GitLab

* [Performance] improve coo2csr space complexity when row is not sorted

* [Perf] replace std::vector<> by NDArray

* keep both impl of unsorted coo to csr and choose according to graph density dynamically

* refine criteria to choose btw Unsorted algos
Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-27.us-west-2.compute.internal>

* Fixes bug #3312

* Fixing lint errors
Co-authored-by: Mufei Li <mufeili1996@gmail.com>

* Added binary builtinMsgFunc forward() for heterograph

* Added backward for u_op_v

* Supports all binary builtin forward

* Supports binary message funcs with reduce func sum

* lint check

* removed import torch from unittest

* enabled GPU test

* lint check

* Fixed docstrings

* rename func get_hs_id

* edited comment
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

* remove

* remove

* fix

* remove

* remove

* [CPU, Parallel] Rewriting omp pragmas with parallel_for

* [CPU, Parallel] Decrease number of calls to task function

* c[CPU, Parallel] Modify calls to new interface of parallel_for

[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>

* Optimize sampling

* Stop initialization of array

* Fix includes for linting

* Move comment

* Fix replace
Co-authored-by: Da Zheng <zhengda1936@gmail.com>

* Update filter code

* Add unit tests

* Fixes

* Switch to indices

* Rename functions

* Fix linting

* Fix whitespace

* Add doc

* Fix heterograph

* Change workspace allocation

* Fix linting

* Fix docs in filter.py

* Add todo
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* Add pytorch-direct version

* remove

* add documentation for UnifiedTensor

* Revert "add documentation for UnifiedTensor"

This reverts commit 63ba42644d4aba197c1cb4ea4b85fa1bc43b8849.

* alignment fix for UnifiedTensor access

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

* Split out separate generators for each thread

* Amortize cost of curand_init

* Improve readability
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.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>

* remove redundant fill

* trigger ci

[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>

* optimizations of spmm for CPU

* Added names of contributors

* Minor code cleanup

* Moved the spmm optimization code to a new header file

* Moved to DGL's logging method

* removed duplicate code between SpMMSumCsr and SpMMCmpCsr

* Changes made to follow Google coding style

* Fixed lint errors in spmm.h

* Fixed some lint errors from spmm_blocking_libxsmm.h

* Fixed lint errors from spmm_blocking_libxsmm.h

* Added comments to SpMMCreateLibxsmmKernel

* to enable building of tests, and other cosmetic changes

* disabling libxsmm on windows

* Put a condition to avoid opt impl for FP64 as libxsmm does not have FP64 support yet

* cosmetic changes and documentation

* cosmetic changes

* to pass lint tests

* replaced multiple allocations for buffers of indices and edges with a single allocation
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

[Feature] Add Heterograph support on Python for builtin unary msg functions (copy_u, copy_e) (#2989)

* heterograph for binary func

* Added SDDMM support

* Added unittest

* added binary test cases

* unary mfuncs works

* Fixed lint err

* lint check and others

* link check

* fixed import *_hetero issue

* lint check

* replace torch with dgl backend

* lint cehck

* removed torch from test

* skip mxnet unittest

* skip gpu test

* Remove unused/duplicated code

* minor

* changed data structure of ndata and edata

* link check

* reorganized

* minor lint

* minor lint

* raise error for udf func

* lint check

* fix for CUDA 10.1

* add a note for future cross-type max/min reducing

* Add support CUDA < 11

* lint check

* tidied C code

* remove dummy GSDDMM_hetero backward implementation
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>
Co-authored-by: Quan Gan <coin2028@hotmail.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>

* Added heterograph support SpMM, SDDMM

* bug fix cuda stream

* add cudaStrm destroy and fix whitespace

* Added heterograph support SpMM, SDDMM

* bug fix cuda stream

* add cudaStrm destroy and fix whitespace

* changed max stream = 1

* Fixed ctx

* using default stream

* Added heterograph support SpMM, SDDMM

* bug fix cuda stream

* add cudaStrm destroy and fix whitespace

* changed max stream = 1

* Fixed ctx

* using default stream

* fix bug in copy_rhs

* changed by mistake

* minor datatype change

* added datatype check
Co-authored-by: Israt Nisa <nisisrat@amazon.com>

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Update

* Add files via upload

* Add files via upload

* Add files via upload

* Add files via upload

* Update

* Update

* Add files via upload

* Add files via upload

* Update

* Lint

* Add files via upload

* Lint

* Update

* Update

* Update

* Update

* Update

* Lint Fix

* Lint
Co-authored-by: Ubuntu <ubuntu@ip-172-31-12-161.us-west-2.compute.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* SpMM for heterograph

