c7c0fd0e37
[Feature] Accessing node/edge types in UDFs. ( #1243 )
...
* typed udf
* docstrings
2020-02-17 16:02:56 +08:00
b133abb82e
[KVStore] New kvstore used by DGL-KE ( #1263 )
...
* new kvstore
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* test warning
* update
* update
* udpate
* update
* update
* update
* update
* small fix
* small fix
* get group count
* update
* update
* make file
* update
* use addr
* get id
* partition book
* update
* partition
* barrier
* update
* loop count
* update
* update
* update
* update
* update
* update
* update
* update
* update
* add mxnet demo
* update ip
* update
* update
* update
* random
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* fix lint
2020-02-17 13:39:13 +08:00
77ae4d5321
[Example] Fix Rgcn hetero nonedetermistic in graph and model initialization ( #1244 )
...
* Fix model save and load problem.
Add offline inference example
* Fix test
* Fix randomness problem between test runs
* Make rdf loader deterministic
2020-02-07 11:07:09 +08:00
eeeb52f464
[Feature] Preference to COO for "hypersparse" unit graphs & graph compaction ( #1238 )
...
* unit graph that prefers coo queries
* auto detect coo preference
* forgot some functions
* disable lint on detect_prefer_coo
* reorg
* change comment
* lint
* fix
* move array_utils.h to src
* compact graph impl
* fix redundant copying in idhashmap
* docstring
* moving preference detection to C
* lint
* fix unit test & address comments
* hypersparse autorestrict
* docstring & fix
* revert copyto and asnumbits
* fix stupid bug
* lint
* leave a TODO for sorted COO
* fixing same node type mapping to different id in different graphs
* addresses comments
* made induced nodes a feautre column
* lint?
2020-02-04 22:39:28 +08:00
828a5e5bc6
[DGL-LifeSci] Migration and Refactor ( #1226 )
...
* First commit
* Update
* Update splitters
* Update
* Update
* Update
* Update
* Update
* Update
* Migrate ACNN
* Fix
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* Finish classification
* Update
* Fix
* Update
* Update
* Update
* Fix
* Fix
* Fix
* Update
* Update
* Update
* trigger CI
* Fix CI
* Update
* Update
* Update
* Add default values
* Rename
* Update deprecation message
2020-02-04 01:38:09 +08:00
e4948c5cbc
fix regression in #1237 ( #1239 )
2020-02-03 11:50:06 +08:00
c167373e1e
[Doc] Fix the doc of NeighborSampler. ( #1236 )
...
* fix.
* fix.
2020-01-31 13:36:17 -08:00
a9dabcc769
[Feature] Random Walk for 0.5 ( #1209 )
...
* trying to refactor IndexSelect
* partial implementation
* add index select and assign for floats as well
* move to random choice source
* more updates
* fixes
* fixes
* more fixes
* adding python impl
* fixes
* unit test
* lint
* lint x2
* lint x3
* update metapath2vec
* debugging performance
* still debugging for performance
* tuning
* switching to succvec
* redo
* revert non-uniform sampler to use vector
* still not fast
* why does this crash with OpenMP???
* because there was a data race!!!
* add documentations and remove assign op
* lint
* lint x2
* lol what have i done
* lint x3
* fix and disable gpu testing
* bugfix
* generic random walk
* reorg the random walk source code
* Update randomwalks.h
* Update randomwalks_cpu.cc
* rename file
* move internal function to anonymous ns
* reorg & docstrings
* constant restart probability
* docstring fix
* more commit
* random walk with restart, tested
* some fixes
* switch to using NDArray for choice
* massive fix & docstring
* lint x?
* lint x??
* fix
* export symbols
* skip gpu test
* addresses comments
* replaces another VecToIdArray
* add randomwalks.h to include
* replace void * with template
2020-01-31 19:52:08 +08:00
f1a8f926a4
[Feature] Add environment variable to switch on/off MXNet set_np_shape ( #1207 )
...
