66eb240d15
[Bugfix] Include NCCL as a submodule ( #2934 )
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* Add NCCL as a submodule
* Allow using third_party/nccl or system nccl
* Add nccl_external as a dependency
* Fix conditional
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-25 09:46:16 +08:00
06b9ec2e8e
[Doc] Add two papers to awesome paper list ( #2936 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
* Update data.rst
* image in dataset userguide
* update links using ref
* modify the link of save_graphs and load_graphs in dataset user guide
* move image to s3 server.
* fix links and ref
* Hide implementations that may cause confusions to the user
* add papers
* fix number of classes in Amazon Cobuy datasets
* add two papers to Awesome paper list
* Update README.md
* add four papers
* add two papers
* Add awesome papers
* Fix index in paper list
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-05-24 14:38:12 +08:00
c46602d7d8
[Doc] Fix a typo in the tutorial for link prediction ( #2928 )
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Fix a typo in the tutorial for "Link Prediction using Graph Neural Networks".
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-05-23 22:43:45 +08:00
ae8dbe6d3c
[Feature][Performance] Implement NCCL wrapper for communicating NodeEmbeddings and sparse gradients. ( #2825 )
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* Split NCCL wrapper from sparse optimizer and sparse embedding
* Add more unit tests for single node nccl
* Fix unit test for tf
* Switch to device histogram
* Fix histgram issues
* Finish migration to histogram
* Handle cases with zero send/recieve data
* Start on partition object
* Get compiling
* Updates
* Add unit tests
* Switch to partition object
* Fix linting issues
* Rename partition file
* Add python doc
* Fix python assert and finish doxygen comments
* Remove stubs for range based partition to satisfy pylint
* Wrap unit test in GPU only
* Wrap explicit cuda call in ifdef
* Merge with partition.py
* update docstrings
* Cleanup partition_op
* Add Workspace object
* Switch to using workspace object
* Move last remainder based function out of nccl_api
* Add error messages
* Update docs with examples
* Fix linting erros
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-05-20 10:58:17 -07:00
0e9259b472
Add ED-GNN to Awesome Papers in DGL. ( #2903 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-20 12:05:06 +08:00
5d7e80f413
[Feature] Add bruteforce implementation for KNN with O(Nk) space complexity ( #2892 )
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* add bruteforce impl
* add support for bruteforce-sharemem
* modify python API
* add tests
* change file path
* change python API
* fix lint
* fix test
* also check worst_dist in the last few dim
* use heap and early-stop on CPU
* fix lint
* fix lint
* add device check
* use cuda function to determine max shared mem
* use cuda to determine block info
* add memory free for tmp var
* update doc-string and add dist option
* fix lint
* add more tests
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-05-19 18:27:43 +08:00
db0fb4eaef
Update README.md ( #2927 )
...
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-05-19 15:45:07 +08:00
1968adbaf7
Update README.md ( #2924 )
2021-05-19 15:18:39 +08:00
6e7f19f27b
[Distributed] add distributed in-degree and out-degree. ( #2918 )
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* add distributed in-degree and out-degree.
* update comments.
* fix a bug.
* add tests.
* add tests.
* fix a bug.
* fix docstring.
* update doc.
