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nv-dlasalle 4d9beb3b7b [Fix] FIx check for num_workers for using ScalarDataBatcher (#3219) 
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-08-06 17:56:15 +08:00
Mufei Li 8c2f8ff84a Update citation_graph.py (#3221) 2021-08-06 15:57:42 +08:00
freeliuzc 45858d6803 [feature] add count_nonzero function for DistTensor (#3203) 
* add count_nonzero function for DistTensor

* change the load method of local data

Co-authored-by: liuzichang04 <liuzichang04@meituan.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Da Zheng <zhengda1936@gmail.com>
 2021-08-05 10:47:50 -07:00
Yuchen 4ae13bd270 [bugfix] Fix force_reload parameter of FraudDataset (#3210) 
* enable force_reload of FraudDataset

* rewrite hash_key in FraudDataset
 2021-08-03 13:14:17 +08:00
David Min b78acd67ce [Doc] Add an official documentation of UnifiedTensor (#3194) 
* 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
Quan (Andy) Gan 213e27f05c Bump nightly version (#3146) 2021-08-02 17:24:18 +08:00
Quan (Andy) Gan 100eb57c45 [Doc] Fix random_walk documentation inconsistency (#3188) 
* 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
nv-dlasalle 6001001fed Improve usage of pinned memory in sparse_optimizer (#3207) 
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2021-08-02 14:16:23 +08:00
Jinjing Zhou 8bc91414e9 [Distributed] Fix distributed training hang with multiple samplers (#3169) 
Rewrite the multiprocessing worker pool
 2021-08-01 21:31:04 +08:00
Kay Liu a107993f10 [Model] add model example CARE-GNN (#3187) 
* [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
Rhett Ying c4791fd46e [bugfix] fix default ntypes/etypes consistency between dgl.DGLGraph and dgl.graph (#3198) 2021-07-29 14:05:28 +08:00
Da Zheng cb4a83a233 [Distributed] Enable distributed EdgeDataLoader (#3192) 
* 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
xiang song(charlie.song) ba7e7cf931 [New Feature] Per edge type sampler for to_homogeneous graphs. (#3131) 
* 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
Lu Lu d70beba762 Bug fix: change th to tf (#3182) 
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-07-27 17:23:21 +08:00
Xiangkun Hu bbb6d4eed0 [Dataset] Fix the edge numbers in the GNNBenchmarkDataset doc string (#3163) 
* 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
Da Zheng 34426a98e9 [Distributed] Distributed heterograph training (#3069) 
* 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
David Min 905c0aa578 [Feature][Performance][GPU] Introducing UnifiedTensor for efficient zero-copy host memory access from GPU (#3086) 
* 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
Jingcheng Yu b379dbd6c8 Optimize dist_graph/_split_even_to_part memory usage (#3132) 
Co-authored-by: yujingcheng02 <yujingcheng02@meituan.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2021-07-15 11:51:56 +08:00
Rhett Ying 5cdf7cfa98 [Doc] refine metis part of dgl.reorder_graph() (#3136) 
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
 2021-07-15 10:14:39 +08:00
Mufei Li 3f6f694159 [Bug fix] Various fix from bug bash (#3133) 
* 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
Quan (Andy) Gan 066bef21f0 [Doc] Fix CoraFull number of edges inconsistency in doc (#3139) 2021-07-14 15:06:57 +08:00
xiang song(charlie.song) d7390763f0 [Distributed] Deprecate old DistEmbedding impl, use synchronized embedding impl (#3111) 
* 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
Mufei Li f0fafa2062 [Bug fix] Fix batch information with remove_nodes/edges applied (#3119) 
* 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
Quan (Andy) Gan 2e19ba8025 add exclude self option for EdgeDataLoader (#3122) 
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-07-13 13:30:16 +08:00
Quan (Andy) Gan b576e617ad [Feature] Add left normalizer for GCN (#3114) 
* add left normalizer for gcn

