f9fd7fd7f7
[BugFix] extract gz into target dir ( #3389 )
2021-09-30 11:35:40 +08:00
e234fcfa8f
[Feature] enable create/set/free cuda stream for internal use ( #3334 )
...
* [Feature] enable create/set/free cuda stream for internal use
* add unit test
* fix unit test failure on mxnet and tf
* refactor stream wrapper
* fix lint error
* fix lint error
2021-09-29 15:35:02 +08:00
5cf48fc69c
[Feature] Implement one thread multiple socket ( #3200 )
...
Co-authored-by: JingchengYu94 <jingchengyu94@gmail.com >
2021-09-27 21:45:52 -07:00
bc14829fb3
[Feature] Exclude edges in sample_neighbors ( #2971 )
...
* [Feature] Exclude edges in sample_neighbors
Extending sample_neighbors and sample_frontier
API to support exclude_edges parameter.
exclude_edges support tensor and dict data
Feature enable excluding certain edges
during neighborhood sampling
Exclude_edges contains EID's of edges
which will be excluded
during neighbor picking for seed nodes.
Added test case for heterograph and homograph
RFC issue id: 2944
* compatibility
* fix
* fix
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2021-09-22 02:15:56 +08:00
fecd6f3c50
[BugFix] fix typo in fakenews dataset variable name ( #3363 )
2021-09-21 22:06:26 +08:00
bc5cac4426
fix broadcast tensor dim ( #3351 )
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-09-19 21:49:56 +08:00
2647afc9b3
[Performance][Feature] Add src_nodes paramter to to_block() to avoid cost running unique() when available. ( #2973 )
...
* Add lhs_nodes are paremeter to to_block
* Update unit test
* Switch to simplified node conversion
* Switch lhs_nodes to be in/out parameter
* Update docs
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-09-16 09:05:16 +08:00
a609b4f023
[Bugfix] Fix #3291 ( #3333 )
...
* Fix #3291
* update
* fix
* Unit key
* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-09-14 08:57:20 +08:00
6454c791b8
[Bugfix] Fix bugs of farthest_point_sampler ( #3327 )
...
* fix start_idx
* fix the bug when cuda > 0
Co-authored-by: Tong He <hetong007@gmail.com >
2021-09-10 17:50:06 +08:00
d17b299a13
[Feature] Update edge features (apply_edge) for heterogeneous graph ( #3250 )
...
* rgcn with new heterograph API
* apply_edge() forward for multi relation
* undoing changes from rgcn-hetero
* backward apply_edge(copy_u) added
* unittest for apply_edge(copy_e)
* Compatible with new PRs
* resolving conflict with master
* Bringing back change after resolving conflict
* minor
* minor
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
2021-09-09 22:39:08 +08:00
298e4fa627
[Feature] Support builtin binary message function for heterogenenous graph ( #3273 )
...
* Added binary builtinMsgFunc forward() for heterograph
* Added backward for u_op_v
* Supports all binary builtin forward
* Supports binary message funcs with reduce func sum
* lint check
* removed import torch from unittest
* enabled GPU test
* lint check
* Fixed docstrings
* rename func get_hs_id
* edited comment
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
2021-09-07 10:01:33 -07:00
75d793a1bc
Update dataloader.py ( #3322 )
2021-09-06 12:16:03 +08:00
f4fe518ff7
[Feature] Add a HINT for the per edge type sampler of heterogeneous DistGraph that highlighting the etypes are sorted already. ( #3260 )
...
* pass cpp test
* distgraph use sorted edge flag.
* lint
* triger
* update test
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal >
2021-09-01 15:36:01 +08:00
a53783c81d
[Performance] Only copy and slice index's in subcolumn when data is used. ( #2930 )
...
* Make column double indices lazy
* Copy indices to proper contexts
* Fix initialization
* Add unit test
* Fix unit test for tensorflow
* Remove unused member
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-08-30 19:17:25 -07:00
e5ed7adc12
[Distributed] Fix a bug in sampling an empty frontier ( #3298 )
...
* handle empty frontiers.
