af61e2fbb4
[Feature] Support nn modules for bipartite graphs. ( #1392 )
...
* init gat
* fix
* gin
* 7 nn modules
* rename & lint
* upd
* upd
* fix lint
* upd test
* upd
* lint
* shape check
* upd
* lint
* address comments
* update tensorflow
Co-authored-by: Quan Gan <coin2028@hotmail.com >
Co-authored-by: Jinjing Zhou <VoVAllen@users.noreply.github.com >
Co-authored-by: Minjie Wang <wmjlyjemaine@gmail.com >
2020-03-29 16:48:38 +08:00
3efb5d8ecf
[NN] Add HeteroGraphConv module for cleaner module definition ( #1385 )
...
* Add HeteroGraphConv
* add custom aggregator; some docstring
* debugging
* rm print
* fix some acc bugs
* fix initialization problem in weight basis
* passed tests
* lint
* fix graphconv flag; add error message
* add mxnet heteroconv
* more fix for mx
* lint
* fix torch cuda test
* fix mx test_nn
* add exhaust test for graphconv
* add tf heteroconv
* fix comment
2020-03-27 18:47:06 +08:00
4af02022b2
[Bug] Multiple fixes ( #1374 )
...
* multiple fixes
* lint
* lint x2
2020-03-19 11:19:44 +08:00
a9520f71ce
[Model][Sampler] GraphSAGE model, bipartite graph conversion & remove edges API ( #1297 )
...
* remove edge and to bipartite and graphsage with sampling
* fixes
* fixes
* fixes
* reenable multigpu training
* fixes
* compatibility in DGLGraph
* rename to compact_as_bipartite
* bugfix
* lint
* add offline inference
* skip GPU tests
* fix
* addresses comments
* fix
* fix
* fix
* more tests
* more docs and unit tests
* workaround for empty slice on empty data
2020-03-08 02:38:29 +08:00
93ac29ce34
[Refactor] Unify DGLGraph, BatchedDGLGraph and DGLSubGraph ( #1216 )
...
* upd
* upd
* upd
* lint
* fix
* fix test
* fix
* fix
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd tutorial
* upd
* upd
* fix kg
* upd doc organization
* refresh test
* upd
* refactor doc
* fix lint
Co-authored-by: Minjie Wang <minjie.wang@nyu.edu >
2020-03-05 18:03:57 +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
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
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
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
9a0511c8e9
[NN] nn modules & examples update ( #890 )
...
* upd
* damn it
* fuck
* fuck pylint
* fudge
* remove some comments about MXNet
* upd
* upd
* damn it
* damn it
* fuck
* fuck
* upd
* upd
* pylint bastard
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
* upd
2019-11-03 17:29:42 -05:00
6a4b5ae98a
[Feature] Edge softmax on a subset of edges in the graph. ( #842 )
...
* upd
* add test
* fix
* upd
* merge
* hotfix
* upd
* fix
2019-09-09 13:44:56 +08:00
e17add5602
[NN] Add MXNet impl for TAGCN module. ( #799 )
...
* 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
* Add TAGCN nn.module and example
* Now tagcn can run on CPU.
* Add unitest for TGConv
* Fix style
* For pubmed dataset, using --lr=0.005 can achieve better acc
* Fix style
* Fix some descriptions
* trigger
* Fix doc
* Add nn.TGConv and example
* Fix bug
* Update data in mxnet.tagcn test acc.
* Fix some comments and code
* delete useless code
* Fix namming
* Fix bug
* Fix bug
* Add test code for mxnet TAGCov
* Update some docs
* Fix some code
* Update docs dgl.nn.mxnet
* Update weight init
* Fix
2019-08-28 13:19:17 +08:00
9314aabd1f
[Refactor] Interface of nn modules ( #798 )
...
* refactor
* upd mpnn
2019-08-27 22:29:25 +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
11fb217a76
[NN] Add TAGCN nn.module and example ( #788 )
...
* 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
* Add TAGCN nn.module and example
* Now tagcn can run on CPU.
* Add unitest for TGConv
* Fix style
* For pubmed dataset, using --lr=0.005 can achieve better acc
* Fix style
* Fix some descriptions
* trigger
* Fix doc
2019-08-25 22:17:46 +08:00
708765f0a1
[NN] RGCN modules ( #744 )
...
