文件历史

提交图

705 次代码提交

作者 SHA1 备注 提交日期
czkkkkkk dd4335c342 [Sparse][Compile] Add GAT example 2023-03-17 09:37:52 +00:00
czkkkkkk 2dee62b521 [Sparse] Support torchscript 2023-03-17 09:20:49 +00:00
Minjie Wang 8d99d30a82 add a link about the removed TGN example (#5456) 2023-03-15 22:08:38 +08:00
DominikaJedynak b7ce4b6a0c Tensorflow examples fix (#5433) 2023-03-09 10:38:19 +08:00
Tingyu Wang bcf9923b32 [Model] Add dgl.nn.CuGraphSAGEConv model (#5137)
* add CuGraphSAGEConv model

* fix lint issues

* update model to reflect changes in make_mfg_csr(), move max_in_degree to forward()

* lintrunner

* allow reset_parameters()

* remove norm option, simplify test

* allow full graph fallback option, add example

* address comments

* address reviews

---------

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2023-02-22 13:43:28 +08:00
Hongzhi (Steve), Chen 9fe5092c17 lintrunner (#5326)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal>
2023-02-19 22:50:07 +08:00
Hongzhi (Steve), Chen 704bcaf6dd examples (#5323)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal>
2023-02-19 08:35:15 +08:00
Tingyu Wang 19b3cea166 [Model] Update CuGraphRelGraphConv to use pylibcugraphops=23.02 (#5217)
* update cugraph_relgraphconv

* update equality test

* update cugraph rgcn example

* update RelGraphConvAgg based on latest API changes

* enable fallback option to fg when fanout is large

---------

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2023-02-15 20:11:20 +08:00
Hongzhi (Steve), Chen b3308ae795 Cleanup mock_sparse related code. (#5230)
* remove_mock_sparse_example

* mock_sparse_test

* remove_mock_sparse

---------

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2023-02-01 15:17:14 +08:00
Hongzhi (Steve), Chen 30fb03a6bc Update example with spmatrix. (#5219)
* update

* graph

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2023-01-20 15:39:55 +08:00
Xin Yao cdfd1e382f Delete train_sampling_unsupervised.py (#5161) 2023-01-12 11:15:48 -08:00
peizhou001 56ffb650fe [API Deprecation]Deprecate contrib module (#5114) 2023-01-06 20:16:01 +08:00
peizhou001 436de3d120 [API Deprecation] Remove _dataloading and tgcn example (#5118) 2023-01-06 19:51:55 +08:00
peizhou001 c55ab2d147 deprecate candidates in dataloader (#5117) 2023-01-06 16:18:32 +08:00
Chang Liu a506ebe82b [Example][Refactor] Multi-gpu graphsage link prediction example refactor (#5091) 2023-01-05 20:59:39 +08:00
rudongyu ec3934d0d1 [Example] Sparse Graph Transformer (#5069)
* gt example

* update

* update

* update

* update

* lint

* Update examples/sparse/graph_transformer.py

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

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2023-01-05 08:50:38 +08:00
Mufei Li 9169fc3541 [Sparse] Polish sparse matrix creation functions (#5093)
* update

* Update

* Update

* Update

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
2023-01-03 22:59:57 +08:00
Mufei Li 37bd092587 [Sparse] Namespace migration and doc update (#5088)
* update

* lint

* lint

* comments

Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
2022-12-29 20:34:29 +08:00
Minjie Wang 025e43210f [Sparse] Add tests for sparse examples; Migrate from mock_sparse to mock_sparse2 (#5073)
* pass gcn

* example tests

* pass gcnii, hgnn, sgc, sign

* black

* test file

* add torchmetrics

* migrate appnp, c_and_s, twirls

* fix style

* minor fix

* fix hypergraphatt and twirls

* pass gat

* fix torchmetric

* lintrunner

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2022-12-29 08:55:25 +08:00
Hongzhi (Steve), Chen bda6a816be rename (#5058)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2022-12-28 13:27:52 +08:00
paoxiaode 6bd8175890 [Sparse] GCNII example (#5008) 2022-12-18 14:44:22 +08:00
Hongzhi (Steve), Chen 236fac4fb9 [Misc] Small fix in sparse GCN example (#5006)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2022-12-12 15:30:49 +08:00
paoxiaode e28f07812b [Sparse] GCN Example (#4996)
* add GCN sparse matrix example