* fix lint.
* fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-202.us-west-1.compute.internal >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-08-29 10:54:46 -07:00
152760f66d
[Doc] Note for HeteroGraphConv / Doc build problems ( #3149 )
...
* Doc: HetGConv note for `edge_type_subgraph`
For the rational behind this note see the discussion in #3003 .
* WIP: Requirements for building the docs.
Had to install all these packages to get further with building the docs.
Didn't successfully build them yet, tho.
* Test
* Update
* Update hetero.py
* Update hetero.py
Co-authored-by: Ubuntu <ubuntu@ip-172-31-13-32.us-west-2.compute.internal >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-08-29 03:14:43 +08:00
79305862ec
allow for configuring default_dir ( #3277 )
...
* allow for configuring default_dir
* allow for using DGLDEFAULTDIR environment variable
* Update env_var.rst
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-08-27 01:29:49 +08:00
9cc85aed62
[Doc] fix formula in RelGraphConv ( #3285 )
...
* [Doc] fix formula in RelGraphConv
* refine descriptions
2021-08-25 17:59:17 +08:00
b4cd60a952
fix relgraphconv bug ( #3256 )
2021-08-23 17:29:14 +08:00
8341244a2d
[Doc] fix formula display issue in EdgeWeightNorm ( #3275 )
...
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-08-21 21:59:26 +08:00
7f9279397a
[Feature][DistDGL] Add NCCL support for range based partitions ( #3213 )
...
* Implement range based NDArrayPartition
* Finish implement range based partition support
* Add unit test
* Fix whitepace
* Add Kernel suffix
* Fix argument passing
* Add doxygen docs and improve variable naming
* Add unit test
* Add function for converting a partition book
* Add example to partition_op docs
* Fix dtype conversion for mxnet and tensorflow
2021-08-19 21:17:55 -07:00
75fca8e4e8
[bugfix] fix the bug of DotGatConv when compute the edge_softmax ( #3272 )
...
Co-authored-by: Zihao Ye <expye@outlook.com >
2021-08-20 09:19:00 +08:00
f634950825
[Performance][Feature] Implement edge excluding in EdgeDataLoader on GPU ( #3226 )
...
* Update filter code
* Add unit tests
* Fixes
* Switch to indices
* Rename functions
* Fix linting
* Fix whitespace
* Add doc
* Fix heterograph
* Change workspace allocation
* Fix linting
* Fix docs in filter.py
* Add todo
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-08-19 12:24:15 -07:00
76af2a2ef3
[perf] Remove activation cache if not required. ( #3258 )
...
* upd
* fix
* upd
2021-08-17 17:14:51 +08:00
31772b142e
fixed typos in docs and docstring ( #3231 )
...
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-08-16 13:58:45 +08:00
6f36dd6366
Cleanup some code in graph_services.py ( #3238 )
...
* Fix bug
* Fix
* Fix
* upd
* Merge some code
* lint
2021-08-15 11:58:37 -07:00
1b350e9319
Fix small typo in knn_graph() documentation ( #3244 )
2021-08-12 14:23:27 +08:00
cd2cf606db
[Bugfix] Fix bug introduced by https://github.com/dmlc/dgl/pull/3131 ( #3234 )
...
* Fix bug
* Fix
* Fix
* upd
* trigger
2021-08-10 11:36:57 +08:00
bcf92f6c21
[Bugfix] Distributed training can not work with dgl.dataloading.negative_sampler ( #3215 )
...
* Fix dist negative data loader bug
* upd
* Fix
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2021-08-06 20:41:20 +08:00
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
8c2f8ff84a
Update citation_graph.py ( #3221 )
2021-08-06 15:57:42 +08:00
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
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
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
213e27f05c
Bump nightly version ( #3146 )
2021-08-02 17:24:18 +08:00
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
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
8bc91414e9
[Distributed] Fix distributed training hang with multiple samplers ( #3169 )
...
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 )
...
* 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 )
...
* 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 )
...
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 )
...
* 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 )
...
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 )
...
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 )
...
* 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
Rhett Ying