36c6c64957
Replace QM9_v2 with built-in QM9Edge Dataset ( #3026 )
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Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-06-16 14:35:40 +08:00
305d5c16df
[Example] update ogbn-arxiv and ogbn-proteins results ( #3018 )
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* [Example] GCN on ogbn-arxiv dataset
* Add README.md
* Update GCN implementation on ogbn-arxiv
* Update GCN on ogbn-arxiv
* Fix typo
* Use evaluator to get results
* Fix duplicated
* Fix duplicated
* Update GCN on ogbn-arxiv
* Add GAT for ogbn-arxiv
* Update README.md
* Update GAT on ogbn-arxiv
* Update README.md
* Update README
* Update README.md
* Update README.md
* Add GAT implementation for ogbn-proteins
* Add GAT implementation for ogbn-proteins
* Add GAT implementation for ogbn-proteins
* Add GAT implementation for ogbn-proteins
* Add GAT implementation for ogbn-proteins
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Update examples for ogbn-arxiv
* Add examples for ogbn-products.
* Update examples for ogbn-proteins.
* Update examples for ogbn-proteins.
* Update examples for ogbn-proteins.
* Update examples for ogbn-proteins.
* Update examples for ogbn-proteins.
* Update examples for ogbn-proteins.
* Update examples for ogbn-proteins.
* Update examples for ogbn-proteins.
* Update examples for ogbn-proteins.
* Update examples for ogbn-products.
* Update examples for ogbn-products.
* Update examples for ogbn-arxiv.
* Update examples for ogbn-arxiv.
* Update examples for ogbn-arxiv.
* Update examples for ogbn-proteins.
* Update examples for ogbn-products.
* Update examples for ogbn-proteins.
* Update examples for ogbn-arxiv.
* Update examples for ogbn-proteins.
* Update README.md
* [Example] ogbn-arxiv & ogbn-proteins
* [Example] ogbn-arxiv & ogbn-proteins
* [Example] ogbn-arxiv & ogbn-proteins
* [Example] ogbn-arxiv & ogbn-proteins
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: Zihao Ye <expye@outlook.com >
2021-06-16 12:33:43 +08:00
8932285652
[bugfix] Fix sparse_optim when the state is stored on the CPU ( fixes #2760 ) ( #3013 )
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* Fix sparse optimizer to wait on copies to the CPU
* Fix linting
* Fix typo
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-06-15 11:37:32 -07:00
b4ad59d77f
[Model] reformat and update performance of grace ( #3009 )
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* reformat and update performance
* Update README.md
* Fix typos
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-06-15 17:02:37 +08:00
63aed58204
[Doc] Fix typo in DGL base dataset class ( #2977 ) #3017
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-15 16:15:52 +08:00
64d0f3f355
[Feature] Add NN-descent support for the KNN graph function in dgl ( #2941 )
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* add bruteforce impl
* add nn descent implementation
* change doc-string
* remove redundant func
* use local rng for cuda
* fix lint
* fix lint
* fix bug
* fix bug
* wrap nndescent_knn_graph into knn
* fix lint
* change function names
* add comment for dist funcs
* let the compiler do the unrolling
* use better blocksize setting
* remove redundant line
* check the return of the cub calls
Co-authored-by: Tong He <hetong007@gmail.com >
2021-06-15 14:25:02 +08:00
a303f07819
fix #2952 ( #3010 )
2021-06-14 15:09:14 +08:00
17141dd372
[Fix] Fix to_homo for graph with zero nodes ntype ( #3011 )
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* fix #2870
* lint
* fix
2021-06-14 14:34:13 +08:00
8b64ae59b8
[Performance] Perform to_block on the GPU when the dataloader is created with a GPU device. ( #3016 )
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* add output device for dataloading
* Update dataloader
* Get sampler device from dataloader
* Fix line length
* Update examples
* Fix to_block GPU for empty relation types
* Handle the case where the DistGraph has None for the underlying graph
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-06-13 18:51:00 +08:00
79b057f0cf
