a613ad8806
Refactor code for retaining formats in message-passing. ( #2570 )
2021-01-25 16:55:16 +08:00
25ac334403
[Distributed] Heterogeneous graph support ( #2457 )
...
* 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 >
2021-01-24 19:18:00 -08:00
aa884d43b6
[doc][fix] Improve the docstring and fix its behavior in DGL's kernel ( #2563 )
...
* upd
* fix
* lint
* fix
* upd
2021-01-25 00:18:57 +08:00
a6abffe303
[Fix] Don't create extra formats in dataloader ( #2551 )
...
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-24 20:59:24 +08:00
2288098ba6
[Feature] Converting a block to a graph and allow block construction ( #2555 )
...
* first commit
* more commit
* fix and docstring
* add to api reference
* address comments
* Update convert.py
2021-01-24 12:44:54 +08:00
7ff2662b88
[Fix] Better Error Message for node_type_subgraph ( #2554 )
...
* Update
* Update
* Update
2021-01-21 15:12:05 +08:00
2c6d071617
[Feature] QM9 Dataset Support ( #2521 )
...
* [Model] MixHop for Node Classification task
* [docs] update
* [docs] update
* [fix] remove seed option
* [fix] update readme
* [feature] support qm9 dataset
* [style] update
* [docs] fix the details
* [fix] indexing only support int
* [style] update
* [fix] multiple backends support
* [docs] add qm9
* [fix] Z type: float32 -> int32
* [fix] Z type: int32 -> long
* [docs] add ref
* [docs] fix
* [docs] update
* [docs] update
* [fix] test eval
* [docs] fix example
Co-authored-by: xnuohz@126.com <ubuntu@ip-172-31-44-184.us-east-2.compute.internal >
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2021-01-21 01:33:30 +08:00
917a755291
[Fix] fix version check ( #2544 )
2021-01-19 19:35:43 +08:00
9a9a06eb2f
[Bug Fix] Fix undefined var bug in LegacyTUDataset ( #2543 )
...
* [Bug Fix] Fix undefined var bug in LegacyTUDataset
* upt
* [Bug Fix] Fix cache file name bug in TUDataset
Co-authored-by: Tong He <hetong007@gmail.com >
2021-01-19 13:58:01 +08:00
8c8c5b1dc1
[Bug fix] Stop erasing schemas of frames with no data rows ( #2529 )
...
* added option for batching empty data, fixes #2526
* added option for batching empty data, fixes #2526
* decreased line lengths
* removed trailing whitespace
* fixed wrong feature name
* [Bugfix] stop erasing schema of frames w/ no cols (fixes #2528 )
* removed arg doc
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-17 10:32:47 +08:00
5da3439c16
[Feature] Add Device Flag in Data Loaders ( #2450 )
...
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-15 07:39:26 +08:00
0778766411
[Bug fix] [Feature] added option for batching empty data ( #2527 )
...
* added option for batching empty data, fixes #2526
* added option for batching empty data, fixes #2526
* decreased line lengths
* removed trailing whitespace
* fixed wrong feature name
* now default behavior when all graphs are empty
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-14 15:25:13 +08:00
bedccc2392
fix 2532 ( #2533 )
2021-01-14 13:40:25 +08:00
54f186bba0
Fix ( #2524 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-59-204.ec2.internal >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-13 15:09:21 +08:00
498505bafb
[Doc] fix docserver build for tutorials ( #2518 )
...
* fix doc build
* hide GPU code
2021-01-12 17:55:58 +08:00
a9f8f2589c
[Doc] Update GraphDataLoader in our docs ( #2504 )
...
* update graphdataloader in docs
* fix
* update examples
* fix sagpool
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-01-11 13:11:19 +08:00
bdb88df576
[Performance] Allow DataLoaders to return indices of the seed array ( #2495 )
...
* return indices from dataloader
* fixes
* fix
* fix distgraph and added some todos
* Update dataloader.py
* Update dataloader.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2021-01-08 14:30:52 +08:00
e2e524df41
[Feature] Add GraphDataLoader implementation ( #2496 )
...
* add graph dataloader
* add to doc
* fix
* fix
* fix docstring
* update according to torch default_collate
* add unittest
* fix
* fix lint
* fix
2021-01-07 13:38:21 +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 )
...
* fix
* fix test
2021-01-06 17:18:37 +08:00
0c2a2ea1e2
[Bugfix] Handle a Corner Case of Batching after Removing Nodes/Edges ( #2465 )
...
* Update
* Update
* Update
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2021-01-05 22:22:03 +08:00
21e90cbf48
[Doc] Fix number of classes in Amazon Cobuy datasets ( #2488 )
...
* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update gnn_benckmark.py
* Hide implementations that may cause confusions to the user
* fix number of classes in Amazon Cobuy datasets
2021-01-05 13:08:05 +08:00
f960468f50
[feature] APIs for manually set batch_num_nodes and batch_num_edges ( #2430 )
...
* 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
d3c1645550
[Performance][Test] New low memory implementation for RGCN and related regression tests ( #2468 )
...
* WIP
* finish lowmem impl; benchmarking
* wip
* wip
* fix benchmarks
* fix bug in searchsorted
* update readme
* update
* lint and ogb dependency
* add flags to to_homogeneous
* fix docstring
* address comments
2021-01-04 22:23:59 +08:00
9fabc9b8c5
[Doc] fix simple typo, tranfer -> transfer ( #2464 )
...
