GitLab

* WIP: TypedLinear and new RelGraphConv

* wip

* further simplify RGCN

* a bunch of tweak for performance; add basic cpu support

* update on segmm

* wip: segment.cu

* new backward kernel works

* fix a bunch of bugs in kernel; leave idx_a for future

* add nn test for typed_linear

* rgcn nn test

* bugfix in corner case; update RGCN README

* doc

* fix cpp lint

* fix lint

* fix ut

* wip: hgtconv; presorted flag for rgcn

* hgt code and ut; WIP: some fix on reorder graph

* better typed linear init

* fix ut

* fix lint; add docstring

* Update (#5)

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* FIx

* Try

* Update

* Update

* Update

* Fix

* Update

* Fix

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update README.md

* Update

* Fix

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Update

* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-6-240.us-west-2.compute.internal>

* Update

* Update

* Fix

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* CI
Co-authored-by: Ubuntu <ubuntu@ip-172-31-6-240.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-123.us-west-2.compute.internal>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* initial update

* more

* more

* multi-gpu example

* cluster gcn, finalize homogeneous

* more explanation

* fix

* bunch of fixes

* fix

* RGAT example and more fixes

* shadow-gnn sampler and some changes in unit test

* fix

* wth

* more fixes

* remove shadow+node/edge dataloader tests for possible ux changes

* lints

* add legacy dataloading import just in case

* fix

* update pylint for f-strings

* fix

* lint

* lint

* lint again

* cherry-picking commit fa9f494

* oops

* fix

* add sample_neighbors in dist_graph

* fix

* lint

* fix

* fix

* fix

* fix tutorial

* fix

* fix

* fix

* fix warning

* remove debug

* add get_foo_storage apis

* lint

* Update

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix lint

* lint

* Update

* Update

* lint fix

* Fix CI

* Fix

* Fix CI

* Update

* Fix

* Update

* Update

* Augmentation (#10)

* Update

* PPR

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* CI

* lint

* lint

* Update

* Update

* Fix AddEdge

* try import

* Update

* Fix

* CI
Co-authored-by: Ubuntu <ubuntu@ip-172-31-31-136.us-west-2.compute.internal>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Fix lint

* lint

* Update

* Update

* lint fix

* Fix CI

* Fix

* Fix CI

* Update

* Fix

* Update

* Update

* resolve conflict

* Fix CI
Co-authored-by: Ubuntu <ubuntu@ip-172-31-31-136.us-west-2.compute.internal>

* gpu compact graph template

* cuda compact graph draft

* fix typo

* compact graphs

* pass unit test but fail in training

* example using EdgeDataLoader on the GPU

* refactor cuda_compact_graph and cuda_to_block

* update training scripts

* fix linting

* fix linting

* fix exclude_edges for the GPU

* add --data-cpu & fix copyright

[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>

* 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>

* [Feature] enable edge reorder in dgl.reorder_graph()

* refine doc string

* refine doc string for dgl.reorder_graph

* refine doc string further

* [Feature] Add dgl.reorder() to re-order graph according to specified strategy

* fix unit test failure for metis reorder

* fix unit test failure on mxnet_cpu

* refine unit test for dgl.reorder

* fix unit test failure on mxnet

* fix array_equal error for mxnet unit test

* fix unit test failure for mxnet

* convert metis output to numpy array explicitly
Co-authored-by: Tong He <hetong007@gmail.com>

* add distributed in-degree and out-degree.

* update comments.

* fix a bug.

* add tests.

* add tests.

* fix a bug.

* fix docstring.

* update doc.

* fix

* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* return mapping.

* support heterogeneous graph.

* more test.

* fix lint.

* fix for diff backends.

* fix.

