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

* fixes

* fix

* more fixes

* update

* oops

* lint?

* temporarily revert - will fix in another PR

* more fixes

* skipping mxnet test

* address comments

* fix DDP

* fix edge dataloader exclusion problems

* stupid bug

* fix

* use_uvm option

* fix

* fixes

* fixes

* fixes

* fixes

* add evaluation for cluster gcn and ddp

* stupid bug again

* fixes

* move sanity checks to only support DGLGraphs

* pytorch lightning compatibility fixes

* remove

* poke

* more fixes

* fix

* fix

* disable test

* docstrings

* why is it getting a memory leak?

* fix

* update

* updates and temporarily disable forkingpickler

* update

* fix?

* fix?

* oops

* oops

* fix

* lint

* huh

* uh

* update

* fix

* made it memory efficient

* refine exclude interface

* fix tutorial

* fix tutorial

* fix graph duplication in CPU dataloader workers

* lint

* lint

* Revert "lint"

This reverts commit 805484dd553695111b5fb37f2125214a6b7276e9.

* Revert "lint"

This reverts commit 0bce411b2b415c2ab770343949404498436dc8b2.

* Revert "fix graph duplication in CPU dataloader workers"

This reverts commit 9e3a8cf34c175d3093c773f6bb023b155f2bd27f.
Co-authored-by: xiny <xiny@nvidia.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

* modify hetero

* modify rst document

* update hetero

* update hetero

* update hetero

* update hetero

* Update

* Update

* Update

* Update

* 20220216

* Update

* Update

* Fix
Co-authored-by: Mufei Li <mufeili1996@gmail.com>
Co-authored-by: ShelkerX <925089962@qq.com>

* implement pin_memory/unpin_memory/is_pinned for dgl.graph

* update python docstring

* update c++ docstring

* add test

* fix the broken UnifiedTensor

* XPU_SWITCH for kDLCPUPinned

* a rough version ready for testing

* eliminate extra context parameter for pin/unpin

* update train_sampling

* fix linting

* fix typo

* multi-gpu uva sampling case

* disable new format materialization for pinned graphs

* update python doc for pin_memory_

* fix unit test

* UVA sampling for link prediction

* dispatch most csr ops

* update graphsage example to combine uva sampling and UnifiedTensor

* update graphsage example to combine uva sampling and UnifiedTensor

* update graphsage example to combine uva sampling and UnifiedTensor

* update doc

* update examples

* change unitgraph and heterograph's PinMemory to in-place

* update examples for multi-gpu uva sampling

* update doc

* fix linting

* fix cpu build

* fix is_pinned for DistGraph

* fix is_pinned for DistGraph

* update graphsage unsupervised example

* update doc for gpu sampling

* update some check for sampling device switching

* fix linting

* adapt for new dataloader

* fix linting

* fix

* fix some name issue

* adjust device check

* add unit test for uva sampling & fix some zero_copy bug

* fix linting

* update num_threads in graphsage examples
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.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

* 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

* Update ginconv.py

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

* 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

* Update

* Update

* Update

* Update

* Update

* CI

* CI

* CI
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

* Fix a bug in TWIRLS, add unittest

* reformatting the code

* modify unittest for TWIRLS
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

* Update

* Update

* Fix

* Update

* Update

* update

* Fix test

* CI

* CI

* add

* fix optional docing

* fix

* lint

* add normalized by edge weight

* add test

* fix

* lint

* fix docs

* fix

* fix docs

* Update

* Fix

* [Feature] enable async transfer in NodeDataLoader for homograph

* fix lint issues

* fix device choose when creating stream

* fix test on cpu only machine

* fix pin_memory config

* support homo only

* avoid creating stream in each step and sync via event

* fix lint

* enable graph copy on non-default stream

* fix lint

* refine arg description

* fix conflicts

* first commit

* next commit

* third commit

* add ShaDow-GNN sampler and unit tests

* fixes

* lint

* cr*p

* lint

* fix lint

* fixes and more unit tests

* more tests

* fix docs

* lint

* fix

* fix

* fix

* fixes

* fix doc

* Update

* Update

* Update

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* Fix

* Fix

* Update

* Update

* Update

* Update

* Update

* Update

* lint fix

* lint fix

* Fix lint

* Update

* Fix CI

* Fix CI

* Fix

* CI

* Fix

* Update

* Fix

* Fix

* Fix CI

* Fix CI

Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com>

* enable unit tests for dataloader on the GPU

* fix compatibility

* copyright

* fix linting
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com>

* [Model][Core] GATv2

* lint

* gatv2conv.py

* lint

* lint

* style and docs

* lint

* gatv2conv fix
Co-authored-by: Shaked Brody shakedbr@campus.technion.ac.il <shakedbr@tangerine.cslcs.technion.ac.il>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* added nn pytorch egatconv