* fix

* fixes and some bug stuff
 2021-07-13 12:49:35 +08:00
Rhett Ying 186ef59283 [Feature] apply dgl.reorder() onto several node classification datase… (#3102) 
* [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
Rhett-Ying 175f53decf [Feature] enable edge reorder in dgl.reorder_graph() (#3113) 
* [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
Kay Liu 0ce92a86ed [BugFix] fix problems found in bug bash (#3116) 
* 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
Wilfried L. Bounsi c7449818a1 Update documentation for remove_edges function (#3123) 
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2021-07-12 12:54:21 +08:00
Quan (Andy) Gan 5798ee8d98 [Performance] Add a warning for ChebConv (#3099) 
* 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
Quan (Andy) Gan 2f41fcd986 [Build] fix various build problems (#3117) 2021-07-08 11:39:33 +08:00
Kay Liu bb89dee7ff [BugFix] fix problems in data split (#3082) 
* [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
Rhett-Ying 32d1f3ac97 [BugFix] skip frames whose num_rows is zero in dgl.heterograph.combine_frames() (#3110) 
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-07-07 14:15:06 +08:00
Quan (Andy) Gan 751685a979 [Doc] Add documentation for DGLGraph.adj_sparse (#3096) 
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-07-07 11:24:47 +08:00
Israt Nisa 188152b853 [Feature] Add Heterograph support on Python for builtin unary msg functions (copy_u, copy_e) (#2989) 
* 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
Jinjing Zhou 4556fab8e6 [Fix] Use logging to print warning message in socket creation (#3098) 
* fix

* fix

* lint

* fix

Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2021-07-06 15:33:43 +08:00
Minjie Wang d3e4460b98 [Doc] Add docstring for missing APIs (#3088) 
* add docstring for missing API; fix some docstring

* rename apis; address comments
 2021-07-05 18:40:07 +08:00
Da Zheng 485c04cff6 [Distributed] Fix a few bugs in distributed API (#3094) 
* 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
WangYQ 0851b4df5d Sageconv doc (#3093) 
* revise the doc of forward function in SAGEConv

* remove trailing space
 2021-07-05 09:25:56 +08:00
Da Zheng 0884d02465 [Distributed] Fix bugs in partitioning on heterogeneous graphs. (#3085) 
* 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
Rhett-Ying 04dce1e630 [Doc] refine doc and optimize metis part for dgl.reorder() (#3090) 
Co-authored-by: Tong He <hetong007@gmail.com>
 2021-07-02 20:14:47 +08:00
nv-dlasalle a0390dde93 [Feature] Add dgl.utils.is_sorted_srcdst() (#2685) 
* 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
Rhett-Ying 95f8ec83b5 [Doc] fix docstring in to_block() (#3081) 2021-07-02 09:45:45 +08:00
Quan (Andy) Gan a97aaa4903 fix (#3076) 2021-06-30 18:27:05 +08:00
Quan (Andy) Gan 7823ae2dbb add TUDataset notice (#3075) 
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-06-30 14:22:45 +08:00
Rhett-Ying 4307fe8895 [Feature] Add dgl.reorder() to re-order graph according to specified … (#3063) 
* [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
Tong He 789b03f433 [Doc] Add KNN Benchmark Results (#3055) 
* add knn benchmark result

* update
 2021-06-28 16:13:56 +08:00
Quan (Andy) Gan 427a5a96e0 [Doc] Update NodeDataLoader and EdgeDataLoader for GPU-based neighbor sampling (#3046) 
* update docstrings and tidy code

* add docs

* address comments

* Update __init__.py

* address comments
 2021-06-25 10:46:21 +08:00
Quan (Andy) Gan acd21a6d60 [Feature] Support direct creation from CSR and CSC (#3045) 
* 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
xiang song(charlie.song) 2f7ca41459 [Bug fix] Use shared memory for grad sync when NCCL is not avaliable as PyTorch distributed backend. (#3034) 
* 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