* fix.
Co-authored-by: Zheng <dzzhen@3c22fba32af5.ant.amazon.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* fix

* refactor

* upd test

* large feat_len or n in segment reduce

* lint

* Add start of to_block gpu implementation

* Pull in more changes from 0.4.2 cuda_to_block

* Move more code to IdArray

* Refactor DeviceNodeMapMaker

* Updates

* get compiling

* Integrate to_block

* Fix ID allocation

* Minor fixes

* Cleanup cuda calls to use cuda_common

* Reduce kernel calls

* Lint cleanup

* Expand documentation

* Remove unused function

* Rename variables for consistency

* Add doxygen comments

* Fix file extension

* Remove raw asynccopy for deviceapi

* Remove unused function

* Fix block/tile configuration

* Add cuda_device_common.cuh

* Add basic hashtable

* Migrate part of hashtable

* Refactor to use external hashtable

* Make functions members

* Format hash table functions

* Migrate duplicate filling

* Move last function over

* Refactor with cu file

* lint c++ code

* Move context check to C++ code

* Use macro switch

* Add missing files

* Update docstring

* update docs

* Move atomic functions

* Refactor hashtable

* Fix linting

* Expand docs

* Fix mismatched argument names

* Switch doxygen comments from using @param to \param
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* [Bug] add_edges() crashes if the input tensor is empty

* lint

* fix

* Update graph

* Fix for dgl.graph

* from_scipy

* Replace canonical_etypes with relations

* from_networkx

* Update for hetero_from_relations

* Roll back the change of canonical_etypes to relations

* heterograph

* bipartite

* Update doc

* Fix lint

* Fix lint

* Fix test cases

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix test

* Fix

* Update

* Use DGLError

* Update

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* rewrite sanity checks

* delete unnecessary checks

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Fix

* Fix

* Fix

* Update

* Fix

* Update

* Fix

* Fix

* Update

* Fix

* Update

* Fix
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>

* update knn graph docs

* more docs

* [Doc] transform module docstrings

* remove copy_ndata and copy_edata

* fix

* lint

* fix

* fix

* fix

* clean up docstrings

* fix docstring

* dtype specifications

* addresses comments

* fix
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* clean commit

* oops forgot the most important files

* use einsum

* copy feature from frontier to block

* Revert "copy feature from frontier to block"

This reverts commit 5224ec963eb6a3ef1b6ab74d8ecbd44e4e42f285.

* temp fix

* unit test

* fix

* revert jtnn

* lint

* fix win64

* docstring fixes and doc indexing

* revert einsum in sparse bidecoder

* fix some examples

* lint

* fix due to some tediousness in remove_edges

* addresses comments

* fix

* more jtnn fixes

* fix

* fix perf.

* fix.

* accelerate metis.

* fix lint.

* use gklib.

* fix perf.

* fix.

* update metis.

* update launch script

* handle synchronized API.

* fix.

* fix example.

* fix dataloader.

* temp fix.

* temp fix omp.

* distinguish roles.

* initialize iterator of DistDataloader correctly.

* check the correctness of launch script.

* move feature copy to sampler.

* measure mem/network copy time.

* remove

* Revert "measure mem/network copy time."

This reverts commit 86cefdc14b7815fcf5aad6496af912dba48e4aa6.

* fix.

* fix

* fix.

* fix cmake.

* disable metis in windows.

* disable metis tests in windows.

* remove test for multigraph.

* fix test.

* fix.

* fix cmake.

* fix.

* revert.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-115.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal>

* WIP: frame refactor

* new frame

* simple update_all builtin

* move all subgraph routines into the same file

* sddmm & spmm schedule; node & edge udf

* degree bucketing

* some tricky 0deg corner cases

* bug in frame append

* merge test_hetero_basics and test_basics

* some code rearange

* fix test_heterograph

* add mean spmm

* enable all builtin combinations

* pass gpu test

* pass pytorch tests

* wip

* fix some pt debugging codes

* fix bug in mxnet backward

* pass all mxnet utests

* passed tf tests

* docstring

* lint

* lint

* fix broadcasting bugs

* add warning and clamp for mean reducer

* add test for zero-degree mean

* address comments

* lint

* small fix

* Hot fix

* more test
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* Add add_reverse_edges and is_simple_graph
Update to_bidirected

* remove is_simple_graph

* Fix lint

* to bidirected only support cpu

* support copy ndata

* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* Merge

* [Graph][CUDA] Graph on GPU and many refactoring (#1791)

