465828cdbc
[CI] pre-install required py packages in image for unit/tutorial test ( #5276 )
2023-02-10 19:11:30 +08:00
f0b7cc96bd
[Performance]Add concurrent cpu id hashmap ( #5241 )
...
Add Id hash map
2023-02-09 08:51:08 +08:00
5598503aa0
[Transform] Add SVDPE Transform Module ( #5121 )
...
* add SVD positional encoding
* modify importing module
* Fixed certain problems
* Change the test unit to a nonsigular one
* Fixed typo and make accord with lintrunner
* added svd_pe into dgl.rst
* Modified dgl.rst
2023-02-08 12:29:03 +08:00
b3308ae795
Cleanup mock_sparse related code. ( #5230 )
...
* remove_mock_sparse_example
* mock_sparse_test
* remove_mock_sparse
---------
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal >
2023-02-01 15:17:14 +08:00
0c5d6f1b00
[BUILD] enable dgl sparse build in default ( #5175 )
...
* enable dgl sparse build in default
* disable sparse build on cugraph
* update
2023-01-16 14:01:39 +08:00
27010dbc55
[Sparse] Sparse matrix subtraction ( #5164 )
...
* use NotImplemented
* format
* sparse sub
* address comments
* lint
* Update elementwise_op_diag.py
* ugh
Co-authored-by: Rhett Ying <85214957+Rhett-Ying@users.noreply.github.com >
2023-01-16 11:37:42 +08:00
acc567aa08
[Sparse] Support sparse matrix dividing scalar ( #5173 )
...
* use NotImplemented
* format
* extend to pytorch scalar
* sparse div scalar
* oops
* Apply suggestions from code review
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2023-01-13 22:54:58 +08:00
b5c5c860f6
[Sparse] Refactor matmul interface. ( #5162 )
...
* [Sparse] Refactor matmul interface.
* Update
2023-01-13 20:08:40 +08:00
9334421d2b
[Sparse] Rename as_sparse to to_sparse, dense to to_dense. ( #5170 )
...
* as_sp_to_sp
* dense
* revert_mock
* test
* revert
Co-authored-by: Steve <ubuntu@ip-172-31-34-29.ap-northeast-1.compute.internal >
2023-01-13 17:03:20 +08:00
5f5db2dfc7
[Sparse] Make functions compatible with PyTorch scalar tensors ( #5163 )
...
* use NotImplemented
* format
* extend to pytorch scalar
* reformat
* reformat
* lint
2023-01-13 14:00:52 +08:00
8abf9d54e3
[Sparse] Use NotImplemented to let Python dispatch types ( #5160 )
...
* use NotImplemented
* add TypeError tests
* format
* lint
* fix type
* fix docstring
* lint
* remove redundant condition
2023-01-12 21:12:29 +08:00
751b4c269d
[Bugfix] Replace global cudaStream in Filter with runtime calls ( fix #5153 ) ( #5157 )
...
* Add failing unit test
* Add fix
* Remove extra newline
* skip cpu test
Co-authored-by: Xin Yao <yaox12@outlook.com >
2023-01-12 16:27:29 +08:00
bff32a0986
[Sparse] Use efficient implementation for Diag @ Sparse and Sparse @ Diag. ( #5147 )
2023-01-12 11:53:46 +08:00
491c19fe4a
[Bugfix] Fix the call of tar.extractall() method ( #5139 )
2023-01-10 23:11:56 -08:00
580c702417
[DataLoader] Allow batch_size=None for GraphDataLoader ( #4483 )
...
* overwrite default_collate_fn
* Update dataloader.py
* Update dataloader.py
* Update dataloader.py
* Update dataloader.py
* Update test_dataloader.py
* revert the test code being reverted in #4956
2023-01-09 00:44:46 +08:00
56ffb650fe
[API Deprecation]Deprecate contrib module ( #5114 )
2023-01-06 20:16:01 +08:00
c8bc558880
[Sparse] Remove SparseMatrix.indices and add device/dtype conversions ( #5108 )
...
* Update
* Update
* Update
* lint
* lint
* Update
* CI
* Update diag_matrix.py
* Update sparse_matrix.py
* Update sparse_matrix.py
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com >
2023-01-06 17:37:13 +08:00
c55ab2d147
deprecate candidates in dataloader ( #5117 )
2023-01-06 16:18:32 +08:00
3a2a5031e9
[API Deprecation]Deprecate candidates in dgl.distributed ( #5116 )
2023-01-06 16:17:44 +08:00
9890201d58
[Dist] Allow reading and writing single-column vector Parquet files. ( #5098 )
...