* add env var
* Trigger CI
* simplification
* add doc
2020-01-20 13:54:14 +08:00
a00636a02b
[Tensorflow] Several nn & example ( #1191 )
...
* several nn example
* appnp
* fix lint
* lint
* add dgi
* fix
* fix
* fix
* fff
* docs
* 111
* fix
* change init
* change result
* tiaocan+1
* fix
* fix lint
* fix
* fix
2020-01-19 22:48:40 +08:00
31a7d50964
[Bug Fix] Add boundary check for heterograph build with card as input ( #1192 )
...
* Add boundary check for heterograph build with card as input
* Fix when u or v is empty
* fix test_kernel.py error print
* Revert "fix test_kernel.py error print"
This reverts commit a71c20292549c0ac62a5326c30669ca4bde8febc.
* Turn op validation check on graph and bipartite by default
* upd
* udp
* upd
* update test
2020-01-18 17:18:40 +08:00
86fe58ebb8
[Bug] Another fix on PyTorch memory leakage issue ( #1139 )
...
* another fix
* another try
* fix
* rewriting with kernel functions
* revert mxnet softmax changes
* lint fix
Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com >
2020-01-14 22:54:19 +08:00
28a24414c8
[BUG] Fix empty heterograph creation with list & tuple ( #1188 )
...
* [BUG] Fix empty heterograph creation with list & tuple
* more fix
2020-01-09 22:40:27 +08:00
aa06e4579f
[Doc] Improve the docstring of several nn modules. ( #1187 )
...
* upd
* upd
* upd
* upd
* lint
* upd
* upd
* upd
* upd
* upd
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com >
2020-01-09 21:14:33 +08:00
3ef757dbff
[Feature] Pickle support for heterograph ( #1177 )
...
* [Feature] Pickle support for heterograph
* fix lint
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com >
2020-01-09 13:27:29 +08:00
ca302a13ac
[Feature] Add dgl.nn.*.Sequential for usability ( #1166 )
...
* upd
* upd
* upd
* upd
* lint
* upd
* upd
* upd
* upd
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com >
2020-01-09 12:39:22 +08:00
319118341d
[Dataset] Change download repo link to https://data.dgl.ai (CDN) ( #1175 )
...
* change download link to cdn
* Update env_var.rst
2020-01-07 17:16:45 +08:00
38d292e541
[KVStore] Fix memory leak bug. ( #1174 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
* add multiple NICs support for kvstore
* test
* fix lint
* update
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* update
* fix lint
* delete msg
* clear kv msg
* update
* update
* update
* update
* update
* update
* is not None
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
2020-01-06 19:47:54 +08:00
6d0a9c4297
[Fix issue] Fix issue 1170 ( #1171 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
* add multiple NICs support for kvstore
* test
* fix lint
* update
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* update
* fix lint
2020-01-05 14:31:41 +08:00
1022d5d64d
[KG] PBG's way of constructing negative edges ( #1159 )
...
* attach positive.
* add neg_deg_sample.
* add comment.
* add neg_deg_sample for eval.
* change the edge sampler.
* rename edge sampler in KG.
* allow specifying chunk size and negative sample size separately.
* fix bugs in KG.
* add check in sampler.
* add more checks.
* fix
* add comment.
* add comments.
2020-01-04 19:25:06 -08:00
61b78e6ee7
[Bug Fix]edge sample hotfix ( #1152 )
...
* hot fix
* Fix docs
* Fix ArrayHeap float overflow bug
* Fix
* Clean some dead code
* Fix
* FIx
* Add some comments
* run test
2019-12-30 19:42:57 -08:00
6731ea3af7
[KVStore] Reduce memory cost of kvstore ( #1156 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
* add multiple NICs support for kvstore
* test
* fix lint
* update
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
2019-12-30 20:25:32 +08:00
4f02bb751b
[KVStore] Made kvstore can support multiple NICs ( #1150 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
* add multiple NICs support for kvstore
* test
* fix lint
* update
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* update
* update
* update
* update
2019-12-30 15:17:31 +08:00
655d75688a
fix deprecation warning ( #1147 )
2019-12-28 12:42:16 +08:00
d57ff78da1
[Small Fix] Change default message queue size of communicator to 2GB ( #1140 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
* change default queue size to 2GB
* OMP_NUM_THREADS=1
2019-12-25 17:03:52 +08:00
e4ef8d1a80
[KVStore] API change of kvstore ( #1058 )
...