* rgcn module
* support id input
* WIP: model codes
* use faster index select
* dropout
* self loop
* WIP: link prediction
* fix lint
* WIP: docs
* docstring
* docstring
* merge two child classes
* mxnet rgcn module
* fix lint
* fix lint
* fix rename bug
* add uniform edge sampler
* fix fn name
* docstring
* fix mxnet rgcn module
* fix mx rgcn
* enable test on cuda
2019-08-23 16:38:48 -04:00
2bff8339dd
[Test] Provid a frame agnostic API to test nn modules on both CPU and CUDA side. ( #775 )
...
* 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
2019-08-21 16:40:41 +08:00
5d3f470b72
[Feature] DGL Pooling modules ( #669 )
...
* removal doc
* glob
* upd
* rm knn
* add softmax
* upd
* upd
* add broadcast and s2s
* optimize max_on
* forsaken changes to heterograph
* upd
* upd
* upd
* upd
* upd
* bugfix
* upd
* upd
* upd
* upd
* format upd
* upd format
* upd doc
* upd
* import order
* upd
* rm warnings
* fix
* upd test
* upd
* upd
* fix device
* upd
* upd
* upd
* upd
* remove 1.1
* upd
* trigger
* trigger
* add more tests
* fix device
* upd
* upd
* refactor
* fix?
* fix
* upd docstring
* refactor
* upd
* fix
* upd
* upd
* upd
* fix
* upd docs
* add shape
* refactor & upd doc
* upd doc
* upd
2019-08-06 01:43:25 +08:00
fc9d30fae4
[Graph] add local scope function ( #735 )
...
* add local scope function
* fix lint
* fix docstring
* change local_scope to local_var; add context manager
* address comments
2019-08-02 00:11:48 -04:00
8ecedfb369
[Fix] Bugfix in docs and check gradient of edge_softmax in test ( #686 )
...
* upd
* Add stronger test
* Update test_nn.py
* Update test_nn.py
* trigger
* trigger
* trigger
2019-06-27 00:43:26 +08:00
74e13eea61
[Model] Update GAT model code ( #622 )
...
* fix gat code to use latest edge softmax module
* avoid transpose
* update README
* use edge_softmax op
* mxnet edge softmax op
* mxnet gat
* update README
* fix unittest
* fix ci
* fix mxnet nn test; relax criteria for prod reducer
2019-06-08 21:41:38 -04:00
653428bdc7
[Feature][Kernel] DGL kernel support ( #596 )
...
* [Kernel] Minigun integration and fused kernel support (#519 )
* kernel interface
* add minigun
* Add cuda build
* functors
* working on binary elewise
* binary reduce
* change kernel interface
* WIP
* wip
* fix minigun
* compile
* binary reduce kernels
* compile
* simple test passed
* more reducers
* fix thrust problem
* fix cmake
* fix cmake; add proper guard for atomic
* WIP: bcast
* WIP
* bcast kernels
* update to new minigun pass-by-value practice
* broadcasting dim
* add copy src and copy edge
* fix linking
* fix none array problem
* fix copy edge
* add device_type and device_id to backend operator
* cache csr adj, remove cache for adjmat and incmat
* custom ops in backend and pytorch impl
* change dgl-mg kernel python interface
* add id_mapping var
* clean up plus v2e spmv schedule
* spmv schedule & clean up fall back
* symbolic message and reduce func, remove bundle func
* new executors
* new backend interface for dgl kernels and pytorch impl
* minor fix
* fix
* fix docstring, comments, func names
* nodeflow
* fix message id mapping and bugs...