Fix example to test_acc is always computed at last epoch ( #3014 )
2021-06-12 18:02:00 -07:00
2570d412f9
[NN] Add fast path for GateGCNConv when it has only one edge type ( #2994 )
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* fix gatedgcn
* fix lint
2021-06-12 01:13:18 +08:00
411bef5498
[CPU, Parallel] parallel_for with default grain size ( #3004 )
2021-06-11 17:09:30 +08:00
17d604b5c7
[Feature] Allow using NCCL for communication in dgl.NodeEmbedding and dgl.SparseOptimizer ( #2824 )
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* Split from NCCL PR
* Fix type in comment
* Expand documentation for sparse_all_to_all_push
* Restore previous behavior in example
* Re-work optimizer to use NCCL based on gradient location
* Allow for running with embedding on CPU but using NCCL for gradient exchange
* Optimize single partition case
* Fix pylint errors
* Add missing include
* fix gradient indexing
* Fix line continuation
* Migrate 'first_step'
* Skip tests without enough GPUs to run NCCL
* Improve empty tensor handling for pytorch 1.5
* Fix indentation
* Allow multiple NCCL communicator to coexist
* Improve handling of empty message
* Update python/dgl/nn/pytorch/sparse_emb.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
* Update python/dgl/nn/pytorch/sparse_emb.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
* Keepy empty tensor dimensionaless
* th.empty -> th.tensor
* Preserve shape for empty non-zero dimension tensors
* Use shared state, when embedding is shared
* Add support for gathering an embedding
* Fix typo
* Fix more typos
* Fix backend call
* Use NodeDataLoader to take advantage of ddp
* Update training script to share memory
* Only squeeze last dimension
* Better handle empty message
* Keep embedding on the target device GPU if dgl_sparse if false in RGCN example
* Fix typo in comment
* Add asserts
* Improve documentation in example
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-06-10 21:19:00 -07:00
9497a9be85
[Bugfix][Examples] Fix graphsage multigpu training example training set size ( #3002 )
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* Make multigpu graphsage use whole datset
* Specify queeze dimension
* Remove squeeze dimension
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-06-10 16:35:08 -07:00
5be937a7fb
[Kernel] Slicing Batched Graphs ( #2965 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Add files via upload
* Add files via upload
* Add files via upload
* Add files via upload
* Update
* Update
* Add files via upload
* Add files via upload
* Update
* Lint
* Add files via upload
* Lint
* Update
* Update
* Update
* Update
* Update
* Lint Fix
* Lint
Co-authored-by: Ubuntu <ubuntu@ip-172-31-12-161.us-west-2.compute.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-06-10 12:07:44 +08:00
ba1549244c
[Performance][Kernel] Eliminating ctor&dtor zand IsNullArray overhead in random walks ( #2990 )
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* Added a special implementation for MetapathBasedRandomWalkStep for the Uniform randomwalk case
* Fixed all linting issues
* add comment
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-06-10 10:10:15 +08:00
f91a97d067
[Dataloader] Fix compatibility of DistributedSampler for older PyTorch versions ( #2997 )
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* fix compatibility
* fix
* lint
2021-06-09 20:14:26 +08:00
a7fe461c1c
[Doc] Single-machine Multi-GPU node classification tutorial ( #2976 )
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* multi-GPU node classification tutorial
* Update 2_node_classification.py
* fixes
* elaborate a bit more
* address comments
* address comments
2021-06-08 10:28:02 +08:00
6c59fee99b
[Model] HetGNN/GTN/HAN/NSHE/MAGNN examples ( #2993 )
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* commit hetgnn
* Update README.md
* Delete examples/pytorch/hetgnn directory
* Update README.md
* Update README.md
* Update README.md
* Revert "Update README.md"
This reverts commit 14cdb3da76c58665ff879eae17ecf9eb28b66cce.
