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
c49582c996
[Test] Fix the random seed in test_kernel.py and fix the _print_error ( #1194 )
...
* Fix the random seed and fix the _print_error
* Fix check_positive_edge_sampler sample weight.
Co-authored-by: Zihao Ye <zihaoye.cs@gmail.com >
Co-authored-by: VoVAllen <VoVAllen@users.noreply.github.com >
2020-01-17 13:48:47 +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
cd9599ab04
[KG][Optimization] Remove copy from parent in minibatch generation ( #1193 )
...
* remote copy from parent
* upd
* make test_sampler easier to pass
2020-01-10 15:59:09 -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
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
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
913e324903
Add device check for sampler input ( #1145 )
...
current samplers only support working on CPU
2019-12-27 22:50:52 +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
0d9acc9d58
hot fix ( #1135 )
2019-12-24 00:19:25 +08:00
a1b28b3954
[Hot fix] Fix build threads ( #1133 )
...
* 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
* try node
* try
* fix
* try new ci
* try new ci
* try new ci
* try new ci
* ci
* try
* try
* fix
* hot fix
* fix
* fix cpp test
* add comments
2019-12-23 21:42:59 +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
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
6ae93e5c6a
[Bug] Fix #1088 ( #1089 )
...
* [Bug] Fix #1088
* fix
* add comment
2019-12-11 10:27:57 +08:00
fa0ee46a01
[hotfix] node id validity check ( #1073 )
...
* fix
* improve
* fix lint
* upd
* fix
* upd
2019-12-06 01:36:41 +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
a0193fd539
Small change for kvstore api ( #981 )
...
* Small change for kvstore api
* fix ci
* fix ci
2019-11-08 16:25:12 +08:00
0b4935d4c3
Test shared-mem on kvstore ( #976 )
2019-11-05 17:09:35 +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
a6d5a0cbdd
[BUG] Fix #717 ( #946 )
...
* [BUG] Fix #717
* fix mxnet test
2019-10-28 09:29:07 +08:00
70ee4b5e28
Add more test to kvstore ( #944 )
2019-10-21 17:46:43 +08:00
ff9f67ee0d
Send any shape of tensor rather than matrix ( #942 )
2019-10-21 17:27:03 +08:00
e2b7f745ca
[Hetero] Doc ( #892 )
...
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* Update
* style fixes & undefined name fix
* transpose=False in test
2019-10-06 20:17:40 +08:00
bce51cbd65
[BUGFIX] check the number of columns in subgraph.copy_from_parent ( #903 )
...
* check the number of columns.
* add test.
2019-10-05 18:35:56 -07:00
d0eae92e5a
[Test] reduce test. ( #895 )
...
* reduce test.
* increase timeout for unittest.
2019-10-02 00:20:39 -07:00
3e454476b6
edge sampler return head nodes and tail nodes. ( #889 )
...
* edge sampler return head nodes and tail nodes.
* edge subgraph.
* use VecToIdArray
* example.
* fix compile error.
2019-09-30 21:25:16 -07:00
0ca52bfc88
[Hetero] Create heterograph from dictionary of edge lists ( #882 )
...
* [Hetero] Create heterograph from dictionary of edge lists
* rename
* address comments
2019-09-30 15:41:41 +08:00
65e1ba4f60
Sort csr ( #886 )
...
* sort
* sort in parallel.
* fix a bug in sorting adj
* rename.
* add more comments.
* accelerate GetData
* fix tests.
* avoid sorting multiple times.
* add test.
* change back.
* sort.
* add sort_csr.
* Fix a bug.
* fix.
* revert modifcation.
* rename
* speed up EdgeIds.
2019-09-28 10:52:12 -07:00
c03046a08f
[Model][Hetero] HAN ( #868 )
...
* Add HAN
* Fix
* WIP; load raw ACM dataset
* DGL's own preprocessing with metapath coalescer
* various fixes
* comparison against simple logistic regression
* rename
* fix test
2019-09-27 12:53:16 +08:00
e16667bfb9
[Fix] Fix Transform ( #876 )
...
* add transform
* lint
* lint
* fix
* fixmx
* fix
* add test
* fix typo
* fix default num_classes
* change to non-inplace operation
* fix lint
* fix
* fix
* fix lint
* fixlint
2019-09-26 21:21:53 -04:00
e3921d5dec
[Sampler] Metapath sampler for metapath2vec ( #861 )
...
