d18274885d
autofix2 ( #5333 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-63.ap-northeast-1.compute.internal >
2023-02-20 23:27:27 +08:00
611393021a
[API Deprecation] Remove candidates in DGLGraph ( #4946 )
2022-12-01 16:41:53 +08:00
3132da2826
Deprecate ( #4864 )
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rename DGLHeteroGraph to DGLGraph
2022-11-15 10:01:01 +08:00
2630d2eb02
[Performance][bugfix] Implement is_unibipartite in C++ with caching. ( #4556 )
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* updates
* Enable caching C++ result
* Add missing docstring
* Remove unused function
* Add unit test
* Address comments
2022-09-19 16:46:27 -07:00
9a00cf194f
[Feature] Import PyTorch's CUDA stream management ( #4503 )
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* add set_stream
* add .record_stream for NDArray and HeteroGraph
* refactor dgl stream Python APIs
* test record_stream
* add unit test for record stream
* use pytorch's stream
* fix lint
* fix cpu build
* address comments
* address comments
* add record stream tests for dgl.graph
* record frames and update dataloder
* add docstring
* update frame
* add backend check for record_stream
* remove CUDAThreadEntry::stream
* record stream for newly created formats
* fix bug
* fix cpp test
* fix None c_void_p to c_handle
2022-09-15 16:54:52 +08:00
077e002fe5
[Bugfix][Rework] Automatically unpin tensors pinned by DGL (rework #3997 ) ( #4135 )
...
* Explicitly unpin tensoradapter allocated arrays
* Undo unrelated change
* Add unit test
* update unit test
* add pinned_by_dgl flag to NDArray::Container
* use dgl.ndarray for holding the pinning status
* update multi-gpu uva inference
* reinterpret cast NDArray::Container* to DLTensor* in MoveAsDLTensor
* update unpin column and examples
* add unit test for unpin column
Co-authored-by: Dominique LaSalle <dlasalle@nvidia.com >
Co-authored-by: nv-dlasalle <63612878+nv-dlasalle@users.noreply.github.com >
2022-06-23 13:56:54 +08:00
a0e8cf0d3e
[Bugfix] Fix UVA sampling with lazy feature slicing ( #3862 )
...
* 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
3f138ebaaf
[Bugfix] Bug fixes in new dataloader ( #3727 )
...
* 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
738e8318fd
[Feature] CUDA UVA sampling for MultiLayerNeighborSampler ( #3674 )
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* 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 >
2022-02-09 14:06:17 +08:00
701b4fccc2
[Sampling] New sampling pipeline plus asynchronous prefetching ( #3665 )
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* 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
2022-01-30 16:13:00 +08:00
40b44a43a9
[Feature] Pin dgl.graph to the page-locked memory ( #3616 )
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* implement pin_memory/unpin_memory/is_pinned for dgl.graph
* update python docstring
* update c++ docstring
* add test
* fix the broken UnifiedTensor
* eliminate extra context parameter for pin/unpin
* fix linting
* fix typo
* disable new format materialization for pinned graphs
* update python doc for pin_memory_
* fix unit test
* update doc
* change unitgraph and heterograph's PinMemory to in-place
* update comments for NDArray's PinMemory_ and PinData
* update doc
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2022-01-21 16:13:12 +08:00
6c81634b29
[Bugfix] Fixes wrong output in multi_update_all for reduce op max/min (Issue#3564)) ( #3581 )
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* fixed bug
* added in test cases
* unittest resolved
* bugfix
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-12-17 08:54:15 +08:00
02880e9f86
Fix unnecessary trigger of lazy copy ( #3585 )
...
