00c09b9f91
Revert "[bugfix] Explicitly unpin tensoradapter allocated arrays ( #3997 )" ( #4061 )
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This reverts commit fdd1fe1908
2022-05-28 20:44:20 +08:00
c577dc9fc3
add sanity check ( #4050 )
2022-05-28 18:51:33 +08:00
7a065a9c56
[Build][Tests] Enable FP16 for GPU builds in CI ( #4030 )
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* Enable FP16 for GPU builds in CI
* Limit default GPU archs to pascal and above
* Disable FP16 dispatching for cuda architectures less than 60
* Fix linting
* Fix typos
2022-05-26 09:48:28 -07:00
3c129ad71f
[Bugfix] Cython CAPI holding GIL causes deadlock when Python callback is asynchronous ( #4036 )
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* cython nogil
* move APIs to internal and add unit test
* fix lint
* disable callback array test
2022-05-25 10:02:44 +08:00
230b886ec5
[Bug fix] Misc Fix for Transforms and NN Modules ( #4038 )
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* Update module.py
* Update utils.py
* Update utils.py
* Update utils.py
* Update module.py
* Update
* Update
* Update
2022-05-24 18:08:08 +08:00
1425150459
Fix test naming ( #4023 )
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Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-05-23 17:21:06 +08:00
3fe5eea791
[NN] Label Propagation & Directional Graph Networks ( #4017 )
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* add label propagation module
* fix prev bug in example
* add dgn
* fix linting and doc issues
* update label propagation & dgn
* update label propagation & dgn
* update example
* fix unit test
* fix agg heritage issue
* fix agg issue
* fix lint
* fix idx
* fix lp gpu issue
* Update
* Update
Co-authored-by: mufeili <mufeili1996@gmail.com >
2022-05-20 15:23:19 +08:00
53835bdb75
[Dist][BugFix] enable sampling on bipartite ( #4014 )
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* [Dist][BugFix] enable sampling on bipartite
* add comments for tests
2022-05-18 10:14:54 +08:00
e0e8736fa0
[Feature] Added floating-point conversion functions to dgl.transforms.functional ( #3890 )
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* * Added half_(), float_(), and double_() functions to DGLHeteroGraph, HeteroNodeDataView, and HeteroEdgeDataView, for converting floating-point tensor data to float16, float32, or float64 precision
* * Extracted out private functions for floating-point type conversion, to reduce code duplication
* * Added test for floating-point data conversion functions, half_(), float_(), and double_()
* * Moved half_(), float_(), and double_() functions from HeteroNodeDataView and HeteroEdgeDataView to Frame class
* * Updated test_float_cast() to use dgl.heterograph instead of dgl.graph
* Added to CONTRIBUTORS.md
* * Changed data type conversion to be deferred until the data is accessed, to avoid redundant conversions of data that isn't used.
* * Addressed issues flagged by linter
* * Worked around a bug in the old version of mxnet that's currently used for DGL testing
* * Only defer Column data type conversion if there is a pending device transfer or index sampling to be done. This is expected to be the desired behaviour based on discussions of a few use cases, as described in the comments.
* * Moved floating-point feature data conversion functions to dgl.transforms.functional
* Changed them from in-place behaviour to shallow copy (out-of-place) behaviour
* * Fixed linter issues
* * Removed lines that unintentionally added to_half, to_float, and to_double to DGLHeteroGraph
* Moved _init_api line to the end of the file again
* * Removed one of the two leading underscores from Frame.__astype_float, making it not fully private
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com >
2022-05-16 18:17:15 -07:00
1f2e696080
Prevent users from attempting to pin PyTorch non-contiguous tensors or views only encompassing part of tensor. ( #3992 )
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* Disable pinning non-contiguous memory
* Prevent views from being converted for write
* Fix linting
* Add unit tests
* Improve error message for users
* Switch to pytest function
* exclude mxnet and tensorflow from inplace pinning
* Add skip
* Restrict to pytorch backend
* Use backend to retrieve device
* Fix capitalization in decorator
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2022-05-16 14:49:36 -07:00
fdd1fe1908
[bugfix] Explicitly unpin tensoradapter allocated arrays ( #3997 )
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* Explicitly unpin tensoradapter allocated arrays
* Undo unrelated change
* Add unit test
* update unit test
2022-05-16 13:02:02 -07:00
65b0b9e8c3
[Dataset & Transform] Synthetic Datasets for Explainability and SIGNDiffusion Transform ( #3982 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Update
* Update
* Update
2022-05-16 22:32:09 +08:00
03024f9587
[Peformance] Remove unnecessary induced vertices in EdgeSubgraph ( #3978 )
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* remove unnecessary induced vertices in EdgeSubgraph
* add unit test
