b78acd67ce
[Doc] Add an official documentation of UnifiedTensor ( #3194 )
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* Add pytorch-direct version
* remove
* add documentation for UnifiedTensor
* Revert "add documentation for UnifiedTensor"
This reverts commit 63ba42644d4aba197c1cb4ea4b85fa1bc43b8849.
* add UnifiedTensor documentation
* Update python/dgl/contrib/unified_tensor.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: shhssdm <shhssdm@gmail.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-08-02 22:40:51 +08:00
213e27f05c
Bump nightly version ( #3146 )
2021-08-02 17:24:18 +08:00
100eb57c45
[Doc] Fix random_walk documentation inconsistency ( #3188 )
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* Update randomwalks.py
* Update randomwalks.py
FIx lint
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-08-02 16:16:29 +08:00
6001001fed
Improve usage of pinned memory in sparse_optimizer ( #3207 )
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Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-08-02 14:16:23 +08:00
8bc91414e9
[Distributed] Fix distributed training hang with multiple samplers ( #3169 )
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Rewrite the multiprocessing worker pool
2021-08-01 21:31:04 +08:00
a107993f10
[Model] add model example CARE-GNN ( #3187 )
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* [Model] add model example CARE-GNN
* update README
* improvements based on the review feedback
* fix missing item()
Co-authored-by: zhjwy9343 <6593865@qq.com >
2021-07-29 15:24:15 +08:00
c4791fd46e
[bugfix] fix default ntypes/etypes consistency between dgl.DGLGraph and dgl.graph ( #3198 )
2021-07-29 14:05:28 +08:00
cb4a83a233
[Distributed] Enable distributed EdgeDataLoader ( #3192 )
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* make heterogeneous find_edges
* add distributed EdgeDataLoader.
* fix.
* fix a bug.
* fix bugs.
* add tests on distributed heterogeneous graph sampling.
* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
2021-07-28 15:28:27 +08:00
ba7e7cf931
[New Feature] Per edge type sampler for to_homogeneous graphs. ( #3131 )
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* fix.
* fix.
* fix.
* fix.
* Fix test
* Deprecate old DistEmbedding impl, use synchronized embedding impl
* Basic imple of heterogeneous on homogenenous sampling
* make pass
* Pass C++ test
* Add python test code
* lint
* lint
* Add MultiLayerEtypeNeighborSampler
* Add unitest for single machine dataloader
* Add dist dataloader test for edge type sampler
* Fix lint
* fix
* support for per etype sample
* Fix some bug and enable distributed training with per edge sample
* fix
* Now distributed training works
* turn off some mxnet
* turn off mxnet for some dist test
* fix
* upd
* upd according to the comments
* Fix
* Fix test and now distributed works.
* upd
* upd
* Fix
* Fix bug
* remove dead code.
* upd
* Fix
* upd
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal >
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-07-28 11:51:32 +08:00
d70beba762
Bug fix: change th to tf ( #3182 )
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Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-07-27 17:23:21 +08:00
bbb6d4eed0
[Dataset] Fix the edge numbers in the GNNBenchmarkDataset doc string ( #3163 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Hide implementations that may cause confusions to the user
* fix number of classes in Amazon Cobuy datasets
* add four papers
* Fix doc string
* fix readme
* fix readme
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-07-21 17:31:32 +08:00
34426a98e9
[Distributed] Distributed heterograph training ( #3069 )
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* support hetero RGCN.
* fix.
* simplify code.
* sample_neighbors return heterograph directly.
* avoid using to_heterogeneous.
* compute canonical etypes in advance.
* fix tests.
* fix.
* fix distributed data loader for heterograph.
* use NodeDataLoader.
* fix bugs in partitioning on heterogeneous graphs.
* fix lint.
* fix tests.
* fix.
* fix.
* fix bugs.
* fix tests.
* fix.
* enable coo for distributed.
* fix.
* fix.
* fix.
* fix.
