3d65484323
Fix mxnet gin ( #2048 )
...
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-19 00:05:15 +08:00
65866989c0
[NN] [Doc] Fix nn api doc ( #2047 )
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* fix mxnet nn doc and no note on chebconv
* change notes to note to highlight
2020-08-18 23:47:16 +08:00
dacc7afeb2
[Convert] Reserve node/edge IDs in to_heterogeneous ( #2045 )
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* Fix
* Fix
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-18 23:16:33 +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
edfbee2ca8
[Feature] Make sample_neighbors copy features on demand ( #2042 )
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* fix
* fix
* lint
* fix
* test
* fix
* fix
2020-08-18 22:25:19 +08:00
aa19df1bbb
[Bugfix] Fix batching isolated node types ( #2035 )
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* [Bugfix] Fix batching isolated ntypes
* fix test
* remove test.py
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-18 09:29:05 +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
0afc3cf8e1
[NN] Add ChebConv for Tensorflow ( #2038 )
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* add chebconv
* fix
* lint
* fix lint
* docs
2020-08-17 22:12:27 +08:00
b35388020d
[Bugfix] fix vocab not saved bug in SSTDataset ( #2036 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update tree.py
2020-08-17 21:59:14 +08:00
a8b27b475c
disable batching blocks ( #2034 )
2020-08-17 16:45:57 +08:00
b1e69105d4
[Doc] API Doc update for mxnet and tf, remove some degree check ( #2028 )
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* mx tf relconv
* use method instead of private attr
* src and dst have different fc for gat
* update edgeconv
* change sage and sgconv
* no degree check on gin
* add remainding API doc
* fix pylint
* infer fc_src and fc_dst, only one tensor for block
* fix pytest
2020-08-17 13:23:44 +08:00
4f1da61b58
[Doc] fix inconsistencies in minibatch user guide ( #2032 )
2020-08-17 12:43:43 +08:00
e291f503f2
[Fix] Update libinfo.py ( #1830 )
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* Update libinfo.py
fix `if search_path is list` error, and improve the code.
* change string format for compatibility with py35
change string format
* Update libinfo.py
* Update libinfo.py
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Quan (Andy) Gan <coin2028@hotmail.com >
2020-08-17 10:52:11 +08:00
1f7b219594
[Doc] User guide section 5 and 6 ( #2029 )
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* [Doc] User guide section 5 and 6
* oops
* fix
2020-08-17 09:47:01 +08:00
2fc280ba65
only filling zeros for min/max reducer ( #2026 )
2020-08-15 12:43:36 +08:00
63e2ba23c6
[WIP][Kernel] Set the built-in reduce result of zero-degree nodes to 0 in C ( #2017 )
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* test idea
* cuda kernels
* lint and fixes
* lint
* change to another strategy
* use infinity
* fix
Co-authored-by: Zihao Ye <expye@outlook.com >
2020-08-14 22:59:24 +08:00
2fa7f71ad5
[Doc] new nn api doc ( #2019 )
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* Add dotproduct attention
* [Feature] Add dotproduct attention
* [Feature] Add dotproduct attention
* [Feature] Add dotproduct attention
* [New] Update landing page
* [New] Update landing page
* [New] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Doc] Update landing page
* [Improvement] use dgl build-in in dotgatconv
* [Doc] review API doc string bottom up
* [Doc] Add doc of input and output features
* [Doc] Update doc string for pooling and transformer.
* [Doc] Reformat doc string and change some wordings.
* [Doc] Doc string refactoring.
* [Doc] Doc string refactoring.
* [Doc] Doc string refactoring.
* [Doc] Doc string refactoring.
* [Doc] Doc string refactoring.
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-14 18:00:38 +08:00
c113a5a0d7
Update dgl_dataset.py ( #2021 )
2020-08-14 16:17:37 +08:00
efa95d8673
[Distributed] Fix bugs ( #2009 )
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* fix.
* add tests.
* fix.
* fix.
2020-08-13 23:51:11 -07:00
1ad46fd015
[Distributed] support distributed sampling in NodeDataLoader ( #2012 )
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* fix.
* doesn't support EdgeDataLoader
* add test.
* fix.
* fix test.
* catch errors in the test.
* fix.
* fix error message
* add print.
* join the server processes.
* update test.
* fix test.