2022-05-16 15:03:42 +08:00
65e6b04d8b
[Build] enable USE_AVX in CI and regression tests ( #4004 )
2022-05-12 21:29:11 -07:00
cb39eae1c4
Supporting DGL build with arch specific optimization ( #3996 )
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Based on the pull request: https://github.com/dmlc/dgl/pull/3983
2022-05-11 12:38:42 -07:00
22e218d335
[Dist] Enable maximum try times for socket backend via DGL_DIST_MAX_T… ( #3977 )
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* [Dist] Enable maximum try times for socket backend via DGL_DIST_MAX_TRY_TIMES
* reset env before/after test
* print log for info when trying to connect
* fix
* print log in python instead of cpp
2022-05-11 13:03:06 +08:00
22d7f92407
[CI] print commit/build ID into comment ( #3989 )
2022-05-10 16:04:21 +08:00
b2ec5a2ea6
[Transform] Add FeatMask and RowFeatNormalizer transforms ( #3968 )
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* [Model]P-GNN
* updata
* [Example]P-GNN
* Update README.md
* Add NodeFeatureMasking and NormalizeFeatures
* Update
* Update transforms.rst
* Update
* Update
* Update
* Update test_transform.py
* Update
* Update
* Update test_transform.py
* Update module.py
* Update module.py
* Update module.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-05-07 11:59:39 +08:00
334e6434d2
[DGL-Go] CI for DGL-Go ( #3959 )
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* Update
* Update
* Fix
* Update
* CI
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
2022-05-06 12:26:50 +08:00
3f792071f6
[BugFix] fix CI status ( #3963 )
2022-04-29 14:47:19 +08:00
56614f320f
[BugFix] fix job status in master CI ( #3962 )
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* [BugFix] fix job status in master CI
* finalize
2022-04-29 12:54:13 +08:00
5561af4517
[Feature] Dataloader worker affinitization ( #3723 )
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* PR3355 + CSR conversion workaround
* Remove debug code
* Fix convention errors
* Remove wrongly added code section during merge
* Update to reflect dataloading changes
* Fix missing changes
* Remove comment
* Fix linter errors
* Fix trailing whitespace
* Add wrapper around worker init function
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2022-04-28 13:00:04 +08:00
37be02a486
[Feature] enable socket net_type for rpc ( #3951 )
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* [Feature] enable socket net_type for rpc
* fix lint
* fix lint
* fix build issue on windows
* fix test failure on windows
* fix test failure
* fix cpp unit test failure
* net_type blocking max_try_times
* fix other comments
* fix lint
* fix comment
* fix lint
* fix cpp
2022-04-28 00:10:06 +08:00
2eaa58e047
[CI] refine status check ( #3958 )
2022-04-27 15:28:26 +08:00
248bece633
[NN] GINEConv ( #3934 )
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* Update
* Update
* Update
* Update
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2022-04-25 14:41:05 +08:00
764b5d0524
Fix test_module_heat_kernel test ( #3941 )
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Signed-off-by: Serge Panev <spanev@nvidia.com >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-04-23 13:32:29 +08:00
338db32d21
[Feature] Try upload report to s3 ( #3891 )
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refactor CI report and log
2022-04-22 16:02:12 +08:00
e06e63d5d5
[Feature] Enable UVA sampling with CPU indices ( #3892 )
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* enable UVA sampling with CPU indices
* add docs
* add more docs
* lint
* fix
* fix
* better error message
* use mp.Barrier instead of queues
* revert
* revert
* oops
* revert dgl.multiprocessing.spawn
* Update pytorch.py
2022-04-12 20:56:51 +08:00
0d878ff8ef
[Example] Cleaned GraphSAGE node classification example with PyTorch Lightning ( #3863 )
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* cleaned pl node classification example
* conform to PL's method of updating the dataloader
* update
* lint
* fix test
* fix
2022-04-12 17:26:23 +08:00
baa9292899
[bugfix] Fix EdgePredictionSampler for UVA sampling ( #3904 )
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* Add failing unit test
* Fix negative sampler edge types
* fix test
* oops
* revert
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2022-04-12 15:25:21 +08:00
5fcd7f290f
[Feature] Enable UVA for GPU PinSAGE and RandomWalk ( #3857 )
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* enable uva for pinsage sampler
* unit test
* modify some checks on the python side
* remove legacy random walk code
* update unit test
* update unit test
* fix unit test
* adjust checks
* move some checks to c++
* move max_nodes check to cuda kernel
* fix ci for tf
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com >
2022-04-11 20:01:23 +08:00
adb3a7c11e
[BugFix] record/restore pin status when pickle/unpickle ( #3914 )
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* [BugFix] record/restore pin status when pickle/unpickle
* disable test on TF
* set version as expected
* unpin memory in test
2022-04-09 11:42:23 +08:00
dc5035b1f3