There is a small typo in python/dgl/dataloading/async_transferer.py.
Should read `transfer` rather than `tranfer`.
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2021-01-02 19:26:09 +08:00
4464b9734c
Fix kg dataset len() ( #2475 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-59-204.ec2.internal >
2020-12-31 23:33:21 +08:00
3d1f2e870a
delete shared memory when receiving signals. ( #2419 )
...
* 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 >
2020-12-26 10:41:10 -08:00
e805470101
addressing post-merge comments ( #2455 )
2020-12-26 17:58:15 +08:00
9a7235faf2
[Performance] Use allocator from PyTorch if possible ( #2328 )
...
* 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
2020-12-25 13:57:51 +08:00
baace710cf
[documentation] Improve the docstring of global pooling layer ( #2437 )
...
* upd
* fix-link
* lint
2020-12-21 10:12:54 +08:00
492ad9be81
[Fix] Avoid Overloading Nonzero for PyTorch Backend ( #2434 )
...
* Update gatedgraphconv.py
* Update entity_classify.py
* Update data-process.rst
* Update reading_data.py
* Update data-process.rst
* Update utils.py
* Update knowledge_graph.py
* Update entity_classify.py
* Update rdf.py
* Update entity_classify_mb.py
* Update test_classify.py
* Update tensor.py
* Update sparse.py
* Update entity_classify_mp.py
* Update 6_line_graph.py
2020-12-20 13:12:17 +08:00
9d7bf4ea89
Fix citation data loading ( #2421 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-57-25.ec2.internal >
2020-12-14 14:58:01 +08:00
1c976222d5
fix doc mistake in dgl/core.py ( #2404 )
...
The variable name 'eid' should be 'nid'
2020-12-08 22:05:55 +08:00
013d145663
[NN] Attention Retrieval for NN Modules ( #2397 )
...
* Update
* Update
2020-12-07 23:42:25 +08:00
fcf1193579
[Doc] Hidden implementations that may cause confusion to the user. ( #2378 )
...
* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* data pipeline user guide
* remove chapter numbers
* Update data.rst
* image in dataset userguide
* update links using ref
* modify the link of save_graphs and load_graphs in dataset user guide
* move image to s3 server.
* fix links and ref
* Hide implementations that may cause confusions to the user
2020-12-03 13:09:19 +08:00
98e11533e2
[hotfix] Produce empty tensor in data frame for emtpy graphs. ( #2387 )
...
* upd
* lint
* lint1
2020-12-03 12:00:29 +08:00
38077e298b
installation and doc fix ( #2379 )
2020-11-30 19:47:40 +08:00
edb978772c
[Doc, UG, Tutorial] Misc Fix ( #2376 )
...
* Update
* Update
* Update
* Update
* Update
2020-11-30 13:40:10 +08:00
6b02babbad
[doc] Add docstring for segment reduce. ( #2375 )
2020-11-27 18:04:13 +08:00
00edb94982
[Performance] Accelerate batching ( #2363 )
...
* speed up batching
* more fix
* lint
* fix
2020-11-24 17:39:00 +08:00
58775ada1f
Remove redundant print information in #2361 ( #2362 )
2020-11-23 03:41:58 +08:00
3adbfa1812
[Performance] Use segment operators for graph readout. ( #2361 )
...
* upd
* upd
* update
* upd
* upd
* upd
* fix
* lint
* lint
* pylint
* doc
2020-11-23 01:45:33 +08:00
45e3e9af2c
[WIP] Misc Fix ( #2359 )
...
* Update
* Update
* Update
2020-11-19 23:54:55 +08:00
fe4ada23f9
Update knowledge_graph.py ( #2329 )
...
The l in "bool" is lost.
Co-authored-by: Zihao Ye <expye@outlook.com >
2020-11-10 17:33:55 +08:00
812f597096
Update appnpconv.py ( #2324 )
2020-11-10 15:37:30 +08:00
4fb0241bfb
[CUDA] Add CUDA11 support ( #2308 )
...
* add support for cuda 11
* fix inc bug in pytorch 1.8
* poke ci
* fix
* small fix
* try fix
* try fix
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2020-11-07 22:16:51 +08:00
6eda605ccd
[BugFix][Dataloading] Disable AsyncTransferer copying to anywhere but the GPU ( #2323 )
...
* Disable copying for anywhere but the GPU
* Remove unused import and remove references to transferring from the GPU from the docs
* Skip gpu test in cpu mode
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-11-07 21:34:54 +08:00
5f19876358
[Bugfix] GINDataset check whether labels are all valid ( #2319 )
...
* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* check whether the original labels are valid
* add unit test for gin dataset
* bug of asscalar in mxnet<=1.6
* mxnet<=1.6 asscalar requires ndarray to be shaped (1,)
* skip gpu while testing datasets
* Update test_data.py
* test of gin dataset takes too much time
2020-11-05 09:35:10 +08:00
c6890c231a
[Performance] In HeteroNodeView, build arange on target device, instead of on CPU and copying it ( #2266 )
...
* Build arange on target device
* Utilize arange device in viewpy:HeteroNodeView.__call__
* Work around uint64 error in TF to_dlpack
* Restore else clause
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2020-11-02 14:03:26 -08:00
d453d72dd1
[Doc][Dataloading] Expand documentation of AsyncTransferer ( #2313 )
...
* Update docs
* Make non-default streams non-blocking
2020-11-02 12:28:30 -08:00
Zihao Ye