* Update README.md
* Add files via upload
* Update README.md
* Update README.md
2021-06-08 08:54:27 +08:00
fd72df9a3d
add Contrast-Reg to awesome papers ( #2991 )
2021-06-07 14:43:12 +08:00
972a9f1323
[Doc] Re-organize the code for dgl.geometry, and expose it in the doc ( #2982 )
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* reorg and expose dgl.geometry
* fix lint
* fix test
* fix
2021-06-07 11:19:39 +08:00
e20d895324
[CPU Parallel] implementation of parallel_for with grain size ( #2972 )
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* [CPU Parallel] implementation of parallel_for with grain size
* Create parallel_for.h
* Update parallel_for.h
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-06-06 21:09:24 +08:00
895d6fff72
[Doc] changing of output dimension ( #2981 )
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Co-authored-by: zhjwy9343 <6593865@qq.com >
2021-06-05 22:12:41 +08:00
e2a28a6c8e
[Doc] Revised Two Issues in Message Passing Tutorial ( #2983 )
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* [Doc] modify the dimension of weight to Numpy broadcasting rule
* [Doc] modify the user defined reduce function
Co-authored-by: zhjwy9343 <6593865@qq.com >
2021-06-05 18:54:31 +08:00
849cbec6ee
[Feature] add positive negative statistics ( #2984 )
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Co-authored-by: zhjwy9343 <6593865@qq.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-06-05 15:48:11 +08:00
6e9d16459e
[Fix] Fixed AttributeError with new version of torchtext (0.9+). ( #2985 )
2021-06-05 02:01:20 +08:00
b1628f2398
[Tutorial] Distributed node classification. ( #2969 )
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* add init version.
* fix build.
* fix format.
* fix.
* fix.
* fix format.
* update README.
* avoid running CI on distributed training tutorials.
* Update tutorials/dist/1_node_classification.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
* fix.
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-06-04 21:50:16 +08:00
6a56562a7c
[CI] Use k8s cluster ( #2957 )
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* add
* fix
* set default
* fix
* try master
* try fix
* try
* fix
* 111
* fix
* fix
* update
* ccc
* try
* fix
* fix
* try new machine
* fix
* fix
* fix
* Revert "fix"
This reverts commit e716d66b046f92fe7ae368947a51a036a7a3188a.
* try
* more parrallel
* use k8s for all
* fix name
* try not specify instance type
* ci
* use one yaml
* Revert "use one yaml"
This reverts commit 717d8d852be39fbf2e2e45f9f224aa97907c372c.
* add timeout
* fix permission
* mount efs
* print
* fix pvc
* fix
* restrict num of gpu instances
* check
* fix
* fix
2021-06-04 18:31:11 +08:00
2df4a95f3e
[Feature] Make to_heterogeneous(to_homogeneous(hg)) return hg ( #2958 )
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* make to_heterogeneous and to_homogeneous invertible
* docstring
* oops
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-06-03 18:50:18 +08:00
60426278bf
[Example] TAHIN ( #2864 )
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* tahin
* readme
* readme
* readme
* readme
* readme
* readme
* main
* main
* new_line
* update
Co-authored-by: zhjwy9343 <6593865@qq.com >
2021-06-03 16:03:55 +08:00
7e58236cc7
[Build] Fix NCCL building crashes when using submodules but with system NCCL installed ( #2975 )
2021-06-03 14:41:52 +08:00
75ec58260a
Add heterograph support in C kernels ( #2882 )
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* SpMM for heterograph
* C APIs SDDMM heterograph
* passes initial result
* renamed eid with nid
* aggregation on same ntype for multiple etypes
* fix link check failure
* lint check part 2
* lint check part 3
* Fixed SpMMCmpCsr Min op
* added mem references
* fixed fill(Max/Min), added const
* removed newline
* brought back docstring
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-06-03 12:14:25 +08:00
6383e64937
[Doc] correct the matrix multiplication symbols ( #2961 )
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* correct the matrix multiplication symbols
* modified dimensionality of linear
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-03 08:51:23 +08:00
7a816f4743
[Doc] Minor fix on the distributed training doc. ( #2968 )