* change edge_ids behavior and C++ impl

* fix unittests; remove utils.Index in edge_id

* pass mx and th tests

* pass tf test

* add aten::Scatter_

* Add nonzero; impl CSRGetDataAndIndices/CSRSliceMatrix

* CSRGetData and CSRGetDataAndIndices passed tests

* CSRSliceMatrix basic tests

* fix bug in empty slice

* CUDA CSRHasDuplicate

* has_node; has_edge_between

* predecessors, successors

* deprecate send/recv; fix send_and_recv

* deprecate send/recv; fix send_and_recv

* in_edges; out_edges; all_edges; apply_edges

* in deg/out deg

* subgraph/edge_subgraph

* adj

* in_subgraph/out_subgraph

* sample neighbors

* set/get_n/e_repr

* wip: working on refactoring all idtypes

* pass ndata/edata tests on gpu

* fix

* stash

* workaround nonzero issue

* stash

* nx conversion

* test_hetero_basics except update routines

* test_update_routines

* test_hetero_basics for pytorch

* more fixes

* WIP: flatten graph

* wip: flatten

* test_flatten

* test_to_device

* fix bug in to_homo

* fix bug in CSRSliceMatrix

* pass subgraph test

* fix send_and_recv

* fix filter

* test_heterograph

* passed all pytorch tests

* fix mx unittest

* fix pytorch test_nn

* fix all unittests for PyTorch

* passed all mxnet tests

* lint

* fix tf nn test

* pass all tf tests

* lint

* lint

* change deprecation

* try fix compile

* lint

* update METIDS

* fix utest

* fix

* fix utests

* try debug

* revert

* small fix

* fix utests

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* trigger

* +1s

* [kernel] Use heterograph index instead of unitgraph index (#1813)

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* upd

* trigger

* +1s

* [Graph] Mutation for Heterograph (#1818)

* mutation add_nodes and add_edges

* Add support for remove_edges, remove_nodes, add_selfloop, remove_selfloop

* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* upd

* upd

* upd

* fix

* [Transfom] Mutable transform (#1833)

* add nodesy

* All three

* Fix

* lint

* Add some test case

* Fix

* Fix

* Fix

* Fix

* Fix

* Fix

* fix

* triger

* Fix

* fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* [Graph] Migrate Batch & Readout module to heterograph (#1836)

* dgl.batch

* unbatch

* fix to device

* reduce readout; segment reduce

* change batch_num_nodes|edges to function

* reduce readout/ softmax

* broadcast

* topk

* fix

* fix tf and mx

* fix some ci

* fix batch but unbatch differently

* new checkk

* upd

* upd

* upd

* idtype behavior; code reorg

* idtype behavior; code reorg

* wip: test_basics

* pass test_basics

* WIP: from nx/ to nx

* missing files

* upd

* pass test_basics:test_nx_conversion

* Fix test

* Fix inplace update

* WIP: fixing tests

* upd

* pass test_transform cpu

* pass gpu test_transform

* pass test_batched_graph

* GPU graph auto cast to int32

* missing file

* stash

* WIP: rgcn-hetero

* Fix two datasety

* upd

* weird

* Fix capsuley

* fuck you

* fuck matthias

* Fix dgmg

* fix bug in block degrees; pass rgcn-hetero

* rgcn

* gat and diffpool fix
also fix ppi and tu dataset

* Tree LSTM

* pointcloud

* rrn; wip: sgc

* resolve conflicts

* upd

* sgc and reddit dataset

* upd

* Fix deepwalk, gindt and gcn

* fix datasets and sign

* optimization

* optimization

* upd

* upd

* Fix GIN

* fix bug in add_nodes add_edges; tagcn

* adaptive sampling and gcmc

* upd

* upd

* fix geometric

* fix

* metapath2vec

* fix agnn

* fix pickling problem of block

* fix utests

* miss file

* linegraph

* upd

* upd

* upd

* graphsage

* stgcn_wave

* fix hgt

* on unittests

* Fix transformer

* Fix HAN

* passed pytorch unittests

* lint

* fix

* Fix cluster gcn

* cluster-gcn is ready

* on fixing block related codes

* 2nd order derivative

* Revert "2nd order derivative"

This reverts commit 523bf6c249bee61b51b1ad1babf42aad4167f206.

* passed torch utests again

* fix all mxnet unittests

* delete some useless tests

* pass all tf cpu tests

* disable

* disable distributed unittest

* fix

* fix

* lint

* fix

* fix

* fix script

* fix tutorial

* fix apply edges bug

* fix 2 basics

* fix tutorial
Co-authored-by: yzh119 <expye@outlook.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-7-42.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-5.us-west-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal>

* slice dstdata from srcdata within nn module

* a bunch of fixes

* add comment

* fix gcmc layer

* repr for blocks

* fix

* fix context

* fix

* do not copy internal columns

* docstring

* metis for hetero

* fix partition

* save mem.

