GitLab

* add ToLevi transform

* fix parameter typo

* fix lint issues

* fix device issue

* refine according to dongyu's comments
Co-authored-by: rudongyu <ru_dongyu@outlook.com>

rename DGLHeteroGraph to DGLGraph

* update accumulator

* rename half to __half

* add bfloat16

* simplify code

* fix another case

* add unit test

* disable half-precision SpMMCoo

* fix lint

* add bf16 specializations

* remove SWITCH_BITS

* enable amp for bf16

* remove SWITCH_BITS for cpu kernels

* enbale bf16 based on CUDART

* fix compiling for sm<80

* fix cpu build

* enable unit tests

* update doc

* disable test for CUDA < 11.0

* address comments

* address comments

* shortest dist

* update

* address issues

* update

* fix indent

* lint

* fix indent

* [Dist] deprecate etype and always use canonical etype for partition and load

* enable canonical etypes in dist part pipeline

* resolve rebase conflicts

* fix lint

* fix test failure

* throw exception if outdated part config is loaded

* refine

* refine

* revert unnecessary change

* fix typo

* sample neighbors with masks

* oops

* refactor again

* remove

* remove debug code

* rename macro

* address comments

* more stuff

* remove

* fix

* try fix unit test

* oops

* fix test

* oops

* change name

* rename a lot of stuff

* oops

* ugh

* misc fixes

* lint

* address a lot of comments

* lint

* lint

* fix

* that was silly

* fix

* fix

* fix

* oops

* sample neighbors with masks

* oops

* refactor again

* remove

* remove debug code

* rename macro

* address comments

* address comment

* address comments

* rename a lot of stuff

* oops

* Update

* Update

* Update

* Update

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

* [Feature] enable to save graphs in multiple formats

* use StreamWithCount to accomodate formats

* fix lint

* fix dynamic cast issue

* fix lint

* refine docstring and code naming

* update docstring

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal>

* refactor the function and module of laplacian_pe

* add blank lines between design doc

* 1st approving review

* update the unittest

* fix lint issues

* fix trailing space

* update by mufei's comments and fix backend bugs

* del test file
Co-authored-by: rudongyu <ru_dongyu@outlook.com>
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>

* updates

* Enable caching C++ result

* Add missing docstring

* Remove unused function

* Add unit test

* Address comments

[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>

* 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>

* Remove async_transferer

* remove test

* Remove AsyncTransferer
Co-authored-by: Xin Yao <xiny@nvidia.com>
Co-authored-by: Xin Yao <yaox12@outlook.com>

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

* fix test failure in TF

* bunch of fixes

* Update test_edge_softmax_hetero.py

* Update test_edge_softmax_hetero.py
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* enable use for weighted neighbor sampler and biased random walk

* add unit tests

* fix for mxnet/tf

* fix typo

* add weighted sampling without replacement (A-Chao)

* improve Algorithm A-Chao with block-wise prefix sum

* correctly fill out_idxs

* implement weighted sampling with replacement

* small fix

* merge host-side code of weighted/uniform sampling

* enable unit tests for cuda weighted sampling

* move thrust/cub wrapper to the cmake file

* update docs accordingly

* fix linting

* fix linting

* fix unit test

* Bump external CUB/Thrust versions

* Fix code style and update description of algorithm design

* [Feature] GPU support weighted graph neighbor sampling
commit by pengqirong(OPPO)

* merge pengqirong's implementation

* revert the change to cub and thrust

* fix linting

* use DeviceSegmentedSort for better performance

* add more comments

* add necessary notes

* add necessary notes

* resolve some comments

* define THRUST_CUB_WRAPPED_NAMESPACE

* fix doc
Co-authored-by: 彭齐荣 <657017034@qq.com>

* Update

* Update functional.py

* Update

* Update test_transform.py

* Update

* Update functional.py

* Update functional.py

* Update functional.py

* Update functional.py

* Update

* Update

* Update functional.py

* Update functional.py

* Update functional.py

* Update functional.py

* Update module.py

* Update test_transform.py

* Update test_transform.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* [Feature] Add CUDA Weighted Randomwalk Sampling

* [Feature] Add CUDA Weighted Randomwalk Sampling

* [Feature] Add CUDA Weighted Randomwalk Sampling

* [Feature] Add CUDA Weighted Randomwalk Sampling

* fix empty prob array && enable non-uniform for restart && enable unit tests

* update doc and guide for randomwalk and pinsage

* update comments
Co-authored-by: zhenliangqiu <ubuntu@ip-172-31-24-245.ap-southeast-1.compute.internal>
Co-authored-by: xiny <xiny@nvidia.com>

* Fix test_csrmm for tensor core

* unset allow tf32 flag

* update test unified tensor

* skip fp16 for CPU

* [Feature] extend sort_csr/csc_by_tag to edge

* fix test ffailure in tensorflow

* refine sorting by edges

* fix docstring

* remove unnecessary mem
Co-authored-by: Xin Yao <xiny@nvidia.com>

* try optimize CI

* fix go test; adjust timing report

* disable certain tests for mx/tf backends

* fix ut

* add pydantic

* * Workaround for graph data saving/loading compatibility problem in Column class.  There may be more places in DGL with the same issue, due to using Python serialization, instead of a more cohesive, comprehensive strategy.  This is just a local fix.

* Add checking for non-empty states

* Add unit test

* Handle the case of columns without storage
Co-authored-by: ndickson <ndickson@nvidia.com>
Co-authored-by: Xin Yao <xiny@nvidia.com>

* Update nccl communicator for when NCCL is missing

* Use static_cast

* Add doc string

* Fix whitespace

* Resrtict unit test to GPU runs
Co-authored-by: Xin Yao <xiny@nvidia.com>

* Explicitly unpin tensoradapter allocated arrays

* Undo unrelated change

* Add unit test

* update unit test

* add pinned_by_dgl flag to NDArray::Container

* use dgl.ndarray for holding the pinning status

* update multi-gpu uva inference

* reinterpret cast NDArray::Container* to DLTensor* in MoveAsDLTensor

* update unpin column and examples

* add unit test for unpin column
Co-authored-by: Dominique LaSalle <dlasalle@nvidia.com>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>

* Add Flickr and Yelp dataset

* Update flickr.py

* update

* Update yelp.py

* Update yelp.py

* update

* Update yelp.py

* Update test_data.py

* Update yelp.py

* update

* Update test_data.py

* Update yelp.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* add argument reorder=False for citation_graph

* add description of the argument reorder

* add reordered/un_reordered save_path

* add version number postfix
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* * Added specialization of cublasGemm function for `__half` type, to try to address https://github.com/dmlc/dgl/issues/3988



* * Added USE_FP16 guard

* * Added test cases to test_segment_mm, to test newly-added FP16 specialization of cublasGemm

* * Replaced for loop in test_segment_mm with pytest.mark.parametrize, as recommended
Co-authored-by: Xin Yao <xiny@nvidia.com>

* Fix bugs & Update dataset

* Update

* Update wikics.py

* Update wikics.py

* Update test_data.py

* Update wikics.py

* Update wikics.py

* Update wikics.py

* update

* Update module.py

* Update dgl.data.rst

* Update wikics.py

* Update wikics.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Update

* CI

* Update

* Update

* Fix

* Fix