* fix
* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-05-18 19:46:09 +08:00
50492d56a8
Fixing issue #2921 ( #2922 )
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* fixing #2921
* fixing #2921
2021-05-18 09:54:38 +08:00
c018436588
[Example] add latent dirichlet allocation ( #2883 )
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* add lda model
* tweak latent dirichlet allocation
* Update README.md
* Update README.md
* update example index
* update header
* minor tweak
* add example test
* update doc
* Update README.md
* Update README.md
* add partial_fit for free
* Update examples/pytorch/lda/lda_model.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* Update examples/pytorch/lda/example_20newsgroups.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* Update lda_model.py
* bugfix torch Gamma uses rate parameter
Co-authored-by: Yifei Ma <yifeim@amazon.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-17 20:25:36 +08:00
657c220de7
[Feature] Python interface for adjacency matrix summation and multiplication ( #2893 )
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* test commit
* fixes
* oops
* add docs
* lint
* why does it say I have a trailing whitespace
* oh ok
* fixes
* why there's an invalid argument error
* address comments
* fix
* address comments
2021-05-17 19:47:02 +08:00
29fec7d5db
Update README.md ( #2920 )
2021-05-17 17:30:26 +08:00
7c7113f660
add use_ddp to dataloaders ( #2911 )
2021-05-17 15:46:02 +08:00
b03077b60d
[NN] GCNII model added < https://arxiv.org/pdf/2007.02133.pdf > ( #2874 )
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* Auto stash before rebase of "origin/pytorch-nn-working"
GCNII model added
* linting
* linting
* lint
* Frequency Adaptive gcn init comit
* Revert "Frequency Adaptive gcn init comit"
This reverts commit 86a80586ac0040497c1edfa0e80df719992dcc4a.
* Update python/dgl/nn/pytorch/conv/gcn2conv.py
modified docstring
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* added beta formula and changed param name
* fix docstring
* lint
* white space lint
* update docstring
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* docstring formula update
* added gcn2
* added GCN2Conv
* Update nn.pytorch.rst
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-17 10:25:59 +08:00
ac1536cf92
[Feature] add udf support for cross_reducer ( #2891 )
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* add: udf support for `cross_reducer`
* update: code lint
* update: reducer without stack
* docs: add docs for udf cross_reducer
* chore: fix code lint
* docs: update multi_update_all docstring
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* docs: update reduce_dict_data docstring
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-15 14:00:37 +08:00
9983107384
[Feature] Support multidimensional features for GAT ( #2912 )
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* support multidimensional features for GAT
* docstring
* lint
* fix
2021-05-15 02:47:23 +08:00
caa6d6072c
[Feature] Replacing thread_wrapped_func with minimal mp.Process wrapper ( #2905 )
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* standardizing thread_wrapped_func
* lints
* Update __init__.py
2021-05-14 11:34:49 +08:00
a90296aa9c
fix. ( #2907 )
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Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
2021-05-13 16:55:31 +08:00
e156331b0e
return a list of ntypes/etypes ( #2742 )
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Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-05-13 10:42:50 +08:00
85231dc93b
[Example] Label Propagation and Correct&Smooth ( #2852 )
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* [example] label propagation and correct&smooth
* update
* update
* update
* update
* [docs] add speed for c&s
* update
* [fix] remove gat&consistent with the author's code
* [feat] multi-type adj norm supported
* update
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-05-12 18:45:46 +08:00
5de4edd1fa
[Regression] Add replace_branch.py ( #2884 )
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* fix
* fix
* debug
* fix
* fix
* fix
* fix
* ci
* fix
* fix
* remove duplicate instruction
* need this file in the main branch
* add nightly
* Delete nightly.jenkins
2021-05-12 17:19:35 +08:00
d70ca6eb7c
[Example] graphsaint ( #2792 )
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* graphsaint
* graphsaint
* graphsaint
* graphsaint
* fixed the model
* fixed some bugs
* fixed the computing of normalization and updated the results
* fixed some bugs and updated the results
* Update utils.py
* Update train_sampling.py
* Update train_sampling.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-11 16:25:56 +08:00
103444c58f
Remove __len__ method from DGLGraph ( #2902 )
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* Update heterograph.py
* remove unit tests
* replace tutorial
2021-05-11 14:06:18 +08:00
70695ff8f8
[Model] Training GraphSAGE with PyTorch Lightning ( #2878 )
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* pytorch lightning initial examples
* revert most changes in dataloader to favor #2886 .