* API change of kvstore
* add demo for kvstore
* update
* remove duplicated log
* change queue size
* update
* update
* update
* update
* update
* update
* update
* update
* update
* fix lint
* change name
* update
* fix lint
* update
* update
* update
* update
* change message queue size to a python argument
2019-12-24 17:05:15 +08:00
41f8a162f4
[Feature Improvement]Edge Sampler w and w/o replacement ( #1116 )
...
* Add weight based edge sampler
* Can run, edge weight work.
TODO: test node weight
* Fix node weight sample
* Fix y
* Update doc
* Fix syntex
* Fix
* Fix GPU test for sampler
* Fix test
* Fix
* Refactor EdgeSampler to act as class object not function that it
can record its own private states.
* clean
* Fix
* Fix
* Fix run bug on kg app
* update
* update test
* test
* Simply python API and fix some C code
* Fix
* Fix
* Fix syntex
* Fix
* Update API description
* add replacement for edge sampler
* Now edge sampler support replacement and no-replacement
* Fix
* Fix
* change kg/app to use edge sampler with replacement config
* Update replacement algo
* Fix syntax
* Update
* Update
Co-authored-by: Da Zheng <zhengda1936@gmail.com >
2019-12-24 16:25:40 +08:00
e890a899fc
Partition a graph with HALO nodes ( #1076 )
...
* get subgraph with halo.
* add partition function.
* add comment.
* parallel partition.
* fix a compilation error.
* fix lint error.
* address comments.
* add comments.
* fix for TF.
2019-12-23 08:46:53 -08:00
d30a69bf27
[Backend] TF backend ( #978 )
...
* tf
* add builtin support
* fiix
* pytest
* fix
* fix
* fix some bugs
* fix selecting
* fix todo
* fix test
* fix test fail in tf
* fix
* fix
* fix gather row
* fix gather row
* log backend
* fix gather row
* fix gather row
* fix for pytorch
* fix
* fix
* fix
* fix
* fix
* fix tests
* fix
* fix
* fix
* fix
* fix
* fix
* fix convert
* fix
* fix
* fix
* fix inplace
* add alignment setting
* add debug option
* Revert "add alignment setting"
This reverts commit ec63fb3506ea84fff7d447a1fbdfd1d5d1fb6110.
* tf ci
* fix lint
* fix lint
* add tfdlpack
* fix type
* add env
* fix backend
* fix
* fix tests
* remove one_hot
* remove comment
* remove comment
* fix
* use pip to install all
* fix test
* fix base
* fix
* fix
* add skip
* upgrade cmake
* change version
* change ci
* fix
* fix
* fix
* fix
* fix seg fault
* fix
* fix python version
* fix
* try fix
* fix
* fix
* tf takes longer time in ci
* change py version
* fix
* fix
* fix oom
* change kg env
* change kg env
* 啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊啊
* 我再也不搞各种乱七八糟环境了……
* use pytest
* Chang image
2019-12-20 15:56:51 +08:00
cf9ba90fd4
[Chem] ACNN and various utilities ( #1117 )
...
* Add several splitting methods
* Update
* Update
* Update
* Update
* Update
* Fix
* Update
* Update
* Update
* Update
* Fix
* Fix
* Fix
* Fix
* Fix
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Finally
* CI
2019-12-19 11:54:40 +08:00
6beef85b07
upd ( #1113 )
2019-12-17 15:24:04 +08:00
632a9af8f9
[Feature] No-Uniform Edge Sampler ( #1087 )
...
* Add weight based edge sampler
* Can run, edge weight work.
