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Minjie Wang 8355a47e45 Update README.md 2021-07-28 12:28:02 +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
Jingcheng Yu c8d4d6fbf8 [Bugfix] fix potential starving in socket receiver (#3176) 
Co-authored-by: JingchengYu94 <jingchengyu94@gmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
 2021-07-25 10:25:35 +08:00
Kay Liu 59a7d0d1c0 [Model] add model example GCN-based Anti-Spam (#3145) 
* add model example GCN-based Anti-Spam

* update example index

* add usage info

* improvements as per comments

* fix image invisiable problem

* add image file

Co-authored-by: zhjwy9343 <6593865@qq.com>
 2021-07-24 23:33:25 +08:00
Tianjun Xiao c0719ec574 train test on face use concat bce (#3180) 2021-07-24 20:49:09 +08:00
Minjie Wang 0f257733ad [Doc] New README (#3178) 
New readme structure
 2021-07-23 18:58:00 +08:00
Minjie Wang 73c85b984b [Doc] Fix perf doc (#3177) 2021-07-23 18:07:42 +08:00
Tianjun Xiao 65ecbb9492 change numbers to concat bce (#3175) 2021-07-23 12:54:28 +08:00
Quan (Andy) Gan 460e784b3b Update README.md (#3170) 2021-07-22 15:48:51 +08:00
Jinjing Zhou de174adac4 Remove redundant fill in SPMM kernel (#3166) 
* remove redundant fill

* trigger ci
 2021-07-21 18:47:54 +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
Minjie Wang 9d56d386c8 [Doc] Update the example folder README 2021-07-20 19:12:06 +08:00
Quan (Andy) Gan ddc92f8d5b speed up random walks (#3158) 
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-07-20 18:15:50 +08:00
Minjie Wang d1cc096956 [Doc] Note for performance benchmarks (#3152) 
Co-authored-by: Tong He <hetong007@gmail.com>
 2021-07-20 13:33:32 +08:00
Xiangkun Hu ee1c1a82fa [Doc] Add two papers to Awesome Paper List (#3155) 
* 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

* Add paper to paperlist

* add two papers

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-07-19 15:53:36 +08:00
Mufei Li 13017ed4b2 Update README.md (#3154) 2021-07-19 14:16:47 +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
Quan (Andy) Gan 7e923180c1 [Doc] Add thumbnails to multi-GPU tutorials (#3141) 2021-07-16 14:27:43 +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
Jinjing Zhou 88f20eec4e fix tags (#3140) 
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2021-07-15 11:02:44 +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
Jinjing Zhou 5f2639e230 [Regression] Fix Reddit dataset in regression test (#3106) 
* fix

* fix

* Update run.sh

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-07-14 17:22:19 +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
Wilfried L. Bounsi ee6bc95175 Update a comment in pytorch HGT example (#3101) 
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
 2021-07-13 19:09:17 +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 7c3e1f94b9 Remove march=native flag (#3134) 2021-07-13 15:16:18 +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
sanchit-misra fac75e166b [CPU][Kernel] Single socket spmm (#3024) 
* optimizations of spmm for CPU

* Added names of contributors

* Minor code cleanup

* Moved the spmm optimization code to a new header file

* Moved to DGL's logging method

* removed duplicate code between SpMMSumCsr and SpMMCmpCsr

* Changes made to follow Google coding style

* Fixed lint errors in spmm.h

* Fixed some lint errors from spmm_blocking_libxsmm.h

* Fixed lint errors from spmm_blocking_libxsmm.h

* Added comments to SpMMCreateLibxsmmKernel

* to enable building of tests, and other cosmetic changes

* disabling libxsmm on windows

* Put a condition to avoid opt impl for FP64 as libxsmm does not have FP64 support yet

* cosmetic changes and documentation

* cosmetic changes

* to pass lint tests

* replaced multiple allocations for buffers of indices and edges with a single allocation

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2021-07-13 11:18:29 +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
Jinjing Zhou 3641829211 fix docs (#3126) 
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
 2021-07-12 11:43:15 +08:00
Tomohiro Endo fc55225f08 Fix module name (#3128) 2021-07-12 11:15:02 +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
Jinjing Zhou 183d29de56 fix cub problem (#3121) 2021-07-08 17:57:10 +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
Hengrui Zhang 0d1dcdcd2e [bugfix] fix a bug found in v0.7 bug bash in the 'grace' model (#3109) 
* Update aug.py

* Update aug.py

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
 2021-07-07 14:50:02 +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
Tianjun Xiao 22e8c120be [Example ] fix faiss issue on k 3 for hilander model (#3105) 
* fix faiss issue on k 3

* Add Hilander paper link

Co-authored-by: Tong He <hetong007@gmail.com>
 2021-07-06 13:22:56 +08:00
Zihao Ye c372f0aed6 [doc] Expose dgl.partition APIs (#3103) 2021-07-06 12:17:56 +08:00