* refine GCN example

* refine GCN example

* change train function

* [Bugfix] Turn off `use_alternate_stream` when TensorAdaptor is not enabled (#4987)

* turn off use_alternate_stream when tensoradaptor is not enabled

* add docstring

* Update (#4997)

Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>

* refine GCN example

* add GCN sparse matrix example

* refine GCN example

* refine GCN example

* change train function

* refine GCN example

* add highlight comment

* refine code

* refine code

* refine by black and flake8

* refine the comment to 80 char length

* refine the comment

* refine comment

Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
2022-12-09 09:19:38 +08:00
Minjie Wang c604366d4c [Sparse][Example] Add TWIRLS example in sparse API (#4922)
* add twirls

* update attention part

* update; add val_like to mock_sparse

* black
2022-12-05 16:56:21 +08:00
Dylan b84de903a2 GCN example correction (#4969) (#4976)
Correction like mentioned in #4969 

I noticed that there is a normalisation step on line 97 while the normalised values are not used downstream. Even if this was meant to show the normalisation step, it would not be calculating the normalisation step described in the CGN paper. The paper considers both in and out degrees while the normalisation in the code only describes normalisation using the in degrees.
In the end, the normalised values are assigned to g.ndata["norm"] but these values are not used afterwards.

Having a normalisation step here is also unnecessary since the GraphConv layer that is used already takes care of the normalisation. https://docs.dgl.ai/en/0.9.x/_modules/dgl/nn/pytorch/conv/graphconv.html#GraphConv

It confused me for a second thinking that I had to do the normalisation myself but this is already handled by the GraphConf.
2022-12-05 10:00:57 +08:00
Tingyu Wang 943abba3fb [Example] add entity_sample example of using CuGraphRelGraphConv (#4827)
* add entity_sample example

* update message

* address review, update api call

* Update examples/pytorch/rgcn/entity_sample_cugraph_relgraphconv.py

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

* Update examples/pytorch/rgcn/entity_sample_cugraph_relgraphconv.py

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

* Update examples/pytorch/rgcn/entity_sample_cugraph_relgraphconv.py

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

* address review

* move example and add description

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2022-12-01 21:09:14 +08:00
Mufei Li a5a0d9ed9d [Sparse] C&S Example (#4963)
* Update

* Update

* Update

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
2022-12-01 18:35:53 +08:00
peizhou001 611393021a [API Deprecation] Remove candidates in DGLGraph (#4946) 2022-12-01 16:41:53 +08:00
Quan (Andy) Gan 1edc92336b [Example] Hypergraph attention (#4941)
* hypergraph attention

* address comments
2022-11-28 20:12:37 +08:00
Mufei Li 7469bc9284 [Sparse] GAT Example (#4955)
* Update

* Update

* Update

* CI

Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
2022-11-28 19:23:23 +08:00
Hongzhi (Steve), Chen 0b9f64d607 small (#4954)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2022-11-25 17:56:15 +08:00
Hongzhi (Steve), Chen 226d1159a9 [Misc] Auto fix by black. (#4952)
* black on explain_main

* isort

* add dot

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2022-11-25 09:24:44 +08:00
Hongzhi (Steve), Chen f118ea9537 black (#4951)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2022-11-25 09:19:17 +08:00
Mufei Li c53deb26ab [Sparse] APPNP example (#4919)
* Update

* Update

* Update

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
2022-11-23 14:30:30 +08:00
Mufei Li 61fa640193 [Sparse] SGC example (#4918)
* Update

* Update

* Update

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal>
2022-11-22 17:38:27 +08:00
Quan (Andy) Gan 59f3d6e0b2 [Sparse] Add HGNN example (#4917)
* hgnn example

* desc

* update example index

* address

* replace naming

* address comments
2022-11-22 01:07:05 +08:00
Hongzhi (Steve), Chen 0c70bc23f4 [Sparse] Refactor SIGN model. (#4921)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2022-11-21 23:22:58 +08:00
Hongzhi (Steve), Chen 53895b958a [Sparse] SIGN example. (#4908)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2022-11-17 16:41:35 +08:00
Rhett Ying b377e1b9c1 [Dist][Examples] refactor dist graphsage examples (#4269)
* [Dist][Examples] refactor dist graphsage examples