* address comments
2021-05-11 11:28:13 +08:00
c18f957d0e
[Model] add implementation of twirls ( #2770 )
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* add implementation of twirls
* format the code
* fix some format error, and ignore others
* fix format errors
* fix format errors
* expose unfolding & attention
* Update nn.pytorch.rst
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-11 09:58:48 +08:00
2a3a9a0011
[Bugfix] to() method ignores PyTorch default CUDA device ( #2897 )
2021-05-08 13:23:30 +08:00
bfef789ea1
[Dataloading] Make loader iters iterator ( #2886 )
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* Make loader items iterator
* Update test_dataloader.py
* Update __init__.py
* Update test_dataloader.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-07 10:15:49 +08:00
fbfcf1a8cc
Doc: adapt send_and_recv example ( #2822 )
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* adapt send_and_recv example
* lint fix
* Change title and example order
* Update heterograph.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-07 09:44:11 +08:00
5498cf051e
[Doc]Fix examples on negative graph sampler ( #2863 )
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* Fix examples on negative graph sampler
In heterogeneous graph, the old example may build a negative graph without edges. In dgl.dataloading.dataloader line637, it shows the key of neg_edges dict should be item in g.canonical_etypes.
* poke ci
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-06 21:34:31 +08:00
241b60d489
[Feature][Performance] Accelerate kNN on GPU ( #2868 )
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* topk kNN accelerated on GPU
* Fix src offset
* Fix trailing whitespace
* Update segmented kNN
* Fix src / dst mixup
* Update kNN docstrings
* Fixed lint
Co-authored-by: Tong He <hetong007@gmail.com >
2021-05-06 14:14:09 +08:00
975eb8fc5d
[Distributed] Distributed node embedding and sparse optimizer ( #2733 )
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* Draft for sparse emb
* add some notes
* Fix
* Add sparse optim for dist pytorch
* Update test
* Fix
* upd
* upd
* Fix
* Fix
* Fix bug
* add transductive exmpale
* Fix example
* Some fix
* Upd
* Fix lint
* lint
* lint
* lint
* upd
* Fix lint
* lint
* upd
* remove dead import
* update
* lint
* update unitest
* update example
* Add adam optimizer
* Add unitest and update data
* upd
* upd
* upd
* Fix docstring and fix some bug in example code
* Update rgcn readme
Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-210.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal >
2021-05-03 08:37:40 +08:00
2d372e35e2
[Distributed] Kill training jobs in distributed training ( #2881 )
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* kill training jobs.
* update.
* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-73-81.ec2.internal >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-05-01 12:21:29 +08:00
45ec21b033
[Distributed] fix docs for distributed training. ( #2840 )
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* update distributed training doc.
* explain data split.
* fix message passing.
* id mapping.
* fix.
* test data reshuffling.
* fix a bug.
* fix test.
* Revert "fix test."
This reverts commit 907f1dd88994894db94ffcd77b5995279f76b489.
* Revert "fix a bug."
This reverts commit ff0a4d893bbe4911a75ecb04bcbd9bc65315166b.
* Revert "test data reshuffling."
This reverts commit 99bb2f6405de67fc73652220b02e7184461c3e5e.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
2021-04-29 14:38:41 +08:00
703d4b93c0
Fix cu11 compile ( #2879 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-191.ec2.internal >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-04-28 22:02:01 +08:00
a38bf346db
[CI] Remove duplicate instruction by bot ( #2880 )
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* fix
* fix
* debug
* fix
* fix
* fix
* fix
* ci
* fix
* fix
* remove duplicate instruction
2021-04-28 19:21:35 +08:00
ab2bd1f13d
[Feature] Add cuda support for Sparse Matrix multiplication, summation and masking ( #2782 )
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* init cuda support
* cuSPARSE err
* passed unittest for csr_mm/SpGEMM. int64 not supported
* Debugging cuSPARSE error 3
* csrgeam only supports int32?