* pytorch test case & fix
* backward binary reduce
* fix bug
* WIP: cusparse
* change to int32 csr for cusparse workaround
* disable cusparse
* change back to int64
* broadcasting backward
* cusparse; WIP: add rev_csr
* unit test for kernels
* pytorch backward with dgl kernel
* edge softmax
* fix backward
* improve softmax
* cache edge on device
* cache mappings on device
* fix partial forward code
* cusparse done
* copy_src_sum with cusparse
* rm id getter
* reduce grad for broadcast
* copy edge reduce backward
* kernel unit test for broadcasting
* full kernel unit test
* add cpu kernels
* edge softmax unit test
* missing ref
* fix compile and small bugs
* fix bug in bcast
* Add backward both
* fix torch utests
* expose infershape
* create out tensor in python
* fix c++ lint
* [Kernel] Add GPU utest and kernel utest (#524 )
* fix gpu utest
* cuda utest runnable
* temp disable test nodeflow; unified test for kernel
* cuda test kernel done
* [Kernel] Update kernel branch (#550 )
* [Model] add multiprocessing training with sampling. (#484 )
* reorganize sampling code.
* add multi-process training.
* speed up gcn_cv
* fix graphsage_cv.
* add new API in graph store.
* update barrier impl.
* support both local and distributed training.
* fix multiprocess train.
* fix.
* fix barrier.
* add script for loading data.
* multiprocessing sampling.
* accel training.
* replace pull with spmv for speedup.
* nodeflow copy from parent with context.
* enable GPU.
* fix a bug in graph store.
* enable multi-GPU training.
* fix lint.
* add comments.
* rename to run_store_server.py
* fix gcn_cv.
* fix a minor bug in sampler.
* handle error better in graph store.
* improve graphsage_cv for distributed mode.
* update README.
* fix.
* update.
* [Tutorial] add sampling tutorial. (#522 )
* add sampling tutorial.
* add readme
* update author list.
* fix indent in the code.
* rename the file.
* update tutorial.
* fix the last API.
* update image.
* [BUGFIX] fix the problems in the sampling tutorial. (#523 )
* add index.
* update.
* update tutorial.
* fix gpu utest
* cuda utest runnable
* temp disable test nodeflow; unified test for kernel
* cuda test kernel done
* Fixing typo in JTNN after interface change (#536 )
* [BugFix] Fix getting src and dst id of ALL edges in NodeFlow.apply_block (#515 )
* [Bug Fix] Fix inplace op at backend (#546 )
* Fix inplace operation
* fix line seprator
* [Feature] Add batch and unbatch for immutable graph (#539 )
* Add batch and unbatch for immutable graph
* fix line seprator
* fix lintr
* remove unnecessary include
* fix code review
* [BUGFix] Improve multi-processing training (#526 )
* fix.
* add comment.
* remove.
* temp fix.
* initialize for shared memory.
* fix graphsage.
* fix gcn.
* add more unit tests.
* add more tests.
* avoid creating shared-memory exclusively.
* redefine remote initializer.
* improve initializer.
* fix unit test.
* fix lint.
* fix lint.
* initialize data in the graph store server properly.
* fix test.
* fix test.
* fix test.
* small fix.
* add comments.
* cleanup server.
* test graph store with a random port.
* print.
* print to stderr.
* test1
* test2
* remove comment.
* adjust the initializer signature.
* [API] update graph store API. (#549 )
* add init_ndata and init_edata in DGLGraph.
* adjust SharedMemoryGraph API.
* print warning.
* fix comment.
* update example
* fix.
* fix examples.
* add unit tests.
* add comments.
* [Refactor] Immutable graph index (#543 )
* WIP
* header
* WIP .cc
* WIP
* transpose
* wip
* immutable graph .h and .cc
* WIP: nodeflow.cc
* compile
* remove all tmp dl managed ctx; they caused refcount issue
* one simple test
* WIP: testing
* test_graph
* fix graph index
* fix bug in sampler; pass pytorch utest
* WIP on mxnet
* fix lint
* fix mxnet unittest w/ unfortunate workaround
* fix msvc
* fix lint
* SliceRows and test_nodeflow
* resolve reviews
* resolve reviews
* try fix win ci
* try fix win ci
* poke win ci again
* poke
* lazy multigraph flag; stackoverflow error
* revert node subgraph test
* lazy object
* try fix win build
* try fix win build
* poke ci
* fix build script
* fix compile
* add a todo
* fix reviews
* fix compile
* [Kernel] Update kernel branch (#576 )
* [Model] add multiprocessing training with sampling. (#484 )
* reorganize sampling code.
