GitLab

Co-authored-by: Hesham Mostafa <hesham.mostafa@intel.com>

Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com>

* adding LABOR sampling

* add ladies and pladies samplers

* fix compile error after rebase

* add reference for ladies sampler

* Improve ladies implementation.

* weighted labor sampling initial implementation draft
fix indentation and small bug in ladies script

* importance_sampling currently doesn't work with weights

* fix weighted importance sampling

* move labor example into its own folder

* lint fixes

* Improve documentation

* remove examples from the main PR

* fix linting by not using c++17 features

* fix documentation of labor_sampler.py

* update documentation for labor.py

* reformat the labor.py file with black

* fix linting errors

* replace exception use with if

* fix typo in error comment

* fixing win64 build for ci

* fixing weighted implementation, works now.

* fix bug in the weighted case and importance_sampling==0

* address part of the reviews

* remove unused code paths from cuda

* remove unused code path from cpu side

* remove extra features of labor making use of random seed.

* fix exclude_edges bug

* remove pcg and seed logic from cpu implementation, seed logic should still work for cuda.

* minor style change

* refactor CPU implementation, take out the importance_sampling probability computation into a function.

* improve CUDAWorkspaceAllocator

* refactor importance_sampling part out to a function

* minor optimization

* fix linting issue

* Revert "remove pcg and seed logic from cpu implementation, seed logic should still work for cuda."

This reverts commit c250e07ac6d7e13f57e79e8a2c2f098d777378c2.

* Revert "remove extra features of labor making use of random seed."

This reverts commit 7f99034353080308f4783f27d9a08bea343fb796.

* fix the documentation

* disable NIDs

* improve the documentation in the code

* use the stream argument in pcg32 instead of skipping ahead t times, can discard the use of hashmap now since it is faster this way.

* fix linting issue

* address another round of reviews

* further optimize CPU LABOR sampling implementation

* fix linting error

* update the comment

* reformat

* rename and rephrase comment

* fix formatting according to new linting specs

* fix compile error due to renaming, fix linting.

* lint

* rename DGLHeteroGraph to DGLGraph to match master

* replace other occurrences of DGLHeteroGraph to DGLGraph
Co-authored-by: Muhammed Fatih BALIN <m.f.balin@gmail.com>
Co-authored-by: Kaan Sancak <kaansnck@gmail.com>
Co-authored-by: Quan Gan <coin2028@hotmail.com>

* [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>

* [Misc] clang-format auto fix.

* blabla

* ablabla

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

* replace

* blabla

* balbla

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

* param

* brief

* note

* return

* tparam

* brief2

* file

* return2

* return

* blabla

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

* 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

* 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

* Based on issue #3436. Improving _SegmentCopyKernel s GPU utilization by switching to nonzero based thread assignment

* fixing lint issues

* Update cub for cuda 11.5 compatibility (#3468)

* fixing type mismatch

* tx guaranteed to be smaller than nnz. Hence removing last check

* minor: updating comment

* adding three unit tests for csr slice method to cover some corner cases

* timing repeatkernel

* clean

* clean

* clean

* updating _SegmentMaskColKernel

* Working on requests: removing sorted array check and adding comments to utility functions

* fixing lint issue

* Optimizing disjoint union kernel

* Trying to resolve compilation issue on CI

* [EMPTY] Relevant commit message here

* applying revision requests on cpu/disjoint_union.cc

* removing unnecessary casts

* remove extra space
Co-authored-by: Abdurrahman Yasar <ayasar@nvidia.com>
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* first commit