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-12-13 17:11:03 +08:00
cb0e1103ed
[Feature] Add Min/max reducer in heterogeneous API for unary message functions ( #3514 )
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* min/max support for forward CPU heterograph
* Added etype with each argU values
* scatter_add needs fix
* added scatter_add_hetero. Grads dont match for max reducer
* storing ntype in argX
* fixing scatter_add_hetero
* hetero matches with torch's scatter add
* works copy_e forward+cpu
* added backward for copy_rhs
* Computes gradient for all node types in one kernel
* bug fix
* unnitest for max/min on CPU
* renamed scatter_add_hetero to update_grad_minmax_hetero
* lint check and comment out cuda call for max. Code is for CPU only
* lint check
* replace inf with zero
* minor
* lint check
* removed LIBXSMM code from hetro code
* fixing backward operator of UpdateGradMinMaxHetero
* removed backward from update_grad_minmax_hetero
* docstring
* improved docstring and coding style
* Added pass by pointer for output
* typos and pass by references
* Support for copy_rhs
* Added header <string>
* fix bug in copy_u_max
* Added comments and dimension check of all etypes
* skip mxnet check
* pass by pointer output arrays
* updated docstring
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-12-04 00:39:30 +08:00
d17b299a13
[Feature] Update edge features (apply_edge) for heterogeneous graph ( #3250 )
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* rgcn with new heterograph API
* apply_edge() forward for multi relation
* undoing changes from rgcn-hetero
* backward apply_edge(copy_u) added
* unittest for apply_edge(copy_e)
* Compatible with new PRs
* resolving conflict with master
* Bringing back change after resolving conflict
* minor
* minor
Co-authored-by: Israt Nisa <nisisrat@amazon.com >
2021-09-09 22:39:08 +08:00
298e4fa627
[Feature] Support builtin binary message function for heterogenenous graph ( #3273 )
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* 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 >
2021-09-07 10:01:33 -07:00
c4791fd46e
[bugfix] fix default ntypes/etypes consistency between dgl.DGLGraph and dgl.graph ( #3198 )
2021-07-29 14:05:28 +08:00
3f6f694159
[Bug fix] Various fix from bug bash ( #3133 )
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* Update
* Update
* Update dependencies
* Update
* Update
* Fix ogbn-products gat
* Update
* Update
* Reformat
* Fix typo in node2vec_random_walk
* Specify file encoding
* Working for 6.7
* Update
* Fix subgraph
* Fix doc for sample_neighbors_biased
* Fix hyperlink
* Add example for udf cross reducer
* Fix
* Add example for slice_batch
* Replace dgl.bipartite
* Fix GATConv
* Fix math rendering
* Fix doc
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-17.us-west-2.compute.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-22-156.us-west-2.compute.internal >
2021-07-15 09:17:15 +08:00
f0fafa2062
[Bug fix] Fix batch information with remove_nodes/edges applied ( #3119 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix lint
* Fix
* Update
* Fix test cases
* Fix
* add docstrings
* Update
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-17.us-west-2.compute.internal >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-07-13 16:27:31 +08:00
32d1f3ac97
[BugFix] skip frames whose num_rows is zero in dgl.heterograph.combine_frames() ( #3110 )
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-07-07 14:15:06 +08:00
751685a979
[Doc] Add documentation for DGLGraph.adj_sparse ( #3096 )
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-07-07 11:24:47 +08:00
188152b853
[Feature] Add Heterograph support on Python for builtin unary msg functions (copy_u, copy_e) ( #2989 )
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* 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 >
2021-07-06 20:41:58 +08:00
acd21a6d60
[Feature] Support direct creation from CSR and CSC ( #3045 )
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* 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 >
2021-06-25 10:05:47 +08:00
ff519f98c3
[API] Standardize Subgraph APIs ( #2929 )
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* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Update
* Fix subgraph tests
* Capture stdout for distributed test
* Capture stdout for distributed test
* Update
* Update
* Update
* Update subgraph.cc
Co-authored-by: Ubuntu <ubuntu@ip-172-31-28-17.us-west-2.compute.internal >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-06-21 19:53:37 +08:00
17141dd372
[Fix] Fix to_homo for graph with zero nodes ntype ( #3011 )
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* fix #2870
* lint
* fix
2021-06-14 14:34:13 +08:00
b8fe2b4837
[Feature][Sampler] Sort CSR by tag ( #1664 )
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* 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 >
2021-06-01 23:33:56 +08:00
ac1536cf92
[Feature] add udf support for cross_reducer ( #2891 )
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* add: udf support for `cross_reducer`
* update: code lint
* update: reducer without stack
* docs: add docs for udf cross_reducer
* chore: fix code lint
* docs: update multi_update_all docstring
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
* docs: update reduce_dict_data docstring
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-15 14:00:37 +08:00
103444c58f
Remove __len__ method from DGLGraph ( #2902 )
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* Update heterograph.py
* remove unit tests
* replace tutorial
2021-05-11 14:06:18 +08:00
fbfcf1a8cc
Doc: adapt send_and_recv example ( #2822 )
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* adapt send_and_recv example
* lint fix
* Change title and example order
* Update heterograph.py
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-05-07 09:44:11 +08:00
8a07ab7737
[Doc] Tutorials re-organization ( #2683 )
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* reorg
* change titles
* rm some stale API doc; minor fix