* C APIs SDDMM heterograph

* passes initial result

* renamed eid with nid

* aggregation on same ntype for multiple etypes

* fix link check failure

* lint check part 2

* lint check part 3

* Fixed SpMMCmpCsr Min op

* added mem references

* fixed fill(Max/Min), added const

* removed newline

* brought back docstring
Co-authored-by: Israt Nisa <nisisrat@amazon.com>
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

* fix

* fix

* fix

* fix

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

[Feature][Performance] Implement NCCL wrapper for communicating NodeEmbeddings and sparse gradients. (#2825)

* Split NCCL wrapper from sparse optimizer and sparse embedding

* Add more unit tests for single node nccl

* Fix unit test for tf

* Switch to device histogram

* Fix histgram issues

* Finish migration to histogram

* Handle cases with zero send/recieve data

* Start on partition object

* Get compiling

* Updates

* Add unit tests

* Switch to partition object

* Fix linting issues

* Rename partition file

* Add python doc

* Fix python assert and finish doxygen comments

* Remove stubs for range based partition to satisfy pylint

* Wrap unit test in GPU only

* Wrap explicit cuda call in ifdef

* Merge with partition.py

* update docstrings

* Cleanup partition_op

* Add Workspace object

* Switch to using workspace object

* Move last remainder based function out of nccl_api

* Add error messages

* Update docs with examples

* Fix linting erros
Co-authored-by: xiang song(charlie.song) <classicxsong@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

Co-authored-by: Ubuntu <ubuntu@ip-172-31-1-191.ec2.internal>
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com>

* 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>

* Add row/col sorted flags

* improve sorting paths

* Remove print statement

* Keep track of sorted matrices

* Remove sort check in to_block

* Improve CPU sorted COO->CSR

* Handle the zero edge case

* Remove omp default clause to work with MSVC

* Update comments on sorted COO->CSR cpu implementatoin

* Expose sorted to python interface

* Make check_sorted default to false for dgl.graph()

* remove check sorted; add utests

* remove check_sorted flag
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* Start on uniform GPU sampling

* Save more work

* Get cu file compiling

* Update sampling

* More changes

* Get GPU sampling for uniform probabilities solved

* Fix batch tensor migration

* Fix

* update kernels

* expand blocking

* Undo testing change

* Cut down on sampling overhead

* Fix replacement

* Update unit tests

* Add option to gpu sample in graphsage

* Copy only csc to gpu

* Add ogbn support

* Fix linting

* Remove nvtx from sample

* Improve documentation and error checking

* Expand documentation

* Update assert checking

* delete extra space

* Use standard dataloader when dataset is a dictionary

* ogb -> ogbn

* Fix edge selection determinism

* Fix typos

* Remove nvtx

* Add comment for self.fanout_arrays and assert

* Fix linting

* Migrate to scalarbatcher

* Fix indentation

* Fix batcher

* Fix indexing

* Only use databatcher for GPU

* Convert to DGL NDArray to PyTorch Tensor

* Add optimization for PyTorch's F.tensor() for list of GPU tensors
Co-authored-by: Da Zheng <zhengda1936@gmail.com>

* disable cpu fp16

* spell mistakes

* test

* more stuff

* add test

* fixes

* optimize algo

* replace unordered_map with arrays

* lint

* lint x2

* oops

* disable gpu csrmm tests

* remove gpu invocation

* optimize with openmp

* remove python functions

* add back with docstrings

* lint

* lint

* update python interface

* functionize

* functionize

* lint

* lint

[Bugfix] Wrap cub with CUB_NS_PREFIX and remove dependency on Thrust to linking issues with Torch 1.8 (#2758)

* Wrap cub with prefixes and remove thrust

* Using counting iterator
Co-authored-by: Zihao Ye <expye@outlook.com>
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com>

* finish graph matching gpu version

* use C++ shuffle

* finish graph matching

* fix bug

* fix bug

* change name and use swap

* upt

* fix format problem

* fix format problem

* stronger test

* upt

* upt

* change python api

* upt

* upt

* format check

* upt

* upt

* fix bug
Co-authored-by: Tong He <hetong007@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 tvm as submodule

* compilation is ok but calling fails

* can call now

* pack multiple modules, change names

* upd

* upd

* upd

* fix cmake

* upd

* upd

* upd

* upd

* fix

* relative path

* upd

* upd

* upd

* singleton

* upd

* trigger

* fix

* upd

* count reducible

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* only keep related files

* upd

* upd

* upd

* upd

* lint

* lint

* lint

* lint

* pylint

* upd

* upd

* compilation

* fix

* upd

* upd

* upd

* upd

* upd

* upd

* upd doc

* refactor

* fix

* upd number
Co-authored-by: Zhi Lin <linzhilynn@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-42-78.us-east-2.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-21-156.us-east-2.compute.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.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