2020-08-13 22:49:21 -07:00
15e3ff878c
[Distributed] Fix memory leak in kvstore ( #2016 )
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* Fix memory leak
* update
* update
* update
* update
* update
* update
* update
2020-08-13 17:17:24 +08:00
4672c022a8
[hotfix] no in-degree check on sage ( #2014 )
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* no degre check on sage
* fix pytest
* no in degree check for heteroconv
2020-08-13 13:11:55 +08:00
cd48435206
[Transform] Docstring and subframes ( #1962 )
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* update knn graph docs
* more docs
* [Doc] transform module docstrings
* remove copy_ndata and copy_edata
* fix
* lint
* fix
* fix
* fix
* clean up docstrings
* fix docstring
* dtype specifications
* addresses comments
* fix
Co-authored-by: Mufei Li <mufeili1996@gmail.com >
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-13 10:41:43 +08:00
6294677f8a
[hotfix] Set reduce results to all zero for nodes with zero in-degrees. ( #2011 )
2020-08-13 01:20:56 +08:00
5362908236
Fix save/load for old version files ( #1994 )
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* load hetero
* fix
* more error message
* add warning
* add alias to dgl namespace
* fix tests
2020-08-12 23:45:21 +08:00
69f5869f3b
[Doc] NN doc refactor Conv Layers ( #1672 )
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* go through gcn, relgcn
* fix tagconv formula
* fix doc in sageconv
* fix sgconv doc
* replace hat with tilde
* more comments on gmmconv
* fix agnnconv chebconv doc
* modify nnconv doc
* remove &
* add nn conv examples
* Rebase master
* More merge conflicts
* check homo
* add back self loop for some convs, check homo in tranform
* add example for denseconv
* add example and doc for dotgat and cfconv
* check in-degree for graphconv
* add language fix
* gconv address all comments
* another round of change based on api template
* change agnn
* go through agnn, appnp, atomic, cf, cheb, dense, gat, sage modules
* finish pytorch part of nn conv
* mxnet graphconv done
* tensorflow graphconv works
* add new modules into doc
* add comments to not split code
* refine doc
* resr
* more comments
* more fix
* finish conv and dense conv part api
* pylint fix
* fix pylink
* fix pylint
* more fix
* fix
* fix test fail because zere in degree
* fix test fail
* sage is not update for mxnet tf
Co-authored-by: Ubuntu <ubuntu@ip-172-31-0-81.us-east-2.compute.internal >
2020-08-12 18:47:19 +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
d1cf5c383e
[Distributed] adjust various APIs. ( #1993 )
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* rename get_data_size.
* remove g from DistTensor.
* remove g from DistEmbedding.
* clean up API of graph partition book.
* fix DistGraph
* fix lint.
* collect all part policies.
* fix.
* fix.
* support distributed sampler.
* remove partition.py
2020-08-11 20:22:00 -07:00
4efa332044
[Distributed] Move server start code to initialize. ( #2002 )
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* move server start code to initialize.
* fix.
* fix lint.
* fix examples.
* add more checks.
2020-08-11 16:58:18 -07:00
0f56575938
[feature] Allow copy_e + udf reduce function ( #1996 )
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* up
* pylint
2020-08-11 18:47:40 +08:00
f5eb80d221
[Feature] Edge DataLoader for edge classification & link prediction ( #1828 )
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* clean commit
* oops forgot the most important files
* use einsum
* copy feature from frontier to block
* Revert "copy feature from frontier to block"
This reverts commit 5224ec963eb6a3ef1b6ab74d8ecbd44e4e42f285.
* temp fix
* unit test
* fix
* revert jtnn
* lint
* fix win64
* docstring fixes and doc indexing
* revert einsum in sparse bidecoder
* fix some examples
* lint
* fix due to some tediousness in remove_edges
* addresses comments
* fix
* more jtnn fixes
* fix
2020-08-11 18:00:58 +08:00
d340ea3aa8
[Distributed] Remove server_count from ip_config.txt ( #1985 )
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* remove server_count from ip_config.txt
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* Update dist_context.py
* fix lint.
* make it work for multiple spaces.
* update ip_config.txt.
* fix examples.
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* udpate
* update
* update
* update
* update
* update
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
2020-08-11 17:41:48 +08:00
71f4230a8b
[Fix] OpenMP compatibility issues ( #1992 )
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* fix OpenMP compatibility issues
* typo
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-11 14:26:34 +08:00
a089b91fdf
Remove stale partition code and fix #1949 ( #1984 )
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* remove unused code
* fix litn
* fix
2020-08-11 10:51:07 +08:00
ee30b2aadd
[Distributed] Fix standalone ( #1974 )
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* fix tests.
* fix.
* remove a test.
* make code work in the standalone mode.
* fix example.
* more fix.
* make DistDataloader work with num_workers=0
* fix DistDataloader tests.
* fix.
* fix lint.
* fix cleanup.
