* Update from master (#4584)
* [Example][Refactor] Refactor graphsage multigpu and full-graph example (#4430)
* Add refactors for multi-gpu and full-graph example
* Fix format
* Update
* Update
* Update
* [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>
* [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>
* [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>
* [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>
* [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* Updated out-of-date comments on remove_edges and remove_self_loop, since they now preserve batch information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>
* [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
* [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)
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Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
* [Refactor] Auto fix view.py. (#4461)
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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
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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>
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Co-authored-by: Quan Gan <coin2028@hotmail.com>
* 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>
* [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>
* [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
* [examples]educe memory consumption (#4558)
* [examples]educe memory consumption
* reffine help message
* refine
* [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>
* Revert "[Feature][REVIEW] Enable DGL cugaph nightly CI (#4525)" (#4563)
This reverts commit ec171c648a.
* [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>
* [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>
* [CI] refine stage logic (#4565)
* [CI] refine stage logic
* refine
* refine
* remove (#4570)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
* Add Pylint workflow for flake8. (#4571)
* remove
* Add pylint.
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
* [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>
* Update pylint. (#4574)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
* [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>
* Update pylint. (#4576)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
* Update pylint.yml
* Update pylint.yml
* Delete pylint.yml
* [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>
* [Feature] Bump DLPack to v0.7 and decouple DLPack from the core library (#4454)
* rename `DLContext` to `DGLContext`
* rename `kDLGPU` to `kDLCUDA`
* replace DLTensor with DGLArray
* fix linting
* Unify DGLType and DLDataType to DGLDataType
* Fix FFI
* rename DLDeviceType to DGLDeviceType
* decouple dlpack from the core library
* fix bug
* fix lint
* fix merge
* fix build
* address comments
* rename dl_converter to dlpack_convert
* remove redundant comments
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>
Co-authored-by: Israt Nisa <neesha295@gmail.com>
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: peizhou001 <110809584+peizhou001@users.noreply.github.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-194.ap-northeast-1.compute.internal>
Co-authored-by: ndickson-nvidia <99772994+ndickson-nvidia@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
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Co-authored-by: Zhiteng Li <55398076+ZHITENGLI@users.noreply.github.com>
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
Co-authored-by: Vibhu Jawa <vibhujawa@gmail.com>
* [Deprecation] Dataset Attributes (#4546)
* Update
* CI
* CI
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
* [Example] Bug Fix (#4665)
* Update
* CI
* CI
* Update
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
* Update
* Update (#4724)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-26.ap-northeast-1.compute.internal>
* [API Deprecation]Rename DGLHeterpGraph to DGLGraph in Py files (#4835)
* rename DGLHeterpGraph to DGLGraph
* [Sparse] Add sparse matrix C++ implementation (#4773)
* [Sparse] Add sparse matrix C++ implementation
* Add documentation
* Update
* Minor fix
* Move Python code to dgl/mock_sparse2
* Move headers to include
* lint
* Update
* Add dgl_sparse directory
* Move src code to dgl_sparse
* Add __init__.py in tests to avoid naming conflict
* Add dgl sparse so in Jenkinsfile
* Complete docstring & SparseMatrix basic op
* lint
* Disable win tests
* fix lint issue
* [Misc] clang-format auto fix. (#4831)
* [Misc] clang-format auto fix.
* blabla
* nolint
* blabla
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
* [Dist] enable access DistGraph.edges via canonical etype (#4814)
* [Dist] enable access DistGraph.edges via canonical etype
* refine code
* refine test
* refine code
* Reading files in chunks to reduce the memory footprint of pyarrow (#4795)
All tasks completed.
* [Dist] Create <graph_name>_stats.txt file if it does not exist before ParMETIS execution (#4791)
* check if stats file exists, if not create one before parmetis run
* correct the typo error and correctly use constants.GRAPH_NAME
* alltoall returns tensor list with None values, which is failing torch.cat(). (#4788)
* replace batch_hetero
* [Misc] Add // NOLINT for the very long code. (#4834)
* alternative
* fix
* remove_todo
* blabl
* ablabl
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
* fix (#4841)
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
* a better way to init threadlocal prng (#4808)
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
* [DIST] Message size to retrieve SHUFFLE_GLOBAL_NIDs is resulting in very large messages and resulting in killed process (#4790)
* Send out the message to the distributed lookup service in batches.
