GitLab

[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>

* print error messages.

* fix.

* 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 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>

* 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>

* Add sparse embedding for dgl and update rgcn example

* upd

* Fix

* Revert "Fix"

This reverts commit 4da87cdfb8b8c3506b7fc7376cd2385ba8045c2a.

* Fix

* upd

* upd

* Fix

* Add unitest and update impl

* fix

* Clean up rgcn example code

* upd

* upd

* update

* Fix

* update score

* sparse for sage

* remove model sparse

* upd

* upd

* remove global norm

* revert delete model_sparse.py

* update according to comments

* Fix doc

* upd

* Fix test

* upd

* lint

* lint

* lint

* upd

* upd

* clean up
Co-authored-by: Ubuntu <ubuntu@ip-172-31-56-220.ec2.internal>

* 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

* upd

* upd

* upd

* upd

* fix

* upd

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

* Distributed heterograph (#3)

* heterogeneous graph partition.

* fix graph partition book for heterograph.

* load heterograph partitions.

* update DistGraphServer to support heterograph.

* make DistGraph runnable for heterograph.

* partition a graph and store parts with homogeneous graph structure.

* update DistGraph server&client to use homogeneous graph.

* shuffle node Ids based on node types.

* load mag in heterograph.

* fix per-node-type mapping.

* balance node types.

* fix for homogeneous graph

* store etype for now.

* fix data name.

* fix a bug in example.

* add profiler in rgcn.

* heterogeneous RGCN.

* map homogeneous node ids to hetero node ids.

* fix graph partition book.

* fix DistGraph.

* shuffle eids.

* verify eids and their mappings when loading a partition.

* Id map from homogneous Ids to per-type Ids.

* verify partitioned results.

* add test for distributed sampler.

* add mapping from per-type Ids to homogeneous Ids.

* update example.

* fix DistGraph.

* Revert "add profiler in rgcn."

This reverts commit 36daaed8b660933dac8f61a39faec3da2467d676.

* add tests for homogeneous graphs.

* fix a bug.

* fix test.

* fix for one partition.

* fix for standalone training and evaluation.

* small fix.

* fix two bugs.

* initialize projection matrix.

* small fix on RGCN.

* Fix rgcn performance (#17)
Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal>

* fix lint.

* fix lint.

* fix lint.

* fix lint.

* fix lint.

* fix lint.

* fix.

* fix test.

* fix lint.

* test partitions.

* remove redundant test for partitioning.

* remove commented code.

* fix partition.

* fix tests.

* fix RGCN.

* fix test.

* fix test.

* fix test.

* fix.

* fix a bug.

* update dmlc-core.

* fix.

* fix rgcn.

* update readme.

* add comments.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-202.us-west-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal>

* fix.

* fix.

* add div_int.

* fix.

* fix.

* fix lint.

* fix.

* fix.

* fix.

* adjust.

* move code.

* handle heterograph.

* return pytorch tensor in GPB.

* remove some tests in example.

* add to_block for distributed training.

* use distributed to_block.

* remove unnecessary function in DistGraph.

* remove distributed to_block.

* use pytorch tensor.

* fix a bug in ntypes and etypes.

* enable norm.

* make the data loader compatible with the old format.

* fix.

* add comments.

* fix a bug.

* add test for heterograph.

* support partition without reshuffle.

* add test.

* support partition without reshuffle.

* fix.

* add test.

* fix bugs.

* fix lint.

* fix dataset.

* fix for mxnet.

* update docstring.

* rename to floor_div

* avoid exposing NodePartitionPolicy and EdgePartitionPolicy.

* fix docstring.

* fix error.

* fixes.

* fix comments.

* rename.

* rename.

* explain IdMap.

* fix docstring.

* fix docstring.

* update docstring.

* remove the code of returning heterograph.

* remove argument.

* fix example.

* make GraphPartitionBook an abstract class.

* fix.

* fix.

* fix a bug.