* fix test
* remove unnecessary code.
* remove tests.
* fix.
* fix.
* fix.
* fix example
* fix.
* fix.
* fix launch script.
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
2020-08-10 15:49:28 -07:00
c2cd6eb22e
[Doc] Reorg doc ( #1989 )
2020-08-10 23:19:03 +08:00
e4b4fcffc2
hotfix ( #1987 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-10 22:06:25 +08:00
729ff2ef38
Fix the performance issue of graph partitioning in new DGLGraph ( #1934 )
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* fix perf.
* fix.
* accelerate metis.
* fix lint.
* use gklib.
* fix perf.
* fix.
* update metis.
* update launch script
* handle synchronized API.
* fix.
* fix example.
* fix dataloader.
* temp fix.
* temp fix omp.
* distinguish roles.
* initialize iterator of DistDataloader correctly.
* check the correctness of launch script.
* move feature copy to sampler.
* measure mem/network copy time.
* remove
* Revert "measure mem/network copy time."
This reverts commit 86cefdc14b7815fcf5aad6496af912dba48e4aa6.
* fix.
* fix
* fix.
* fix cmake.
* disable metis in windows.
* disable metis tests in windows.
* remove test for multigraph.
* fix test.
* fix.
* fix cmake.
* fix.
* revert.
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-115.us-west-2.compute.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-19-1.us-west-2.compute.internal >
2020-08-09 18:33:05 -07:00
4ef01dbb05
[Example] Rgcn support ogbn-mag dataset. ( #1812 )
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* rgcn support ogbn-mag dataset
* upd
* multi-gpu val and test
* Fix
* fix
* Add support for ogbn-mag
* Fix
* Fix
* Fix
* Fix
* Add layer_norm
* update
* Fix merge
* Clean some code
* update Readme
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-68-185.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal >
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-09 15:56:15 +08:00
e75157738b
hotfix ( #1980 )
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Co-authored-by: Ubuntu <ubuntu@ip-172-31-87-240.ec2.internal >
2020-08-09 11:25:13 +08:00
b9ef70e5ac
[Distributed] Set the number of threads correctly to speed up ( #1976 )
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* temp fix omp.
* set server threads.
* add CAPI to set up OMP threads.
* fix.
* fix.
* update namesapce.
* set cpi properly.
* allow to config num worker threads.
* set #threads.
* fix.
2020-08-08 19:30:53 -07:00
f7ce48bcd4
[NN] Fix error message of GatedGraphConv ( #1964 )
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Co-authored-by: Zihao Ye <expye@outlook.com >
2020-08-08 23:01:07 +08:00
5454471fc8
[Distributed] Add roles ( #1971 )
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* distinguish roles.
* add comments.
* fix lint.
* move roles to server_state.
* fix text.
* fix tests.
* fix tests.
* Revert "fix tests."
This reverts commit 5baa136b872a4550d4e612bfb1dfe363d7814adf.
2020-08-08 01:41:51 -07:00
2823c61f37
[Distributed] Fix synchronized APIs in kvstore ( #1948 )
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* handle synchronized API.
* fix.
* fix.
* fix.
Co-authored-by: Chao Ma <mctt90@gmail.com >
2020-08-07 19:01:52 -07:00
bab32d5ba1
[Distributed] Fix dataloader ( #1970 )
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* fix dataloader.
* initialize iterator of DistDataloader correctly.
* update test.
2020-08-07 18:09:21 -07:00
264d96cdf5
[bugfix] Fix a bunch of examples to be compatible with dgl 0.5 ( #1957 )
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* upd
* upd
* upd
* upd
* upd
* upd
* fix pinsage also
* upd
* upd
* upd
Co-authored-by: Ubuntu <ubuntu@ip-172-31-29-3.us-east-2.compute.internal >
Co-authored-by: Quan Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
2020-08-08 01:31:23 +08:00
18bfec24cf
[hotfix] Refactor edge softmax module ( #1967 )
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* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
2020-08-07 23:50:12 +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
5d5436ba18
[Dataset] RedditDataset change data.train_mask to numpy array ( #1961 )
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* PPIDataset
* Revert "PPIDataset"
This reverts commit 264bd0c960cfa698a7bb946dad132bf52c2d0c8a.
* Update reddit.py
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com >
2020-08-07 15:22:13 +08:00
35c9473ba5
[HotFix] Fix add_reverse_edges ( #1960 )
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* Hot fix
* more test
Co-authored-by: Ubuntu <ubuntu@ip-172-31-51-214.ec2.internal >
2020-08-07 13:07:06 +08:00
xiang song(charlie.song)