* a bunch of fixes

* add unique

* lint

* lint

* lint

* address comments

* Update negative_sampler.py

* fix

* description

* address comments and fix

* fix

* replace unique with replace

* test pylint

* Update negative_sampler.py

* first commit

* second commit

* spaghetti unit tests

* rewrite test

[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>

* 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>

* update

* update

* update

* update

* lint

* lint

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* lint

* update

* clone

* update

* update

* update

* update

* replace idarray with ndarray

* refactor cpp part

* refactor python part

* debug

* refactor interface

* test and doc

* lint and test

* lint

* fix

* fix

* fix

* const

* doc

* fix

* fix

* fix

* fix

* fix & doc

* fix

* fix

* update

* update

* update

* merge

* doc

* doc

* lint

* fix

* more tests

* doc

* fix

* fix

* update

* update

* update

* fix

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

* update

* update

* update

* update

* lint

* lint

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* update

* lint

* update

* clone

* update

* update

* update

* update

* replace idarray with ndarray

* refactor cpp part

* refactor python part

* debug

* refactor interface

* test and doc

* lint and test

* lint

* fix

* fix

* fix

* const

* doc

* fix

* fix

* fix

* fix

* fix & doc

* fix

* fix

* fix

* fix

* fix

* fix

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

* test commit

* fixes

* oops

* add docs

* lint

* why does it say I have a trailing whitespace

* oh ok

* fixes

* why there's an invalid argument error

* address comments

* fix

* address comments

* init cuda support

* cuSPARSE err

* passed unittest for csr_mm/SpGEMM. int64 not supported

* Debugging cuSPARSE error 3

* csrgeam only supports int32?

* disabling int64 for cuda

* refactor and add CSRMask

* lint

* oops

* remove todo

* rewrite CSRMask with CSRGetData

* lint

* fix test

* address comments

* lint

* fix

* addresses comments and rename BUG_ON
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-30-71.ec2.internal>
Co-authored-by: Quan Gan <coin2028@hotmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* Remove double-checking sorted

* Remove sorting of CSR by default

* Update unit test to use unsorted matix

* delete whitespace

* Expand unit tests

* Replace cusparse sort

* Fix row column sorting

* Explicitly don't sort columns

* Fix linting errors

* Fix bit-width calculation

* Fix sorting assertion and unit test

* Fix linting

* Improve CPU COO2CSR

* Remove references

* Rename and add documentation to edge encoding/decoding funcionts

* Fix sorting keys as 64 bit

* Revert cosmetic changes to unit tests

* Update documentation

* Update complexity documentation for coo to csr conversion

* Remove COOIsSorted check in CPU implementation too

* COO sort

* COOToCSR

* CSR2COO

* CSRSort; CSRTranspose

* pass all CSR tests

* lint

* remove int32 conversion

* fix tensorflow nn tests

* turn on CI

* fix

* addreess comments

* 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>

* 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 union

* Pass test

* Fix lint

* return map for unionCOO/unionCSR

* Revert "return map for unionCOO/unionCSR"

This reverts commit 28e96c40f0659f02b33d88bcf528af6a6267726d.

* Update

* lint

* lint

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

* 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 nonzero op

* 111

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

* start

* coo csr union partition

* lint

* lint

* lint

* Add matrix->data transform

* update

* Fix window compile

* Add CSR support for DisjointPartition

* lint

* Fix

* Use IdArray Op

* Concat ready

* Fix and all pass

* resolve comments

* Add union COO C++ test

* Add C++ test for csr

* lint

* triger

* Update include

* Fix merge

* test
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 cuda utils; change g.to; add g.device