* refine train_dist.py

* update train_dist_unsupervised.py

* fix debug info

* update train_dist_transductive

* update unsupervised_transductive

* remove distgnn

* fix join() in standalone mode

* change batch_labels to long() for ogbn-papers100M

* free unnecessary mem

* lint

* fix lint

* refine

* fix lint

* fix incorrect args

* refine
2022-11-17 08:35:15 +08:00
peizhou001 3132da2826 Deprecate (#4864)
rename DGLHeteroGraph to DGLGraph
2022-11-15 10:01:01 +08:00
Chang Liu 6566c31fba Fix ogb/ogbn-mag/heter-RGCN example (#4839)
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2022-11-09 14:08:01 +08:00
Ereboas 7c788f531c [Example] Update SEAL+NGNN for ogbl-citation2 (#4776)
* Use black for formatting

* limit line width to 80 characters.

* Use a backslash instead of directly concatenating

* file structure adjustment.

* file structure adjustment(2)

* codes for citation2

* format slight adjustment

* adjust format in models.py

* now it runs normally for all datasets.

* add comments; adjust code order.

* adjust indenting.

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2022-11-03 10:24:03 +08:00
Ereboas f9805ef11c [Example] SEAL+NGNN for ogbl-citation2 (#4772)
* Use black for formatting

* limit line width to 80 characters.

* Use a backslash instead of directly concatenating

* file structure adjustment.

* file structure adjustment(2)

* codes for citation2

* format slight adjustment

* adjust format in models.py

* now it runs normally for all datasets.

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2022-10-28 00:31:24 +08:00
Mufei Li ec17136e6e [Deprecation] Examples (#4751)
* 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>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>
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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
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)

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

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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>
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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
Co-authored-by: Vibhu Jawa <vibhujawa@gmail.com>
2022-10-26 21:13:00 +08:00
Chendi.Xue e682fa74ba [EXAMPLE]Add device support in hetero_rgcn (#4677)
* Add device support in hetero_rgcn

Signed-off-by: Xue, Chendi <chendi.xue@intel.com>

* use num_workers instead of hard code and enable cpu_affinity for pytorch > 1.12

Signed-off-by: Xue, Chendi <chendi.xue@intel.com>

* Remove hard code num_workers and use dgl version to check if cpu_affinity is supported

Signed-off-by: Xue, Chendi <chendi.xue@intel.com>

* Remove specified dl_cores and computer_cores

Add error print if num_workers are miss set

Signed-off-by: Xue, Chendi <chendi.xue@intel.com>

* expected num_workers should be less than num_physical_cores

Signed-off-by: Chendi Xue <chendi.xue@intel.com>

* Update examples/pytorch/ogb/ogbn-mag/hetero_rgcn.py

Co-authored-by: Chang Liu <chang.liu@utexas.edu>

* Remove dgl version and num_workers print

Signed-off-by: Xue, Chendi <chendi.xue@intel.com>

* add comment to explain is_support_affinity

* Fix typo

Signed-off-by: Xue, Chendi <chendi.xue@intel.com>

Signed-off-by: Xue, Chendi <chendi.xue@intel.com>
Signed-off-by: Chendi Xue <chendi.xue@intel.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
2022-10-21 17:03:43 -07:00
Chang Liu 98792a8ae3 [Example][Refactor] Refactor RGAT example (#4530)
* RGAT refactor

* File rename

* Address comments

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
2022-10-18 21:49:24 +08:00
Mufei Li e452179c88 [Deprecation] Dataset Attributes (#4666)
* 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>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>
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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
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

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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>
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>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
Co-authored-by: Vibhu Jawa <vibhujawa@gmail.com>
2022-10-13 11:12:45 +08:00
彭卓清 5b2d44faaa [Model] BiPointNet (#4434)
* initial completion

* add binary version of pointnet and pointnet++

* add binary version of pointnet and pointnet++

* add binary version of pointnet and pointnet++

* add binary version of pointnet and pointnet++

* add binary version of pointnet and pointnet++

* finish README

* fix suggestions

* fix suggestions

* fix suggestions

* solve details

* resolve formatting issues

* add accuracy

* revert the changes

Co-authored-by: Tong He <hetong007@gmail.com>
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
2022-10-08 21:24:16 +08:00
Hongzhi (Steve), Chen be8763fa65 [Misc] Black auto fix. (#4679)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
2022-10-08 11:59:37 +08:00
Chang Liu 72cfb9342f [Example][Refactor] RGCN link prediction example refactor (#4548) 2022-09-30 12:57:50 -07:00