* fix.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal >
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
2021-07-17 10:57:00 +08:00
905c0aa578
[Feature][Performance][GPU] Introducing UnifiedTensor for efficient zero-copy host memory access from GPU ( #3086 )
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* Add pytorch-direct version
* Initial commit of unified tensor
* Merge branch 'master' of https://github.com/davidmin7/dgl
* Remove unnecessary things
* Fix error message
* Fix/Add descriptions
* whitespace fix
* add unpin
* disable IndexSelectCPUFromGPU with no CUDA
* add a newline for unified_tensor.py
* Apply changes based on feedback
* add 'os' module
* skip unified tensor unit test for cpu only
* Update tests/pytorch/test_unified_tensor.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
* reflect feedback
Co-authored-by: shhssdm <shhssdm@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-07-17 00:06:20 +08:00
b379dbd6c8
Optimize dist_graph/_split_even_to_part memory usage ( #3132 )
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Co-authored-by: yujingcheng02 <yujingcheng02@meituan.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-07-15 11:51:56 +08:00
5cdf7cfa98
[Doc] refine metis part of dgl.reorder_graph() ( #3136 )
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Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-07-15 10:14:39 +08:00
3f6f694159
[Bug fix] Various fix from bug bash ( #3133 )
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* Update
* Update
* Update dependencies
* Update
* Update
* Fix ogbn-products gat
* Update
* Update
* Reformat
* Fix typo in node2vec_random_walk
* Specify file encoding
* Working for 6.7
* Update
* Fix subgraph
* Fix doc for sample_neighbors_biased
* Fix hyperlink
* Add example for udf cross reducer
* Fix
* Add example for slice_batch
* Replace dgl.bipartite
* Fix GATConv
* Fix math rendering
* Fix doc
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-17.us-west-2.compute.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-22-156.us-west-2.compute.internal >
2021-07-15 09:17:15 +08:00
066bef21f0
[Doc] Fix CoraFull number of edges inconsistency in doc ( #3139 )
2021-07-14 15:06:57 +08:00
d7390763f0
[Distributed] Deprecate old DistEmbedding impl, use synchronized embedding impl ( #3111 )
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* fix.
* fix.
* fix.
* fix.
* Fix test
* Deprecate old DistEmbedding impl, use synchronized embedding impl
* update doc
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal >
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-07-14 00:15:53 +08:00
f0fafa2062
[Bug fix] Fix batch information with remove_nodes/edges applied ( #3119 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix lint
* Fix
* Update
* Fix test cases
* Fix
* add docstrings
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-17.us-west-2.compute.internal >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-07-13 16:27:31 +08:00
2e19ba8025
add exclude self option for EdgeDataLoader ( #3122 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-07-13 13:30:16 +08:00
b576e617ad
[Feature] Add left normalizer for GCN ( #3114 )
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* add left normalizer for gcn
* fix
* fixes and some bug stuff
2021-07-13 12:49:35 +08:00
186ef59283
[Feature] apply dgl.reorder() onto several node classification datase… ( #3102 )
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* [Feature] apply dgl.reorder() onto several node classification datasets in DGL
* rebase on latest dgl.reorder_graph()
2021-07-13 08:52:17 +08:00
175f53decf
[Feature] enable edge reorder in dgl.reorder_graph() ( #3113 )
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* [Feature] enable edge reorder in dgl.reorder_graph()
* refine doc string
* refine doc string for dgl.reorder_graph
* refine doc string further
2021-07-12 14:11:46 +08:00
0ce92a86ed
[BugFix] fix problems found in bug bash ( #3116 )
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* fix breakline in fakenews.py
* fix inconsistent argument name
* modify incorrect example and deprecated graph type
* modify docstring and example in knn_graph
* fix incorrect node type
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-07-12 13:34:50 +08:00
c7449818a1
Update documentation for remove_edges function ( #3123 )
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Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-07-12 12:54:21 +08:00
5798ee8d98
[Performance] Add a warning for ChebConv ( #3099 )
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* add a warning for chebconv
* fix and docstrings
* update bgnn
* fix
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-07-09 14:49:15 +08:00
2f41fcd986
[Build] fix various build problems ( #3117 )
2021-07-08 11:39:33 +08:00
bb89dee7ff
[BugFix] fix problems in data split ( #3082 )
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* [BugFix] fix problems in data split
* fix format problems in docstring
* modify statistics to fit in dgl nature
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: zhjwy9343 <6593865@qq.com >
2021-07-07 16:07:23 +08:00
32d1f3ac97
[BugFix] skip frames whose num_rows is zero in dgl.heterograph.combine_frames() ( #3110 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-07-07 14:15:06 +08:00
751685a979
[Doc] Add documentation for DGLGraph.adj_sparse ( #3096 )
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Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-07-07 11:24:47 +08:00
188152b853
[Feature] Add Heterograph support on Python for builtin unary msg functions (copy_u, copy_e) ( #2989 )
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* heterograph for binary func
* Added SDDMM support
* Added unittest
* added binary test cases
* unary mfuncs works
* Fixed lint err
* lint check and others
* link check
* fixed import *_hetero issue
* lint check
* replace torch with dgl backend
* lint cehck
* removed torch from test
* skip mxnet unittest
* skip gpu test
* Remove unused/duplicated code
* minor
* changed data structure of ndata and edata
* link check
* reorganized
* minor lint
* minor lint
* raise error for udf func
* lint check
* fix for CUDA 10.1
* add a note for future cross-type max/min reducing
* Add support CUDA < 11
* lint check
* tidied C code
* remove dummy GSDDMM_hetero backward implementation
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2021-07-06 20:41:58 +08:00
4556fab8e6
[Fix] Use logging to print warning message in socket creation ( #3098 )
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* fix
* fix
* lint
* fix
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-07-06 15:33:43 +08:00
d3e4460b98
[Doc] Add docstring for missing APIs ( #3088 )
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* add docstring for missing API; fix some docstring
* rename apis; address comments
2021-07-05 18:40:07 +08:00
485c04cff6
[Distributed] Fix a few bugs in distributed API ( #3094 )
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* fix.
