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Quan (Andy) Gan 1eb4923cad Merge branch 'master' into better-conda 2022-09-19 13:53:18 +08:00
Hongzhi (Steve), Chen f1689ad0e1 [Misc]Add pyproject.toml for autopep8 & black. (#4543) 
* Add pyproject.toml for autopep8.

* Add pyproject.toml for autopep8.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-19 11:38:58 +08:00
Hongzhi (Steve), Chen 36dbccee12 Delete pylint.yml 2022-09-16 18:35:41 +08:00
Hongzhi (Steve), Chen d0b04f7eec Update pylint.yml 2022-09-16 18:29:58 +08:00
Hongzhi (Steve), Chen e069549a74 Update pylint.yml 2022-09-16 18:17:39 +08:00
Hongzhi (Steve), Chen 07a465b8be Update pylint. (#4576) 
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-16 17:37:09 +08:00
Hongzhi (Steve), Chen 11a679c085 [Misc] Use another workflow. (#4575) 
* Update pylint.

* Use another workflow.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-16 17:33:17 +08:00
Hongzhi (Steve), Chen d08b28dec1 Update pylint. (#4574) 
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-16 17:11:12 +08:00
Hongzhi (Steve), Chen 5f5739192a [Misc] Update the python version in Pylint workflow for flake8. (#4572) 
* remove

* Add pylint.

* Change the python version for pylint.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-16 17:01:46 +08:00
Hongzhi (Steve), Chen 97b3c5c8a7 Add Pylint workflow for flake8. (#4571) 
* remove

* Add pylint.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-16 16:50:19 +08:00
Hongzhi (Steve), Chen 565bbdbb66 remove (#4570) 
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-16 16:34:29 +08:00
Rhett Ying a3e00c4453 [CI] refine stage logic (#4565) 
* [CI] refine stage logic

* refine

* refine
 2022-09-16 16:28:04 +08:00
Hongzhi (Steve), Chen 795371ad0e [Misc] Try use official pylint workflow. (#4568) 
* polish update_version

* update pylint workflow.

* add

* revert.

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-16 16:10:04 +08:00
Hongzhi (Steve), Chen ec96407c3c [Misc] Add flake8 lint workflow. (#4566) 
* Add pyproject.toml for autopep8.

* Add pyproject.toml for autopep8.

* Add flake8 annotation in workflow.

* remove

* add

* clean up

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
 2022-09-16 15:47:41 +08:00
Rhett Ying 7f984b64b2 Revert "[Feature][REVIEW] Enable DGL cugaph nightly CI (#4525)" (#4563) 
This reverts commit ec171c648a.
 2022-09-16 13:57:50 +08:00
Vibhu Jawa ec171c648a [Feature][REVIEW] Enable DGL cugaph nightly CI (#4525) 
* Added cugraph nightly scripts

* Removed nvcr.io//nvidia/pytorch:22.04-py3 reference

Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
 2022-09-16 11:28:30 +08:00
Rhett Ying 1bc77c5e61 [examples]educe memory consumption (#4558) 
* [examples]educe memory consumption

* reffine help message

* refine
 2022-09-15 19:27:20 +08:00
Xin Yao 9a00cf194f [Feature] Import PyTorch's CUDA stream management (#4503) 
* add set_stream

* add .record_stream for NDArray and HeteroGraph

* refactor dgl stream Python APIs

* test record_stream

* add unit test for record stream

* use pytorch's stream

* fix lint

* fix cpu build

* address comments

* address comments

* add record stream tests for dgl.graph

* record frames and update dataloder

* add docstring

* update frame

* add backend check for record_stream

* remove CUDAThreadEntry::stream

* record stream for newly created formats

* fix bug

* fix cpp test

* fix None c_void_p to c_handle
 2022-09-15 16:54:52 +08:00
Rhett Ying 099b173f6f [DistPart] expose timeout config for process group (#4532) 
* [DistPart] expose timeout config for process group

* refine code

* Update tools/distpartitioning/data_proc_pipeline.py

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-09-15 15:28:36 +08:00
Israt Nisa cf03592743 Move mock version of dgl_sparse library to DGL main repo (#4524) 
* init

* Add api doc for sparse library

* support op btwn matrices with differnt sparsity

* Fixed docstring

* addresses comments

* lint check

* change keyword format to fmt

Co-authored-by: Israt Nisa <nisisrat@amazon.com>
 2022-09-14 12:08:20 -04:00
Hongzhi (Steve), Chen 701c6fe754 [Readability] Auto fix setup.py and update-version.py (#4446) 
* Auto fix update-version

* Auto fix setup.py

* Auto fix update-version

* Auto fix setup.py

* [Doc] Change random.py to random_partition.py in guide on distributed partition pipeline (#4438)