* disabling int64 for cuda
* refactor and add CSRMask
* lint
* oops
* remove todo
* rewrite CSRMask with CSRGetData
* lint
* fix test
* address comments
* lint
* fix
* addresses comments and rename BUG_ON
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-30-71.ec2.internal >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-04-27 16:06:35 +08:00
e18c2ab408
[NN] Fix GATConv for Broadcasting with Residual Connections ( #2867 )
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* Update
* update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-59-108.us-west-2.compute.internal >
2021-04-27 14:36:06 +08:00
b2b531e041
[Example] add implementation of grace ( #2828 )
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* [Example] add implementation of grace
* [Doc] add grace in the index file
* fix
* fix typos
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-04-27 12:43:03 +08:00
e7046f1e0e
[Distributed] Fix a bug in graph partition. ( #2869 )
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* update distributed training doc.
* explain data split.
* fix message passing.
* id mapping.
* fix.
* test data reshuffling.
* fix a bug.
* fix test.
* Revert "fix."
This reverts commit 2d025e9e1a5c05c3da9b803a035a788ced59bd77.
* Revert "id mapping."
This reverts commit 2a6a93ceb81fbdff86e6e9e5a58e1ace1e9d9882.
* Revert "fix message passing."
This reverts commit ed8a86bf2b015e5e4f64ba160e81b207ad2a1d65.
* Revert "explain data split."
This reverts commit 4338ddf8a336014cf92d4cb9a1db02b9badc0e55.
* Revert "update distributed training doc."
This reverts commit dda1c35c44536934c19715534f01f832afda6ad2.
* add more tests.
* fix.
* fix.
* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-04-26 18:17:16 +08:00
2ae891a78c
Update main.py ( #2872 )
2021-04-26 17:12:19 +08:00
756fdd8e90
[Example] DeeperGCN ( #2831 )
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* [example] deepergcn
* update
* update
* update
* update
* update
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-04-25 18:37:41 +08:00
1fe0860750
[Bugfix] Fixes #2844 ( #2847 )
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Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-04-25 18:12:17 +08:00
66182b28ad
[Serialization] Better error message when idx_list out of bound ( #2848 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-04-25 17:27:54 +08:00
c37e036432
[Bug Fix] Fix sparse opt bug ( #2859 )
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* Fix #2856
* upd
* Fix unitest
* upd
* upd
* upd
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal >
2021-04-25 13:40:21 +08:00
3c387988d7
[Example] DCRNN and GaAN ( #2858 )
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* Ready for PR
* refractor code
Co-authored-by: Ubuntu <ubuntu@ip-172-31-45-47.ap-northeast-1.compute.internal >
Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com >
2021-04-23 22:33:39 +08:00
3075b277aa
[CI] Fix regression trigger ( #2862 )
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* fix
* fix
* debug
* fix
* fix
* fix
* fix
* ci
* fix
* fix
2021-04-23 15:47:32 +08:00
ebc6a85a80
[Bugfix] TGN model bugfix and improvement ( #2860 )
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* Add DCRNN Example
* Bugfix DCRNN
* Bugfix DCRNN
* Bugfix Train/eval have different flow
* Performance Matched
* modified tgn for research
* kind of fixed 2hop issue
* remove data
* bugfix and improve the performance
* Refractor Code
Co-authored-by: Ubuntu <ubuntu@ip-172-31-45-47.ap-northeast-1.compute.internal >
Co-authored-by: Tianjun Xiao <xiaotj1990327@gmail.com >
2021-04-23 15:44:22 +08:00
d76af4d4c1
[Distributed] Return the ID mapping in graph partitioning. ( #2857 )
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* return mapping.
* support heterogeneous graph.
* more test.
* fix lint.
* fix for diff backends.
* fix.
* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-04-22 17:51:42 +08:00
6b022d2fe2
[Sampler] BiasedChoice sampler ( #1665 )
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* update
* update
* update
* update
* update
* update
* update
* fix
* fix
* update
* doc
* doc
* fix
* fix
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-04-22 15:12:52 +08:00
nv-dlasalle