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Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
2021-06-02 18:46:52 +08:00
f8d6bf8e07
[Test] Fix regression ram info ( #2964 )
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* fix regression ram info
* fix
2021-06-02 16:14:05 +08:00
0e964ea566
increase timeout for dgl.nn.NodeEmbedding TCPStore get/wait to 10 minutes ( #2967 )
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Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-06-02 14:56:42 +08:00
2ae190d690
[Doc] fix shape mismatch problem in user guide ( #2938 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-02 12:18:10 +08:00
527bbfa8ea
update nightly installation ( #2959 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-02 12:12:01 +08:00
22d0df8b6a
[Doc] Update link_predict.py docstring ( #2960 )
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corrected docstring, the model uses two R-GCN layers
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-02 12:08:28 +08:00
86ba2335c3
[Testing] Enable C++ tests on GPU ( #2945 )
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* Enable C++ tests on GPU
* Add missing '--runtime nvidia'
2021-06-01 11:39:57 -07:00
b8fe2b4837
[Feature][Sampler] Sort CSR by tag ( #1664 )
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* update
* update
* update
* update
* lint
* lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* lint
* update
* clone
* update
* update
* update
* update
* replace idarray with ndarray
* refactor cpp part
* refactor python part
* debug
* refactor interface
* test and doc
* lint and test
* lint
* fix
* fix
* fix
* const
* doc
* fix
* fix
* fix
* fix
* fix & doc
* fix
* fix
* fix
* fix
* fix
* fix
* update
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-01 23:33:56 +08:00
0437b16497
[Doc] Fix a typo in the tutorial for Neighbor Sampling ( #2935 )
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Fix a typo in the tutorial for "Introduction of Neighbor Sampling for GNN Training".
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-06-01 13:59:22 +08:00
fcfe52aee5
fix residual ( #2962 )
2021-06-01 13:50:39 +08:00
2ad7a9e9dd
[Fix] Fix #2808 ( #2917 )
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* Fix #2808
* fix
* fix
* fix
* fix
* fix
* fix
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-31 19:05:58 +08:00
09642d7c21
[Tutorial] Single Machine Multi-GPU Minibatch Graph Classification ( #2940 )
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* Update
* Update
* Update tutorials/multi/1_graph_classification.py
Co-authored-by: Tong He <hetong007@gmail.com >
* Update
* Update
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-4-21.us-west-2.compute.internal >
Co-authored-by: Tong He <hetong007@gmail.com >
2021-05-31 18:36:34 +08:00
9a0e13ac61
Speed up random number generation. ( #2953 )
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* speed up random number generation.
* fix lint.
* Fix
* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
2021-05-28 19:17:53 +08:00
b8b0fd22b2
[Feature] add two fraud datasets ( #2908 )
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* add two fraud dataset
* add comments and modify to heterogenous graph
* modify the node name based on datasets
* add assertion message
Co-authored-by: zhjwy9343 <6593865@qq.com >
2021-05-28 15:45:44 +08:00
64d2a2aff7
[Feature] fix #2876 , add two fake news datasets ( #2939 )
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* [Feature] fix #2876 , add two fake news datasets
* add name assertion
* add assertion message
Co-authored-by: zhjwy9343 <6593865@qq.com >
2021-05-28 14:29:26 +08:00
18dbaebebc
[Distributed] Specify the graph format for distributed training ( #2948 )
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* explicitly set the graph format.
* fix.
* fix.
* fix launch script.
* fix readme.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal >
2021-05-26 18:09:30 +08:00
1db4ad4fcc
Move pointer dereferencing in CDFSampler::draw() and AliasSampler::draw() to inside of conditional ( #2943 )
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Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-25 13:53:53 +08:00
Hengrui Zhang