* save mem.

* reduce mem

* fix test

* fix lint

* fix test

* fix.

* fix.

* fix.

* fix.

* fix lint.

* fix backend operator.

* fix tensorflow operators.

* fix.

* revert change in mxnet operator.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal>

* code

* joint_union

* joint union pass all test

* test case for test_transform

* upd

* lint

* lint

* Fix

* list

* Fix

* Fix

* update to_bidirected impl

* Fix

* Fix

* upd

* remove joint_union
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* To simple

* lint

* upd

* more test

* fix

* Fix

* Fix

* add share edata

* doc

* Fix

* Fix

* Fix

* Fix

* lint

* lint

* Fix

* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* reverse

* Add more test

* Fix lint

* Fix

* move to transform

* upd

* upd

* upd

* Add more test

* lint

* Fix

* Fix doc

* Fix

* test

* doc

* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* line graph

* update docstring

* Add test and compile OK

* Add python API

* Fix linty

* Fix

* Fix

* upd

* upd

* Fix

* merge

* Fix

* fix

* upd

* lint

* Fix
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* Matrix to simple

* Pass test

* new impl

* Fix test

* Fix lint

* trigger

* upd

* Fix comments
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal>

* add cub; array cumsum

* CSRSliceRows

* fix warning

* operator << for ndarray; CSRSliceRows

* add CSRIsSorted

* add csr_sort

* inplace coosort and outplace csrsort

* WIP: coo is sorted

* mv cuda_utils

* add AllTrue utility

* csr sort

* coo sort

* coo2csr for sorted coo arrays

* CSRToCOO from sorted

* pass tests for the new kernel changes

* cannot use inplace sort

* lint

* try fix msvc error

* Fix g.copy_to and g.asnumbits; ToBlock no longer uses CSC

* stash

* revert some hack

* revert some changes

* address comments

* fix

* fix to_block unittest

* add todo note

* add constraint.

* fix bugs.

* temp fix.

* fix lint

* add balance_ntypes and balance_edges

* add comments.

* fix.

* fix

* Fix bugs in partitioning.

* add comment.

* fix lint.

* fix test.

* add more tests.

* simplify the fix

* fix.

* add reorder immutable graph.

* add python API.

* add reorder for csr.

* remove gk version.

* fix

* add cpp test.

* bug fixes

* fix tests.

* fix bugs and add check

* fix test.

* add omp.

* add comments.

* add coo reorder.

* fix a bug.

* handle reorder for different graph structues.

* fix lint.

* fix.

* add original ids.

* reshuffle nodes before metis partition.

* inner nodes are in contiguous Id range.

* reshuffle nodes/edges when partitioning.

* load partition return graph partition book.

* use inner_node/inner_edges

* add and test range partition book.

* count inner_edge correctly.

* fix lint.

* fix lint.

* fix lint.

* fix errors.

* fix errors.

* fix for TF.

* fix.

* fix.

* change docstring.

* support logical and.

* add comments.

* avoid copy.

* fix

* update docstring.

* fix a bug.

* add range search.

* fix

* fix a bug.

* add more tests.

* load graph partition book.

* support shared memory for range partition book.

* fix a bug.

* fix.

* fix lint.

* remove check

* fix test.

* remove num_nodes and num_edges

* fix lint.

* fix graph partition book.

* address comments.

* use makedirs.

* fix compile
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Chao Ma <mctt90@gmail.com>

* 111

* 111

* lint

* lint

* lint

* lint

* fix

* lint

* try

* fix

* lint

* lint

* test

* fix

* ttt

* test

* fix

* fix

* fix

* mxnet

* 111

* fix 64bits computation

* pylint

* roll back

* fix

* lint

* fix hetero_from_relations

* remove index_dtype in to_homo and to_hetero

* fix

* fix

* fix

* fix

* remove default

* fix

* lint

* fix

* fix error message

* fix error

* lint

* macro dispatch

* try

* lint

* remove nbits

* error message

* fix

* fix

* lint

* lint

* lint

* fix

* lint

* fix

* fix random walk

* lint

* lint

* fix

* fix

* fix

* lint

* fix

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

* Update

* Update

* Update