* metapath sampler
* lint & fixes
* lint x2
* lint x3
* fix windows
* remove max_cycle argument
* add todo note
2019-09-26 16:42:33 -04:00
1db697ec65
Improve edge sampler ( #881 )
...
* optimizer for sampling all negative edges.
* allow to disable checking false negative.
* fix lint.
* fix docstring.
* fix for comment.
* add comments.
2019-09-25 22:56:37 -07:00
2d489617dd
[Feature] find the existence of negative edges. ( #875 )
...
* find the existence of negative edges.
* add comment.
* fix test.
2019-09-23 01:59:02 -07:00
f9c0217d27
[Bugfix] Fix number of nodes mismatch in to_homo() conversion ( #874 )
2019-09-22 19:30:24 +08:00
bf8bb58f60
[Transform] Add to_self_loop, remove_self_loop, onehot_degree transform ( #862 )
...
* add transform
* lint
* lint
* fix
* fixmx
* fix
* add test
* fix typo
* fix default num_classes
* change to non-inplace operation
* fix lint
* fix
2019-09-21 00:05:38 +08:00
9b4d60799a
[Hetero] New syntax ( #824 )
...
* WIP. remove graph arg in NodeBatch and EdgeBatch
* refactor: use graph adapter for scheduler
* WIP: recv
* draft impl
* stuck at bipartite
* bipartite->unitgraph; support dsttype == srctype
* pass test_query
* pass test_query
* pass test_view
* test apply
* pass udf message passing tests
* pass quan's test using builtins
* WIP: wildcard slicing
* new construct methods
* broken
* good
* add stack cross reducer
* fix bug; fix mx
* fix bug in csrmm2 when the CSR is not square
* lint
* removed FlattenedHeteroGraph class
* WIP
* prop nodes, prop edges, filter nodes/edges
* add DGLGraph tests to heterograph. Fix several bugs
* finish nx<->hetero graph conversion
* create bipartite from nx
* more spec on hetero/homo conversion
* silly fixes
* check node and edge types
* repr
* to api
* adj APIs
* inc
* fix some lints and bugs
* fix some lints
* hetero/homo conversion
* fix flatten test
* more spec in hetero_from_homo and test
* flatten using concat names
* WIP: creators
* rewrite hetero_from_homo in a more efficient way
* remove useless variables
* fix lint
* subgraphs and typed subgraphs
* lint & removed heterosubgraph class
* lint x2
* disable heterograph mutation test
* docstring update
* add edge id for nx graph test
* fix mx unittests
* fix bug
* try fix
* fix unittest when cross_reducer is stack
* fix ci
* fix nx bipartite bug; docstring
* fix scipy creation bug
* lint
* fix bug when converting heterograph from homograph
* fix bug in hetero_from_homo about ntype order
* trailing white
* docstring fixes for add_foo and data views
* docstring for relation slice
* to_hetero and to_homo with feature support
* lint
* lint
* DGLGraph compatibility
* incidence matrix & docstring fixes
* example string fixes
* feature in hetero_from_relations
* deduplication of edge types in to_hetero
* fix lint
* fix
2019-09-17 15:41:57 -04:00
0a56d65223
[Feature] x_dot_x builtin kernel support ( #831 )
...
* upd
* fig edgebatch edges
* add test
* trigger
* Update README.md for pytorch PinSage example.
Add noting that the PinSage model example under
example/pytorch/recommendation only work with Python 3.6+
as its dataset loader depends on stanfordnlp package
which work only with Python 3.6+.
* Provid a frame agnostic API to test nn modules on both CPU and CUDA side.
1. make dgl.nn.xxx frame agnostic
2. make test.backend include dgl.nn modules
3. modify test_edge_softmax of test/mxnet/test_nn.py and
test/pytorch/test_nn.py work on both CPU and GPU
* Fix style
* Delete unused code
* Make agnostic test only related to tests/backend
1. clear all agnostic related code in dgl.nn
2. make test_graph_conv agnostic to cpu/gpu
* Fix code style
* fix
* doc
* Make all test code under tests.mxnet/pytorch.test_nn.py
work on both CPU and GPU.