* fix.
* fix.
* fix.
* Fix test
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal >
2021-07-05 15:12:02 +08:00
0851b4df5d
Sageconv doc ( #3093 )
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* revise the doc of forward function in SAGEConv
* remove trailing space
2021-07-05 09:25:56 +08:00
0884d02465
[Distributed] Fix bugs in partitioning on heterogeneous graphs. ( #3085 )
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* fix bugs in partitioning on heterogeneous graphs.
* fix.
* fix.
* fix example.
* fix.
* fix test.
* fix.
* fix.
* fix.
* fix tests.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-71-112.ec2.internal >
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com >
2021-07-02 21:16:14 +08:00
04dce1e630
[Doc] refine doc and optimize metis part for dgl.reorder() ( #3090 )
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Co-authored-by: Tong He <hetong007@gmail.com >
2021-07-02 20:14:47 +08:00
a0390dde93
[Feature] Add dgl.utils.is_sorted_srcdst() ( #2685 )
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* Add dgl.utils.is_sorted_srcdst
* Fix linting issues
* delete blank line
* Specify datatype to index tensor in test
* Force integer conversion
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-07-02 11:29:24 +08:00
95f8ec83b5
[Doc] fix docstring in to_block() ( #3081 )
2021-07-02 09:45:45 +08:00
a97aaa4903
fix ( #3076 )
2021-06-30 18:27:05 +08:00
7823ae2dbb
add TUDataset notice ( #3075 )
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Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-06-30 14:22:45 +08:00
4307fe8895
[Feature] Add dgl.reorder() to re-order graph according to specified … ( #3063 )
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* [Feature] Add dgl.reorder() to re-order graph according to specified strategy
* fix unit test failure for metis reorder
* fix unit test failure on mxnet_cpu
* refine unit test for dgl.reorder
* fix unit test failure on mxnet
* fix array_equal error for mxnet unit test
* fix unit test failure for mxnet
* convert metis output to numpy array explicitly
Co-authored-by: Tong He <hetong007@gmail.com >
2021-06-30 13:29:08 +08:00
789b03f433
[Doc] Add KNN Benchmark Results ( #3055 )
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* add knn benchmark result
* update
2021-06-28 16:13:56 +08:00
427a5a96e0
[Doc] Update NodeDataLoader and EdgeDataLoader for GPU-based neighbor sampling ( #3046 )
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* update docstrings and tidy code
* add docs
* address comments
* Update __init__.py
* address comments
2021-06-25 10:46:21 +08:00
acd21a6d60
[Feature] Support direct creation from CSR and CSC ( #3045 )
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* csr and csc creation
* fix
* fix
* fixes to adj transpose
* fine
* raise error if indptr did not match number of nodes
* fix
* huh?
* oh
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-25 10:05:47 +08:00
2f7ca41459
[Bug fix] Use shared memory for grad sync when NCCL is not avaliable as PyTorch distributed backend. ( #3034 )
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* Use shared memory for grad sync when NCCL is not avaliable as PyTorch distributed backend.
Fix small bugs and update unitests
* Fix bug
* update test
* update test
* Fix unitest
* Fix unitest
* Fix test
* Fix
* simple update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-212.ec2.internal >
2021-06-24 12:06:54 +08:00
e56bbafd25
[Feature] Biased Neighbor Sampling ( #2987 )
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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
* update
* update
* update
* merge
* doc
* doc
* lint
* fix
* more tests
* doc
* fix
* fix
* update
* update
* update
* fix
* fix
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-23 17:44:51 +08:00
5961c14026
[Doc] EdgeWeightNorm Fix doc ( #3051 )
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Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-06-23 15:49:31 +08:00
e667545da5
[Feature] Node2vec ( #2992 )
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* add seal example
* 1. add paper infomation in examples/README
2. adjust codes
3. option test
* use latest `to_simple` to replace coalesce graph function
* remove outdated codes
* remove useless comment
* Node2vec
1.implement node2vec random walk c++ op
2.implement node2vec model
3.implement node2vec example
* add CMakeLists file modify
* refine c++ codes
* refine c++ codes
* add missing whitespace
* refine python codes
* add codes
* add node2vec_impl.h
* fix codes
* fix code style problem
* fixes
* remove
* lots of changes
* add benchmark
* fixes
Co-authored-by: smilexuhc <smile.xuhc@gmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-06-23 14:47:56 +08:00
7359481497
[Feature][GPU] Add function for setting weights of a sparse embedding on multiple GPUs. ( #3047 )
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* add unit test
* Extend NDArrayPartition object
* Add method for setting embedding, and improve documentation
* Sync before returning
* Use name unique to sparse embedding class to avoid delete
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-06-22 08:48:12 -07:00
David Min