* aligned with test build

* aligned with test build

* fixed wihite spaces

* fixed wihite spaces

* fixed wihite spaces

* added missing egatconv in imports

* added indentation in forward

* GATConv based implementation

* removed **kw_args

* added dgl relative imports

* PR corrections

* added DGL Error to EGATConv imports

* Update test_nn.py
Co-authored-by: Argusmocny <k.kaminski@cent.uw.edu.pl>
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* [Feature] enable create/set/free cuda stream for internal use

* add unit test

* fix unit test failure on mxnet and tf

* refactor stream wrapper

* fix lint error

* fix lint error

* fix start_idx

* fix the bug when cuda > 0
Co-authored-by: Tong He <hetong007@gmail.com>

* Add pytorch-direct version

* remove

* Add multi-gpu unified tensor test for pytorch

* relocate verification step to each process

* reduce number of workers

* add parameter
Co-authored-by: shhssdm <shhssdm@gmail.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

* 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>

[Feature][Performance][GPU] Introducing UnifiedTensor for efficient zero-copy host memory access from GPU (#3086)

* Add pytorch-direct version

* Initial commit of unified tensor

* Merge branch 'master' of https://github.com/davidmin7/dgl



* Remove unnecessary things

* Fix error message

* Fix/Add descriptions

* whitespace fix

* add unpin

* disable IndexSelectCPUFromGPU with no CUDA

* add a newline for unified_tensor.py

* Apply changes based on feedback

* add 'os' module

* skip unified tensor unit test for cpu only

* Update tests/pytorch/test_unified_tensor.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* reflect feedback
Co-authored-by: shhssdm <shhssdm@gmail.com>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* fix.

* fix.

* fix.

* fix.

* Fix test

* Deprecate old DistEmbedding impl, use synchronized embedding impl

* update doc
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>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

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

* add left normalizer for gcn

* fix

* fixes and some bug stuff

* csr and csc creation

* fix

* fix

* fixes to adj transpose

* fine

* raise error if indptr did not match number of nodes

* fix

* huh?

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

[Bug fix] Use shared memory for grad sync when NCCL is not avaliable as PyTorch distributed backend. (#3034)

* Use shared memory for grad sync when NCCL is not avaliable as PyTorch distributed backend.

Fix small bugs and update unitests

* Fix bug

* update test

* update test

* Fix unitest

* Fix unitest

* Fix test

* Fix

* simple update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-212.ec2.internal>

* add unit test

* Extend NDArrayPartition object

* Add method for setting embedding, and improve documentation

* Sync before returning

* Use name unique to sparse embedding class to avoid delete
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* fix gatedgcn

* fix lint

* Split from NCCL PR

* Fix type in comment

* Expand documentation for sparse_all_to_all_push

* Restore previous behavior in example

* Re-work optimizer to use NCCL based on gradient location

* Allow for running with embedding on CPU but using NCCL for gradient exchange

* Optimize single partition case

* Fix pylint errors

* Add missing include

* fix gradient indexing

* Fix line continuation

* Migrate 'first_step'

* Skip tests without enough GPUs to run NCCL

* Improve empty tensor handling for pytorch 1.5

* Fix indentation

* Allow multiple NCCL communicator to coexist

* Improve handling of empty message

* Update python/dgl/nn/pytorch/sparse_emb.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* Update python/dgl/nn/pytorch/sparse_emb.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* Keepy empty tensor dimensionaless

* th.empty -> th.tensor

* Preserve shape for empty non-zero dimension tensors

* Use shared state, when embedding is shared

* Add support for gathering an embedding

* Fix typo

* Fix more typos

* Fix backend call

* Use NodeDataLoader to take advantage of ddp

* Update training script to share memory

* Only squeeze last dimension

* Better handle empty message

* Keep embedding on the target device GPU if dgl_sparse if false in RGCN example

* Fix typo in comment

* Add asserts

* Improve documentation in example
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* reorg and expose dgl.geometry

* fix lint

* fix test

* fix

* add bruteforce impl

* add support for bruteforce-sharemem

* modify python API

* add tests

* change file path

* change python API

* fix lint

* fix test

* also check worst_dist in the last few dim

* use heap and early-stop on CPU

* fix lint

* fix lint

* add device check

* use cuda function to determine max shared mem

* use cuda to determine block info

* add memory free for tmp var

* update doc-string and add dist option

* fix lint

* add more tests
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* Make loader items iterator

* Update test_dataloader.py

* Update __init__.py

* Update test_dataloader.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* Draft for sparse emb

* add some notes

* Fix

* Add sparse optim for dist pytorch

* Update test

* Fix

* upd

* upd

* Fix

* Fix

* Fix bug

* add transductive exmpale

* Fix example

* Some fix

* Upd

* Fix lint

* lint

* lint

* lint

* upd

* Fix lint

* lint

* upd

* remove dead import

* update

* lint

* update unitest

* update example

* Add adam optimizer

* Add unitest and update data

* upd

* upd

* upd

* Fix docstring and fix some bug in example code

* Update rgcn readme
Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-24-210.ec2.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-66.ec2.internal>

* Update

* update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-59-108.us-west-2.compute.internal>