* Allow reading and writing single-column vector Parquet files.
These files are commonly produced by Spark ML's feature processing code.
* [Dist] Only write single-column vector files for Parquet in tests.
2023-01-05 20:37:28 +08:00
9169fc3541
[Sparse] Polish sparse matrix creation functions ( #5093 )
...
* update
* Update
* Update
* Update
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
2023-01-03 22:59:57 +08:00
0698e91a0e
[Sparse] Use Pytorch dense computation in SpMM tests ( #5096 )
2023-01-03 22:26:06 +08:00
774709d399
[Dist] Add support for Parquet-formatted edges files, remove some assumptions on edge file number. ( #5051 )
...
* [Dist] Add support for Parquet-formatted edges files, remove some assumptions on edge file number.
* [Dist] Add parquet edges option to unit tests.
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2023-01-03 16:01:50 +08:00
cd817a1a00
[NN] Add SpatialEncoder and SpatialEncoder3d ( #4991 )
...
* Add SpatialEncoder and SpatialEncoder3d
* Optimize the code execution efficiency
* Fixed certain problems according to Dongyu's suggestions.
* Fix an error about probability of division by zero in PathEcoder; Change certain designs in SpatialEncoder
* Fix a typo
* polish the docstring
* fix doc
* lint
Co-authored-by: Ubuntu <ubuntu@ip-172-31-14-146.ap-northeast-1.compute.internal >
Co-authored-by: rudongyu <ru_dongyu@outlook.com >
2023-01-03 14:02:14 +08:00
ce378327c7
fix bf16 tests ( #5089 )
2022-12-29 21:36:39 +08:00
37bd092587
[Sparse] Namespace migration and doc update ( #5088 )
...
* update
* lint
* lint
* comments
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
2022-12-29 20:34:29 +08:00
255ad1b35b
[Sparse] New print for SparseMatrix and DiagMatrix ( #5085 )
...
* new print func
* lintrunner
2022-12-29 15:38:10 +08:00
025e43210f
[Sparse] Add tests for sparse examples; Migrate from mock_sparse to mock_sparse2 ( #5073 )
...
* pass gcn
* example tests
* pass gcnii, hgnn, sgc, sign
* black
* test file
* add torchmetrics
* migrate appnp, c_and_s, twirls
* fix style
* minor fix
* fix hypergraphatt and twirls
* pass gat
* fix torchmetric
* lintrunner
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-12-29 08:55:25 +08:00
14429df661
[Sparse] Support BSpMM and BSDDMM ( #5079 )
...
* [Sparse] Support BSpMM and BSDDMM
* Update SpMM and SDDMM error messages
* Use TORCH_CHECK
* Update error string
2022-12-28 17:14:12 +08:00
fa5ff2fceb
[Sparse] Add coalesce and has_duplicate to SparseMatrix ( #5071 )
...
* add coalesce() and has_duplicate()
* Add duplicate check in spspmm
* black
* fix
* clang-format
* lintrunner
* minor fix
* fix
2022-12-28 13:10:10 +08:00
8c3e7830dc
[Sparse] Elementwise multiplication of a SparseMatrix object by a scalar ( #5076 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
2022-12-28 09:37:44 +08:00
0f1bcd9927
[Sparse] Softmax based on Reduction and BroadcastOp ( #5067 )
...
* Update
* update
* Update
* Update
* Update
* format
* Update
* lint
* Update
* lint
* CI
* CI
* Update
* address comments
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
2022-12-27 14:50:15 +08:00
4aff59f775
[Sparse] Rename existing DGL sparse module. ( #5066 )
...
* rename
* next time i should use lintrunner
2022-12-26 13:55:48 +08:00
0159c3c11d
[Sparse] Add SpSpMM for sparse-sparse and sparse-diag matrix multiplication. ( #5050 )
...
* [Sparse] Add SpSpMM
* Update matmul interface
* address comments
* fix test utils to generate only coalesced matrices
* fix linter
* fix ut
* fix
* rm print
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-12-24 15:31:09 +08:00
f0ce2bea22
[Sparse] Sparse matrix reduction Python part ( #5013 )
...