* Fix syntex
* Remove rand
* Start implementing masked-mm kernel.
Add base control flow code.
* Add masked dot declare
* Update func/variable name
* Skeleton compile OK
* Update Implement. Unify BinaryDot with BinaryReduce
* New Impl of x_dot_x, reuse binary reduce template
* Compile OK.
TODO:
1. make sure x_add_x, x_sub_x, x_mul_x, x_div_x work
2. let x_dot_x work
3. make sure backward of x_add_x, x_sub_x, x_mul_x, x_div_x work
4. let x_dot_x backward work
* Fix code style
* Now we can pass the tests/compute/test_kernel.py for add/sub/mul/div forward and backward
* Fix mxnet test code
* Add u_dot_v, u_dot_e, v_dot_e unitest.
* Update doc
* Now also support v_dot_u, e_dot_u, e_dot_v
* Add unroll for some loop
* Add some Opt for cuda backward of dot builtin.
Backward is still slow for dot
* Apply UnravelRavel opt for broadcast backward
* update docstring
2019-09-14 19:27:31 +08:00
4297e6d6ff
[Feature] add PBG's negative edge sampling. ( #836 )
...
* PBG negative edge sampler.
* add a positive edge to make it regular, handle last batch.
* exclude all positive edges in the parent graph.
* just uniformly sample negative nodes.
* fix lint.
* shuffle one-side nodes of positive edges.
* just uniformly sample negative nodes.
* change the data type.
* address comment.
* remove commented code.
2019-09-11 12:52:06 -07:00
7782276962
[KVStore] Distributed kvstore ( #851 )
...
* update
* speedup
* add some comments
2019-09-11 14:54:50 +08:00
0fb13f7b9d
[Feature] Data format ( #728 )
...
* Add serialization
* add serialization
* add serialization
* lalalalalalalala
* lalalalalalalala
* serialize
* serialize
* nnn
* WIP: import tvm runtime node system
* WIP: object system
* containers
* tested basic container composition
* tested custom object
* tmp
* fix setattr bug
* tested object container return
* fix lint
* some comments about get/set state
* fix lint
* fix lint
* update cython
* fix cython
* ffi doc
* fix doc
* WIP: using object system for graph
* c++ side refactoring done; compiled
* remove stale apis
* fix bug in DGLGraphCreate; passed test_graph.py
* fix bug in python modify; passed utest for pytorch/cpu
* fix lint
* Add serialization
* Add serialization
* fix
* fix typo
* serialize with new ffi
* commit
* commit
* commit
* save
* save
* save
* save
* commit
* clean
* Delete tt2.py
* fix lint
* Add serialization
* fix lint 2
* fix lint
* fix lint
* fix lint
* fix lint
* Fix Lint
* Add serialization
* Change to Macro
* fix
* fix
* fix bugs
* refactor
* refactor
* updating dmlc-core to include force flag
* trying tempfile
* delete leaked pointer
* Fix assert
* fix assert
* add comment and test case
* add graph labels
* add load labels
* lint
* lint
* add graph labels
* lint
* fix windows
* fix
* update dmlc-core to latest
* fix
* fix camel naming
2019-09-09 20:57:51 +08:00
8844246aea
[bugfix] Disable shared memory test that may fails CI. ( #810 )
...
* upd
* up
* upd
* upd
2019-08-30 15:42:05 +08:00
ad15947f0e
[bugfix] Fix several issues in test_kernel ( #801 )
...
* upd
* stable
2019-08-28 04:24:00 +08:00
650f6ee1e0
[NN] Add commonly used GNN models from examples to dgl.nn modules. ( #748 )
...
* gat
* upd
* upd sage
* upd
* upd
* upd
* upd
* upd
* add gmmconv
* upd ggnn
* upd
* upd
* upd
* upd
* add citation examples
* add README
* fix cheb
* improve doc
* formula
* upd
* trigger
* lint
* lint
* upd
* add test for transform
* add test
* check
* upd
* improve doc
* shape check
* upd
* densechebconv, currently not correct (?)
* fix cheb
* fix
* upd
* upd sgc-reddit
* upd
* trigger
2019-08-27 18:21:19 +08:00
xiang song(charlie.song)