* fix docs
* add warning
* rm new-tutorial run in ci
* lint
2021-02-20 17:42:45 +08:00
8ccb8206bf
[Doc] Update docs to motivate the use of set_batch_num_nodes and set_batch_num_edges ( #2630 )
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* fix doc
* update docstring for transformation on batch graph
* update cn guide
* fix format
* update rst
2021-02-08 14:43:24 +08:00
878acdb0fc
Revert "Refactor code for retaining formats in message-passing. ( #2570 )" ( #2583 )
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This reverts commit a613ad8806
2021-01-28 14:04:07 +08:00
a613ad8806
Refactor code for retaining formats in message-passing. ( #2570 )
2021-01-25 16:55:16 +08:00
aa884d43b6
[doc][fix] Improve the docstring and fix its behavior in DGL's kernel ( #2563 )
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* upd
* fix
* lint
* fix
* upd
2021-01-25 00:18:57 +08:00
fa5f4d6aa7
[Doc] Hotfix on docstring of set_batch_num_edges ( #2498 )
2021-01-06 21:45:04 +08:00
2caac086c2
[Bug] send_and_recv and pull may write to wrong places ( #2497 )
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* fix
* fix test
2021-01-06 17:18:37 +08:00
0c2a2ea1e2
[Bugfix] Handle a Corner Case of Batching after Removing Nodes/Edges ( #2465 )
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* Update
* Update
* Update
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-01-05 22:22:03 +08:00
f960468f50
[feature] APIs for manually set batch_num_nodes and batch_num_edges ( #2430 )
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* wip
* udp
* upd
* fix typo
* lint
* lint
* upd
* upd
* lint
* lint
* upd
* upd
* tftest
* fix
* fallback numpy
* fix tf
* docstring
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
2021-01-04 23:43:58 +08:00
40caf1ab50
[HeteroGraph] Fix the failure of apply_nodes when the input function changes feature size for all nodes ( #2223 )
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* Fix
* Fix
2020-09-24 08:54:28 +08:00
f3f646bbfd
[Doc and User Guide] Minor Fix ( #2205 )
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* Fix doc and user guide
* Update heterograph.py
Co-authored-by: Ubuntu <ubuntu@ip-172-31-13-9.us-west-2.compute.internal >
2020-09-17 03:01:12 +08:00
7d8522a29f
[Bug] fix cumsum on an empty array with prepend_zero returning an empty array ( #2179 )
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* fix cumsum
* udp
Co-authored-by: Zihao <expye@outlook.com >
2020-09-11 18:23:44 +08:00
ac570c1dae
[Bugfix] Fix flatten not wrapping unit graph ( #2170 )
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* fix flatten not wrapping unit graph
* fix doc
2020-09-10 17:41:52 +08:00
9eaace9216
rename create_format_ to create_formats_ ( #2126 )
2020-08-29 22:49:27 +08:00
b2ac89f2e4
[Bugfix] Fix #2076 ( #2111 )
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* Fix
* Revert "Fix"
This reverts commit 2627630daee33a709a70ef87e1ad9930772430a8.
* Fix
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
2020-08-27 00:23:31 +08:00
bcff14ccde
[Dco] Remove preface in guide ( #2096 )
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* fix
* fix
2020-08-23 10:27:15 +08:00
f13b9b6212
[Doc] Scan the API docs and make many changes ( #2080 )
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* WIP: api
* dgl.sampling, dgl.data
* dgl.sampling; dgl.dataloading
* sampling packages
* convert
* subgraph
* deprecate
* subgraph APIs
* All docstrings for convert/subgraph/transform
* almost all funcs under dgl namespace
* WIP: DGLGraph
* done graph query
* message passing functions
* lint
* fix merge error
* fix test
* lint
* fix
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-20 23:26:49 +08:00
9088c63592
[Feature] Change the Default Value of transpose in DGLGraph.adj ( #2046 )
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* Update adj
* Fix
2020-08-18 22:45:46 +08:00
be444e52d9
[Doc/Feature] Refactor, doc update and behavior fix for graphs ( #1983 )
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* Update graph
* Fix for dgl.graph
* from_scipy
* Replace canonical_etypes with relations
* from_networkx
* Update for hetero_from_relations
* Roll back the change of canonical_etypes to relations
* heterograph
* bipartite
* Update doc
* Fix lint
* Fix lint
* Fix test cases
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Update
* Fix test
* Fix
* Update
* Use DGLError
* Update
* Update
* Update
* Update
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* rewrite sanity checks
* delete unnecessary checks
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Fix
* Update
* Update
* Update
* Fix
* Fix
* Fix
* Update
* Fix
* Update
* Fix
* Fix
* Update
* Fix
* Update
* Fix
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
2020-08-18 04:26:29 +08:00
5e34ca8bb5
[Feature] Lazy copy ndata, edata to device ( #1986 )
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* Lazy to device
* remove print
* lint
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* Fix
* lint
* Fix
* Revert "Fix"
This reverts commit 615c9b8f80f5f6ee2ab43c849a22f0083deedf3b.
* Add test for frame lazy update
* disable tensorflow
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-08-12 13:04:47 +08:00
22167f7203
[Refactor] Enable new kernel in all message passing APIs ( #1953 )
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* WIP: frame refactor
* new frame
* simple update_all builtin
* move all subgraph routines into the same file
* sddmm & spmm schedule; node & edge udf
* degree bucketing
* some tricky 0deg corner cases
* bug in frame append
* merge test_hetero_basics and test_basics
* some code rearange
* fix test_heterograph
* add mean spmm
* enable all builtin combinations
* pass gpu test
* pass pytorch tests
* wip
* fix some pt debugging codes
* fix bug in mxnet backward
* pass all mxnet utests
* passed tf tests
* docstring
* lint
* lint
* fix broadcasting bugs
* add warning and clamp for mean reducer
* add test for zero-degree mean
* address comments
* lint
* small fix
2020-08-07 15:40:25 +08:00
Hongzhi (Steve), Chen