TODO: test node weight
* Fix node weight sample
* Fix y
* Update doc
* Fix syntex
* Fix
* Fix GPU test for sampler
* Fix test
* Fix
* Refactor EdgeSampler to act as class object not function that it
can record its own private states.
* clean
* Fix
* Fix
* Fix run bug on kg app
* update
* update test
* test
* Simply python API and fix some C code
* Fix
* Fix
* Fix syntex
* Fix
* Update API description
2019-12-16 11:26:34 -08:00
dd65ee211e
[CI] Change tests for flexibility
...
* change ci image
* fix
* force bash
* fix
* fix python version
* fix
* fix
* fix
* update gpu
* cuda
* jenkins
* fix build sh
* fix
* Revert "fix"
This reverts commit 6b091914b3ef6b4300fa662ee375aa4b27944f5c.
* try fix
* fix
* Revert "fix"
This reverts commit e42c3035fa4974c6b197aaba0748f7b45113ddaa.
* try fix
* fix
* fix
* fix
* fix
* fix
* fix
* fix tests
* try fix
* fix
* fix
* fix
* fix
* fix
* fix
* fix ctx problem
* fix many tests
* fix typo
* add backend
* move to pytorch folder
* fix?
* fix ci
* try skip
* try false
* try?
* try?
* Revert to 7d9a52f
* fix various
* fix lint
* Revert Jenkinsfile
* revert env
* revert env
* address comment
* remove file
2019-12-16 14:54:37 +08:00
adea4ba1d0
fix doc. ( #1100 )
2019-12-13 05:24:37 -08:00
b599f6ed96
Update ( #1090 )
2019-12-11 13:39:18 +08:00
870857cfba
udp ( #1083 )
2019-12-09 14:52:20 +08:00
a5a052b5bf
[Fix] Fix #1078 , #1077 and add nightly build to readme
2019-12-09 00:03:35 +08:00
fa0ee46a01
[hotfix] node id validity check ( #1073 )
...
* fix
* improve
* fix lint
* upd
* fix
* upd
2019-12-06 01:36:41 +08:00
35653ddd0a
[Fix] Fix karate due to networkx version change
2019-12-04 22:02:10 +08:00
49b406c981
memory leak fix in PyTorch ( #1060 )
2019-11-29 14:37:33 +08:00
365d361725
[Bug] Fix #1036 ( #1037 )
...
* fix
* unit test
2019-11-29 11:53:29 +08:00
4f6063124b
[Graph]To(device) should return updated object ( #1057 )
...
* To(device) should return updated object
* Add test case and doc
* Add another doc
* Add descriptions and a test
* Pass test
2019-11-29 00:15:22 +08:00
ead64de98e
[Hetero] Batching/Unbatching DGLHeteroGraph ( #1017 )
...
* Update
* Update
* Update
* Fix
* CI style fix
* CI fix style
* Fix
* Try CI
* Fix test
* Update
* Update
* Update
* Update
2019-11-26 14:40:50 +08:00
6694f7b945
[Bug] Fix DGLHeteroGraph.edge_type_subgraph ( #1040 )
...
* Update
* Try CI
2019-11-25 03:35:25 +08:00
45aa158408
Fix example code in saving graphs ( #1034 )
2019-11-22 13:38:58 +08:00
f1542b9dfa
Fix ( #1019 )
2019-11-20 15:14:40 +08:00
a0193fd539
Small change for kvstore api ( #981 )
...
* Small change for kvstore api
* fix ci
* fix ci
2019-11-08 16:25:12 +08:00
7897fa3b9c
add init api on kvserver ( #975 )
2019-11-05 16:21:35 +08:00
cccde032f4
[kvstore] Performance improvement for distributed kvstore ( #972 )
...
* Performance improvment for distributed kvstore
* update
* update
2019-11-04 18:27:00 +08:00
fdd0fe651d
hotfix ( #971 )
2019-11-04 12:11:53 +08:00
Quan (Andy) Gan