* split array.h into several headers

* cuda index select

* file

* three cuda kernels

* add cuda elementwise arith and several others

* cuda CSRIsNonZero

* fix lint

* lint

* lint

* fix bug in changing ctx to property

* address comments

* remove unused codes

* address comments

* traversal to new framework

* add new

* Fix compile

* Pass test

* keep old version

* lint

* lint

* Fix

* Fix

* Fix compatability with new master

* Fix test and tutorials

* Update according to comments

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

* 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>

* remove edge and to bipartite and graphsage with sampling

* fixes

* fixes

* fixes

* reenable multigpu training

* fixes

* compatibility in DGLGraph

* rename to compact_as_bipartite

* bugfix

* lint

* add offline inference

* skip GPU tests

* fix

* addresses comments

* fix

* fix

* fix

* more tests

* more docs and unit tests

* workaround for empty slice on empty data

* [WIP] PinSAGE operators

* moved the edge remapping mess into C

* some docstrings

* lint

* lint x2

* lint x3

* skip gpu test on topk

* extend pinsage to any metapath

* lint x4

* addresses #1265

* add always_preserve (fixes #1266) and fix a silly bug

* disable gpu test on compaction

* lint

* fix a horrible bug and add more tests

* lint

* addresses comments

* lint

* bugfix

* addresses comments
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu>

* WIP: working on random choices

* light slice

* basic CPU impl

* add python binding; fix CreateFromCOO and CreateFromCSR returning unitgraph

* simple test case works

* fix bug in slicing probability array

* fix bug in getting the correct relation graph

* fix bug in creating placeholder graph

* enable omp

* add cpp test

* sample topk

* add in|out_subgraph

* try fix lint; passed all unittests

* fix lint

* fix msvc compile; add sorted flag and constructors

* fix msvc

* coosort

* COOSort; CSRRowWiseSampling; CSRRowWiseTopk

* WIP: remove DType in CSR and COO; Restrict data array to be IdArray

* fix all CSR ops for missing data array

* compiled

* passed tests

* lint

* test sampling out edge

* test different per-relation fanout/k values

* fix bug in random choice

* finished cpptest

* fix compile

* Add induced edges

* add check

* fixed bug in sampling on hypersparse graph; add tests

* add ascending flag

* in|out_subgraph returns subgraph and induced eid

* address comments

* lint

* fix

* unit graph that prefers coo queries

* auto detect coo preference

* forgot some functions

* disable lint on detect_prefer_coo

* reorg

* change comment

* lint

* fix

* move array_utils.h to src

* compact graph impl

* fix redundant copying in idhashmap

* docstring

* moving preference detection to C

* lint

* fix unit test & address comments

* hypersparse autorestrict

* docstring & fix

* revert copyto and asnumbits

* fix stupid bug

* lint

* leave a TODO for sorted COO

* fixing same node type mapping to different id in different graphs

* addresses comments

* made induced nodes a feautre column

* lint?

* trying to refactor IndexSelect

* partial implementation

* add index select and assign for floats as well

* move to random choice source

* more updates

* fixes

* fixes

* more fixes

* adding python impl

* fixes

* unit test

* lint

* lint x2

* lint x3

* update metapath2vec

* debugging performance

* still debugging for performance

* tuning

* switching to succvec

* redo

* revert non-uniform sampler to use vector

* still not fast

* why does this crash with OpenMP???

* because there was a data race!!!

* add documentations and remove assign op

* lint

* lint x2

* lol what have i done

* lint x3

* fix and disable gpu testing

* bugfix

* generic random walk

* reorg the random walk source code

* Update randomwalks.h

* Update randomwalks_cpu.cc

* rename file

* move internal function to anonymous ns

* reorg & docstrings

* constant restart probability

* docstring fix

* more commit

* random walk with restart, tested

* some fixes

* switch to using NDArray for choice

* massive fix & docstring

* lint x?

* lint x??

* fix

* export symbols

* skip gpu test

* addresses comments

* replaces another VecToIdArray

* add randomwalks.h to include

* replace void * with template

* sort

* sort in parallel.

* fix a bug in sorting adj

* rename.

* add more comments.

* accelerate GetData

* fix tests.

* avoid sorting multiple times.

* add test.

* change back.

* sort.

* add sort_csr.

* Fix a bug.

* fix.

* revert modifcation.

* rename

* speed up EdgeIds.

* WIP: array refactoring

* WIP: implementation

* wip

* most csr part

* WIP: on coo

* WIP: coo

* finish refactoring immutable graph

* compiled

* fix undefined ndarray copy bug; add COOToCSR when coo has no data array

* fix bug in COOToCSR

* fix bug in CSR constructor

* fix bug in in_edges(vid)

* fix OutEdges bug

* pass test_graph

* pass test_graph

* fix bug in CSR constructor

* fix bug in CSR constructor

* fix bug in CSR constructor

* fix stupid bug

* pass gpu test

* remove debug printout

* fix lint

* rm biparate grpah

* fix lint

* address comments

* fix bug in Clone

* cpp utests