* initial commit
* lint
* rename
* address comments
* add doctests
* address comments
* remove additional test
* add description
* lint
* lint
* lint
* Update test_reduction.py
Co-authored-by: Hongzhi (Steve), Chen <chenhongzhi.nkcs@gmail.com >
2022-12-22 16:49:29 +08:00
56ce60b061
[Sparse] Fix SpMM and SDDMM test precision problem ( #5060 )
2022-12-21 18:02:29 +08:00
1f2fcae3e2
[Sparse] Support SpMM and SDDMM ( #5032 )
...
* [Sparse] Support SpMM and SDDMM
* Add SDDMMAutoGrad
* Rename SpMMImpl and SDDMMImpl and move them to dgl_sparse/src/matmul.h
* Update comments
* Update
* Minor fix
2022-12-21 10:29:23 +08:00
f40db9b743
[Dist][Test] Add exit_code asserts in some distributed tests ( #5053 )
...
Signed-off-by: Serge Panev <spanev@nvidia.com >
Signed-off-by: Serge Panev <spanev@nvidia.com >
2022-12-21 09:03:13 +08:00
11e6190579
[Sparse] Add Two Sparse Matrices with Different Sparsity, DiagMatrix.dense, Add SparseMatrix and DiagMatrix ( #5044 )
...
* Update
* undo wrong edit
* lint
* fix import
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
2022-12-20 20:15:37 +08:00
f4eef72628
[Fix core lib warning] Remove LooseVersion ( #5026 )
...
* replace LooseVersion with packaging.version
* import packaging from setuptools
* import packaging.version in dgl.utils
* format
* revert changes to apps/kg
* revert changes to _dataloading
2022-12-19 09:02:14 +08:00
9731e02325
[Dist] enable to chunk node/edge data into arbitrary number of chunks ( #4930 )
...
* [Dist] enable to chunk node/edge data into arbitrary number of chunks
* [Dist] enable to split node/edge data into arbitrary parts
* refine code
* Format boolean to uint8 forcely to avoid dist.scatter failure
* convert boolean to int8 before scatter and revert it after scatter
* refine code
* fix test
* refine code
* move test utilities into utils.py
* update comment
* fix empty data
* update
* update
* fix empty data issue
* release unnecessary mem
* release unnecessary mem
* release unnecessary mem
* release unnecessary mem
* release unnecessary mem
* remove unnecessary shuffle data
* separate array_split into standalone utility
* add example
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2022-12-15 10:01:39 +08:00
354a211038
[Sparse] Elementwise ops for DiagMatrix and Elementwise Power for SparseMatrix ( #5024 )
...
* Update
* Update
* lint
* CI
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
2022-12-15 08:33:51 +08:00
32dc1af67e
[Dist] generate partition meta for ParMETIS pipeline ( #5020 )
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* [Dist] generate partition meta for ParMETIS
2022-12-14 21:15:54 +08:00
d02e560e07
Revert "[Sparse] Add SpMM and SDDMM." ( #5014 )
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* Revert "[Sparse] Add SpMM and SDDMM. (#4999 )"
This reverts commit 15365d7855
2022-12-12 19:37:08 +08:00
15365d7855
[Sparse] Add SpMM and SDDMM. ( #4999 )
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* [Sparse] Add SpMM and SDDMM
* Update
* Add CSR and CSC SpMM tests
2022-12-12 15:37:09 +08:00
e01580d3b9
[Sparse] Misc fix for existing elementwise ops ( #5003 )
...
* Update
* Update
* Update
* Update
* update
* lint
* CI
* CI
* CI
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
2022-12-09 17:16:59 +08:00
aad3bd0484
[Bugfix] Fix empty tensors may being treated as pinned ( #5005 )
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* fix empty tensor is treated as pinned
* avoid calling cudaHostGetDevicePointer on nullptr
* update empty array
* add a comment
2022-12-09 16:42:59 +08:00
20fb4d4c31
[Lint] Add a formatter GitHub Action for ufmt and clang-format ( #4977 )
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* add lint workflow
* add line number
* address comments
* update package versions
* remove autopep8 config
2022-12-08 13:32:08 +08:00
279e2e8fba
Add Graph Transformer Layer (Dense Computation) ( #4959 )
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* Add GraphTransformerLayer (dense)
* beautify the python code with black
* refine according to mufei's comments
* fix AttributeError in unit test
* rename module as GraphormerLayer
* fix name issue
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-12-07 16:23:14 +08:00
a80bd9e039
Update ( #4997 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-36-188.ap-northeast-1.compute.internal >
2022-12-07 15:07:50 +08:00
Rhett Ying