata <dgl.DGLGraph.ndata>` 를 입력 노드의 피쳐의 경우 :attr:`block.srcdata <dgl.DGLGraph.srcdata>` 로 또는 출력 노드의 피쳐의 경우 :attr:`block.dstdata <dgl.DGLGraph.dstdata>` 로 교체한다.
- 원본 그래프가 여러 종류의 노드 타입을 갖는 경우, :attr:`g.nodes <dgl.DGLGraph.nodes>` 를 입력 노드의 피쳐의 경우 :attr:`block.srcnodes <dgl.DGLGraph.srcnodes>` 로 또는 출력 노드의 피처의 경우 :attr:`block.dstnodes <dgl.DGLGraph.dstnodes>` 로 교체한다.
- :meth:`g.number_of_nodes <dgl.DGLGraph.number_of_nodes>` 를 입력 노드의 개수는 :meth:`block.number_of_src_nodes <dgl.DGLGraph.number_of_src_nodes>` 로 출력 노드의 개수는 :meth:`block.number_of_dst_nodes <dgl.DGLGraph.number_of_dst_nodes>` 로 각각 교체한다.
Heterogeneous 그래프들
~~~~~~~~~~~~~~~~~~~~
Heterogeneous 그래프의 경우도 커스텀 GNN 모듈을 만드는 것은 비슷하다. 예를 들어, 전체 그래프에 적용되는 다음 모듈을 예로 들어보자.
.. 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}
``CustomHeteroGraphConv`` 에서의 원칙은 ``g.nodes`` 를 대상 피쳐가 입력 노드의 것인지 출력 노드의 것인지에 따라서 ``g.srcnodes`` 또는 ``g.dstnodes`` 바꾸는 것이다.
.. 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}
Homogeneous 그래프, 이분 그래프(bipartite graph), 그리고 MFG를 위한 모듈 작성하기
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
DGL의 모든 메시지 전달 모듈들은 homogeneous 그래프, 단방향 이분 그래프 (unidirectional bipartite graphs, 두개 노드 타입을 갖고, 하나의 에지 타입을 갖음), 그리고 하나의 에지 타입을 갖는 MFG에서 동작한다. 기본적으로 DGL 빌트인 뉴럴 네트워크 모듈의 입력 그래프와 피쳐는 아래 경우들 중에 하나를 만족해야 한다.
- 입력 피쳐가 텐서들의 쌍인 경우, 입력 그래프는 단방향 이분(unidirectional bipartite) 그래프이어야 한다.
- 입력 피쳐가 단일 텐서이고 입력 그래프가 MFG인 경우, DGL은 자동으로 출력 노드의 피쳐를 입력 노드 피처의 첫 몇개의 행으로 정의한다.
- 입력 피쳐가 단일 텐서이고 입력 그래프가 MGF가 아닌 경우, 입력 그래프는 반드시 homogeneous여야 한다.
다음 코드는 :class:`dgl.nn.pytorch.SAGEConv` 을 PyTorch로 단순하게 구현한 것이다. (MXNet이나 TensorFlow 버전도 제공함. (이 코드는 normalization이 제거되어 있고, mean aggregation만 사용한다.)
.. 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_ko-nn` 은 단방향 이분 그래프, homogeneous 그래프와 MFG에 적용되는 :class:`dgl.nn.pytorch.SAGEConv` 를 자세히 다루고 있다.