* Update distributed-preprocessing.rst

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>

* fix unpinning when tensoradaptor is not available (#4450)

* [Doc] fix print issue in tutorial (#4459)

* [Example][Refactor] Refactor RGCN example (#4327)

* Refactor full graph entity classification

* Refactor rgcn with sampling

* README update

* Update

* Results update

* Respect default setting of self_loop=false in entity.py

* Update

* Update README

* Update for multi-gpu

* Update

* [doc] fix invalid link in user guide (#4468)

* [Example] directional_GSN for ogbg-molpcba (#4405)

* version-1

* version-2

* version-3

* update examples/README

* Update .gitignore

* update performance in README, delete scripts

* 1st approving review

* 2nd approving review

Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Clarify the message name, which is 'm'. (#4462)

Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>

* [Refactor] Auto fix view.py. (#4461)

Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [Example] SEAL for OGBL (#4291)

* [Example] SEAL for OGBL

* update index

* update

* fix readme typo

* add seal sampler

* modify set ops

* prefetch

* efficiency test

* update

* optimize

* fix ScatterAdd dtype issue

* update sampler style

* update

Co-authored-by: Quan Gan <coin2028@hotmail.com>

* [CI] use https instead of http (#4488)

* [BugFix] fix crash due to incorrect dtype in dgl.to_block() (#4487)

* [BugFix] fix crash due to incorrect dtype in dgl.to_block()

* fix test failure in TF

* [Feature] Make TensorAdapter Stream Aware (#4472)

* Allocate tensors in DGL's current stream

* make tensoradaptor stream-aware

* replace TAemtpy with cpu allocator

* fix typo

* try fix cpu allocation

* clean header

* redirect AllocDataSpace as well

* resolve comments

* [Build][Doc] Specify the sphinx version (#4465)

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* reformat

* reformat

* Auto fix update-version

* Auto fix setup.py

* reformat

* reformat

Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
 2022-09-14 13:36:18 +08:00
Quan (Andy) Gan 1f8c02b31d Merge branch 'master' into better-conda 2022-09-14 09:48:55 +08:00
Rhett Ying 11532198b6 [CI] only known devs are authorized to trigger CI (#4518) 
* [CI] only known devs are authorized to trigger CI

* fix if author is null

* add comments
 2022-09-08 15:37:01 +08:00
ndickson-nvidia 684f66b7aa [Feature] Added exclude_self and output_batch to knn graph construction (Issues #4323 #4316) (#4389) 
* * Added "exclude_self" and "output_batch" options to knn_graph and segmented_knn_graph
* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information

* * Changed defaults on new knn_graph and segmented_knn_graph function parameters, for compatibility; pytorch/test_geometry.py was failing

* * Added test to ensure dgl.remove_self_loop function correctly updates batch information

* * Added new knn_graph and segmented_knn_graph parameters to dgl.nn.KNNGraph and dgl.nn.SegmentedKNNGraph

* * Formatting

* * Oops, I missed the one in segmented_knn_graph when I fixed the similar thing in knn_graph

* * Fixed edge case handling when invalid k specified, since it still needs to be handled consistently for tests to pass
* Fixed context of batch info, since it must match the context of the input position data for remove_self_loop to succeed

* * Fixed batch info resulting from knn_graph when output_batch is true, for case of 3D input tensor, representing multiple segments

* * Added testing of new exclude_self and output_batch parameters on knn_graph and segmented_knn_graph, and their wrappers, KNNGraph and SegmentedKNNGraph, into the test_knn_cuda test

* * Added doc comments for new parameters

* * Added correct handling for uncommon case of k or more coincident points when excluding self edges in knn_graph and segmented_knn_graph
* Added test cases for more than k coincident points

* * Updated doc comments for output_batch parameters for clarity

* * Linter formatting fixes

* * Extracted out common function for test_knn_cpu and test_knn_cuda, to add the new test cases to test_knn_cpu

* * Rewording in doc comments

* * Removed output_batch parameter from knn_graph and segmented_knn_graph, in favour of always setting the batch information, except in knn_graph if x is a 2D tensor

Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-09-07 08:35:26 +08:00
Chang Liu 1c9d2a0302 [Feature] Unify the cuda stream used in core library (#4480) 
* Use an internal cuda stream for CopyDataFromTo

* small fix white space

* Fix to compile

* Make stream optional in copydata for compile

* fix lint issue

* Update cub functions to use internal stream

* Lint check

* Update CopyTo/CopyFrom/CopyFromTo to use internal stream

* Address comments

* Fix backward CUDA stream

* Avoid overloading CopyFromTo()

* Minor comment update

* Overload copydatafromto in cuda device api

Co-authored-by: xiny <xiny@nvidia.com>
 2022-09-06 10:14:55 +08:00
peizhou001 62af41c245 [Bug] Enable turn on/off libxsmm at runtime (#4455) 
* enable turn on/off libxsmm at runtime by adding a global config and related API


Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>
 2022-09-05 17:38:34 +08:00
Israt Nisa 06608f847c [Cleanup] Remove duplicate entries of CUB submodule (issue# 4395) (#4499) 
* remove third_part/cub

* remove from third_party

Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>
 2022-09-05 13:23:08 +08:00
nv-dlasalle 806def67a1 [Cleanup] Remove async_transferer (#4505) 
* Remove async_transferer

* remove test

* Remove AsyncTransferer

Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>
 2022-09-05 11:46:06 +08:00
Chang Liu fce9614089 [Example][Refactor] Refactor graphsage multigpu and full-graph example (#4430) 
* Add refactors for multi-gpu and full-graph example

* Fix format

* Update

* Update

* Update
 2022-09-05 09:05:56 +08:00
Quan (Andy) Gan 2dd06b2152 [Build][Doc] Specify the sphinx version (#4465) 
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-09-01 13:52:08 +08:00
Xin Yao 2b76674002 [Feature] Make TensorAdapter Stream Aware (#4472) 
* Allocate tensors in DGL's current stream

* make tensoradaptor stream-aware

* replace TAemtpy with cpu allocator

* fix typo

* try fix cpu allocation

* clean header

* redirect AllocDataSpace as well

* resolve comments
 2022-08-31 20:09:40 +08:00
Rhett Ying 468c0ca4b4 [BugFix] fix crash due to incorrect dtype in dgl.to_block() (#4487) 
* [BugFix] fix crash due to incorrect dtype in dgl.to_block()

* fix test failure in TF
 2022-08-31 16:09:46 +08:00
Rhett Ying 86656a6b34 [CI] use https instead of http (#4488) 2022-08-31 14:59:40 +08:00
rudongyu b9290e8b2d [Example] SEAL for OGBL (#4291) 
* [Example] SEAL for OGBL

* update index

* update

* fix readme typo

* add seal sampler

* modify set ops

* prefetch

* efficiency test

* update

* optimize

* fix ScatterAdd dtype issue

* update sampler style

* update

Co-authored-by: Quan Gan <coin2028@hotmail.com>
 2022-08-31 11:48:07 +08:00
Hongzhi (Steve), Chen ef93518da3 [Refactor] Auto fix view.py. (#4461) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
 2022-08-30 18:31:03 +08:00
Hongzhi (Steve), Chen ab0af8146f Clarify the message name, which is 'm'. (#4462) 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
 2022-08-30 13:34:54 +08:00
Quan (Andy) Gan d9ec423b87 Merge branch 'master' into better-conda 2022-08-30 13:20:01 +08:00
Zhiteng Li 97b2ab53e2 [Example] directional_GSN for ogbg-molpcba (#4405) 
* version-1

* version-2

* version-3

* update examples/README

* Update .gitignore

* update performance in README, delete scripts

* 1st approving review

* 2nd approving review

Co-authored-by: Mufei Li <mufeili1996@gmail.com>
 2022-08-26 15:37:54 +08:00
Rhett Ying bd311aa68d [doc] fix invalid link in user guide (#4468) 2022-08-25 23:16:44 +08:00
Chang Liu 40a2f3c760 [Example][Refactor] Refactor RGCN example (#4327) 
* Refactor full graph entity classification

* Refactor rgcn with sampling

* README update

* Update

* Results update

* Respect default setting of self_loop=false in entity.py

* Update

* Update README

* Update for multi-gpu

* Update
 2022-08-25 13:19:32 +08:00
Quan (Andy) Gan 518e6c283d Update conda_build_config.yaml 2022-08-24 18:14:26 +08:00
Rhett Ying ea6195c253 [Doc] fix print issue in tutorial (#4459) 2022-08-24 13:34:57 +08:00
Quan (Andy) Gan af7dd95de9 Update build.sh 2022-08-24 13:01:17 +08:00
Quan (Andy) Gan fe83296faf Update build.sh 2022-08-24 12:45:43 +08:00
Quan (Andy) Gan 1c594ef42c Update meta.yaml 2022-08-24 11:18:13 +08:00
Quan Gan 9eea7aaa2c windows stuff 2022-08-23 10:10:05 +00:00
Quan Gan a64ad1b974 update with default build options 2022-08-23 09:40:45 +00:00
Quan Gan 01dedf0308 update conda build scripts 2022-08-23 09:30:52 +00:00
Xin Yao 1947d87dd7 fix unpinning when tensoradaptor is not available (#4450) 2022-08-23 12:08:32 +08:00
Mufei Li 7a41c126f6 [Doc] Change random.py to random_partition.py in guide on distributed partition pipeline (#4438) 
* Update distributed-preprocessing.rst

* Update

Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
 2022-08-22 18:12:55 +08:00