* fix a bug in example

* fix a bug

* reverse heterograph sampling.

* temp fix.

* fix lint.

* Revert "temp fix."

This reverts commit c450717b9f578b8c48769c675f2a19d6c1e64381.

* compute norm.

* Revert "reverse heterograph sampling."

This reverts commit bd6deb7f52998de76508f800441ff518e2fadcb9.

* fix.

* move id_map.py

* remove check

* add more comments.

* update docstring.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-202.us-west-1.compute.internal>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-9-132.us-west-1.compute.internal>
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>
Co-authored-by: Ubuntu <ubuntu@ip-172-31-62-171.ec2.internal>

* fix munmap() using wrong parameter

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

Co-authored-by: Zihao Ye <expye@outlook.com>

* delete shared memory when receive signal.

* rename.

* fix lint.

* fix lint.

* fix compile.

* Fix.

* we need to report error if the shared memory exist.

* disable tensorflow test for shared memory.

* revert.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-202.us-west-1.compute.internal>
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com>

* first commit

* some thoughts

* move around

* more commit

* more fixes

* now it uses torch allocator

* fix symbol export error

* fix

* fixes

* test fix

* add script

* building separate library per version

* fix for vs2019

* more fixes

* fix on windows build

* update jenkinsfile

* auto copy built dlls for windows

* lint and installation guide update

* fix

* specify conda environment

* set environment for ci

* fix

* fix

* fix

* fix again

* revert

* fix cmake

* fix

* switch to using python interpreter path

* remove scripts

* debug

* oops sorry

* Update index.rst

* Update index.rst

* copies automatically, no need for this

* do not print message if library not found

* tiny fixes

* debug on nightly

* replace add_compile_definitions to make CMake 3.5 happy

* fix linking to wrong lib for multiple pytorch envs

* changed building strategy

* fix nightly

* fix windows

* fix windows again

* setup bugfix

* address comments

* change README

* upd cmake

* upd

* format

* reuse.

* fix compile.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-2-202.us-west-1.compute.internal>

* disable openmp in arithmetic operation

* lint

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

* upd

* upd

* update

* upd

* upd

* upd

* fix

* lint

* lint

* pylint

* doc

* support AVX512

* env DGL_CPU_INTEL_KERNEL_ENABLED=1

* env DGL_CPU_INTEL_KERNEL_LOG=1

* Add unittest test_spmm.cc
Co-authored-by: Izabela Mazur <izabela.mazur@intel.com>
Co-authored-by: Michal Szarmach <michal.szarmach@intel.com>

Review patch

* multiple fixes

* fix CI

* fiddle

* revert stubs

* remove stubs

* poke

* remove linking of driver library

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

* multiple fixes

* fix CI

* fiddle

* revert stubs

* upd

* upd

* unmerge

* unmerge
Co-authored-by: Quan Gan <coin2028@hotmail.com>

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* Update docs

* Make non-default streams non-blocking

* Add async transferer class

* Add async ndarray copy interface

* Add python bindings

* Fix comment

* Add python class

* Fix linting issues

* Add python unit test

* Update python interface

* move async_transferer to cuda only directory

* Fix linting issue

* Move out of contrib

* Add doc strings

* Move test compute from backend

* Update comment

* Fix test naming

* Fix argument usage

* Wrap/unwrap backend parameters

* Move to dataloading

* Move to 'dataloading'

* Make GPU/CPU compatible

* Fix unit tests

* Add docs

* Use only backend interface for datamovement in unit test

* OMP pragma was added to support hetero_graph loop, as follows:
pragma omp parallel for

* OMP pragma will be enabled iff the gpu is used for
Co-authored-by: Zihao Ye <expye@outlook.com>

* fix cumsum

* udp
Co-authored-by: Zihao <expye@outlook.com>

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* upd

* fix

* upd

* upd

* upd

* upd

* fix

* upd
Co-authored-by: VoVAllen <jz1749@nyu.edu>