* Update function signature for allgather_sizes function call.
* Removed the unnecessary if statement .
* Removed logging.info message, which is not needed.
* [Misc] Minor code style fix. (#4843)
* [Misc] Change the max line length for cpp to 80 in lint.
* blabla
* blabla
* blabla
* ablabla
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>
* [Sparse] Lint C++ files (#4845)
* [Dist] Fix typo of metis preprocess in dist partitin pipeline
* Fix ogb/ogbn-mag/heter-RGCN example (#4839)
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
* fix issue
* [Misc] Update cpplint. (#4844)
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Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>
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Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>
Co-authored-by: kylasa <kylasa@gmail.com>
Co-authored-by: Muhammed Fatih BALIN <m.f.balin@gmail.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
* [API Deprecate]Remove as_heterograph and as_immutable_graph (#4851)
* Remove batch_hetero and unbatch_hetero
* [API Deprecate]Rename DGLHeterpGraph to DGLGraph in python files (#4833)
* remove training new line
* remove node_attrs and edge_attrs in batch.py (#4890)
* [API Deprecation] Remove copy_src,copy_edge,src_mul_edge in dgl.function (#4891)
* remove emb_tensor in NodeEmbedding (#4892)
* [API Deprecation]Remove 5 APIs in DGLGraph (#4902)
* [API Deprecation]Remove APIs in old dgl section in DGLGraph (#4901)
* [API Deprecation]Remove adjacency_matrix_scipy and inplace args in candidates (#4895)
* [API Deprecation] Remove add_edge in DGLGraph (#4894)
* [API Derepcation]Remove __contains__ in DGLGraph (#4937)
* [API Deprecation]Remove edge_id() and force_multi argument in edge_ids() (#4896)
* fix issue
* remove deprecated_kwargs
* remove unused import
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: Chang Liu <chang.liu@utexas.edu>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>
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Co-authored-by: Israt Nisa <nisisrat@amazon.com>
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Co-authored-by: Muhammed Fatih BALIN <m.f.balin@gmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
* fix uva sampling with features
* fix
* add is_listlike function to distinguish strings from sequence
* fix
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
* fix lint for graph_index.py
* pylint for base.py
* pylint for batched_graph.py
* pylint for frame.py; simplify and fix bugs in frame when index is slice type
* pylint for graph.py
* pylint for immutable_graph_index.py
* pylint for init.py
* pylint for rest files in root package
* pylint for _ffi package
* pylint for function package
* pylint for runtime package
* pylint for runtime.ir package
* add pylint to ci
* fix mx tests
* fix lint errors
* fix ci
* fix as requested
* fix lint
* lazy eval edge ids.
* parallelize node id lookup.
* fix a bug.
* use mxnet for index.
* use update_all in the subgraph training.
* sample neighbors.
* Revert "parallelize node id lookup."
This reverts commit e661f69bb06cb5a7c246f0e106f245e27800e220.
* update README.
* cache subgraphs.
* support all degrees.
* cache adj in CPU.
* fix a bug in sse.
* print.
* raise error on mutable graphs.
* measure train time per epoch.
* fix a bug in graph_index.
* remove readonly in DGLSubGraph.
* cache subgraph properly.
* accelerate getting adjacency.
* split infer.
* lazy eval edges.
* specify inference mode.
* update for new sampler.
* use new mxnet sampling api.
* fix indent.
* remove profiling code.
* remove mxnet from sampler.
* return a lambda function for graph edges.
* add docs for immutable subgraph.
* Revert "return a lambda function for graph edges."
This reverts commit 0de5d7f100e230c518a3fb8976a6227f474d09ee.
* get parent_eid.
* subgraph copy from
* WIP
* cached members
* Change all usage of id tensor to the new Index object; remove set device in DGLGraph;
* subgraph merge API tested
* add dict type reduced msg test
* subgraph
* more test cases
* WIP
* new FrameRef and test
* separate nx init code
* WIP
* subgraph code and test
* line graph code and test
* adding new test for adding new features on line graphs
* no backtracking line graph
* fix inplace relabel
Songqing Zhang