[NN] Add EGNN & PNA ( #3901 )
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* add EGNN & PNA
* fix egnn issues
* fix pna issues
* update pna conv
* add doc strings
* update pnaconv
* fix unused args issue
* fix moment aggregation issue
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-04-07 17:44:57 +08:00
35e66f426a
[Bugfix] Fix UVA sampling with partially specified node types ( #3897 )
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* fix uva with partial node types
* lint
* skip tensorflow unit test
2022-03-31 17:07:02 +08:00
4c7bd314b4
[Feature] Radius Graph ( #3829 )
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* radius graph
* remove trailing whitespaces from docs
* disable invalid name for transform func
* disable radius graph module invalid name
* move pylint disable before init
* fix missing nodes from point set
* update docs indexing
* add compute mode as optional param
* radius graph test
* remove trailing whitespaces
* fix precision when comparing tensors
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-03-30 17:23:29 +08:00
290b7c25c2
[Transform] Random Walk Positional Encoding & Laplacian Positional Encoding ( #3869 )
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* [Transform] Random Walk Positional Encoding & Laplacian Positional Encoding
* Update python/dgl/transforms/module.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
* Update python/dgl/transforms/functional.py & python/dgl/transforms/module.py
* update python/dgl/transforms/functional.py
* update doc indexing
* update unit test
* support weighted graphs for random_walk_pe
* change reference
* fix linter errors
* fix datatype compatibility with MXNet & TF
* fix device errors
* fix result precision errors
* change tensorflow abs api
* reboost CI
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2022-03-30 15:59:28 +08:00
9fee20b91d
[Sampler] [Example] SAINTSampler and Simplify GraphSAINT Example ( #3879 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2022-03-30 13:51:37 +08:00
f758db386f
[Bug] Fix dtype mismatch in heterogeneous DataLoader ( #3878 )
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* fix
* unit test
2022-03-26 13:56:21 +08:00
a0e8cf0d3e
[Bugfix] Fix UVA sampling with lazy feature slicing ( #3862 )
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* fix uva sampling with features
* fix
* add is_listlike function to distinguish strings from sequence
* fix
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com >
2022-03-24 20:13:01 +08:00
e9fd65e9c9
[BugFix] send rpc messages blockingly in case of congestion ( #3867 )
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Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2022-03-24 09:51:45 +08:00
8005978e1e
[NN] Grouped reversible residual connections for GNNs ( #3842 )
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* Update
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
2022-03-23 16:58:39 +08:00
a3fd059537
Fix jenkins ( #3875 )
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* try fix
* try fix
* try fix
* try fix
* Revert "try fix"
This reverts commit a3fa0b1e9c0ab892cc3a22acf3770903db8b14a7.
* try fix shared memory
* try fix shared memory
* try fix image version
* fix
2022-03-23 14:13:45 +08:00
480a4ae35c
[BugFix] pass ntype/etype into partition book when node/edge_split ( #3828 )
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* [BugFix] pass ntype/etype into partition book when node/edge_split
* fix test failure
* fix test failue on mxnet
* fix test failure
2022-03-14 15:11:01 -07:00
1d80d91a32
[BugFix] call g.is_homogenous instead of len(g.etypes) ( #3793 )
2022-03-02 14:27:52 +08:00
e0f0fa2a78
Fix a bug in sparse optimizer. ( #3779 )
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* fix a bug.
* Update pylintrc
* fix.
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2022-02-28 12:04:32 -08:00
6d9433b04f
[Transform] [Doc] Rename transform to transforms and update doc ( #3765 )
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* Update
* Update
* Update
* Fix
* Update
* Update
* Update
* Fix
2022-02-24 21:28:15 +08:00
2f4146a4c2
[Dataset] add train_idx/val_idx/test_idx as dataset attributes ( #3769 )
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* add train_idx/val_idx/test_idx as dataset attributes
* refine docstring
2022-02-24 15:17:40 +08:00
8db2dd3355
[Dataset][Fix] Allow non-numeric values and some fix on doc ( #3757 )
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* [Fix] be able to parse ids if numeric and non-numeric values are used together
* add required package info and cache note into docstring
* duplicate node id is not allowed
2022-02-23 17:26:12 +08:00
0227ddfb66
[NN] Rework RelGraphConv and HGTConv ( #3742 )
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* 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
2022-02-23 12:10:20 +08:00
3f138ebaaf
[Bugfix] Bug fixes in new dataloader ( #3727 )
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* 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 >
2022-02-22 01:30:31 +08:00
Quan (Andy) Gan