* add multi-process training.
* speed up gcn_cv
* fix graphsage_cv.
* add new API in graph store.
* update barrier impl.
* support both local and distributed training.
* fix multiprocess train.
* fix.
* fix barrier.
* add script for loading data.
* multiprocessing sampling.
* accel training.
* replace pull with spmv for speedup.
* nodeflow copy from parent with context.
* enable GPU.
* fix a bug in graph store.
* enable multi-GPU training.
* fix lint.
* add comments.
* rename to run_store_server.py
* fix gcn_cv.
* fix a minor bug in sampler.
* handle error better in graph store.
* improve graphsage_cv for distributed mode.
* update README.
* fix.
* update.
* [Tutorial] add sampling tutorial. (#522 )
* add sampling tutorial.
* add readme
* update author list.
* fix indent in the code.
* rename the file.
* update tutorial.
* fix the last API.
* update image.
* [BUGFIX] fix the problems in the sampling tutorial. (#523 )
* add index.
* update.
* update tutorial.
* fix gpu utest
* cuda utest runnable
* temp disable test nodeflow; unified test for kernel
* cuda test kernel done
* Fixing typo in JTNN after interface change (#536 )
* [BugFix] Fix getting src and dst id of ALL edges in NodeFlow.apply_block (#515 )
* [Bug Fix] Fix inplace op at backend (#546 )
* Fix inplace operation
* fix line seprator
* [Feature] Add batch and unbatch for immutable graph (#539 )
* Add batch and unbatch for immutable graph
* fix line seprator
* fix lintr
* remove unnecessary include
* fix code review
* [BUGFix] Improve multi-processing training (#526 )
* fix.
* add comment.
* remove.
* temp fix.
* initialize for shared memory.
* fix graphsage.
* fix gcn.
* add more unit tests.
* add more tests.
* avoid creating shared-memory exclusively.
* redefine remote initializer.
* improve initializer.
* fix unit test.
* fix lint.
* fix lint.
* initialize data in the graph store server properly.
* fix test.
* fix test.
* fix test.
* small fix.
* add comments.
* cleanup server.
* test graph store with a random port.
* print.
* print to stderr.
* test1
* test2
* remove comment.
* adjust the initializer signature.
* [API] update graph store API. (#549 )
* add init_ndata and init_edata in DGLGraph.
* adjust SharedMemoryGraph API.
* print warning.
* fix comment.
* update example
* fix.
* fix examples.
* add unit tests.
* add comments.
* [Refactor] Immutable graph index (#543 )
* WIP
* header
* WIP .cc
* WIP
* transpose
* wip
* immutable graph .h and .cc
* WIP: nodeflow.cc
* compile
* remove all tmp dl managed ctx; they caused refcount issue
* one simple test
* WIP: testing
* test_graph
* fix graph index
* fix bug in sampler; pass pytorch utest
* WIP on mxnet
* fix lint
* fix mxnet unittest w/ unfortunate workaround
* fix msvc
* fix lint
* SliceRows and test_nodeflow
* resolve reviews
* resolve reviews
* try fix win ci
* try fix win ci
* poke win ci again
* poke
* lazy multigraph flag; stackoverflow error
* revert node subgraph test
* lazy object
* try fix win build
* try fix win build
* poke ci
* fix build script
* fix compile
* add a todo
* fix reviews
* fix compile
* all demo use python-3 (#555 )
* [DEMO] Reproduce numbers of distributed training in AMLC giant graph paper (#556 )
* update
* update
* update
* update num_hops
* fix bug
* update
* report numbers of distributed training in AMLC giant graph paper
* [DEMO] Remove duplicate code for sampling (#557 )
* update
* update
* re-use single-machine code
* update
* use relative path
* update
* update
* update
* add __init__.py
* add __init__.py
* import sys, os
* fix typo
* update
* [Perf] Improve performance of graph store. (#554 )
* fix.
* use inplace.
* move to shared memory graph store.
* fix.
* add more unit tests.
* fix.
* fix test.
* fix test.
* disable test.
* fix.
* [BUGIFX] fix a bug in edge_ids (#560 )
* add test.
* fix compute.
* fix test.
* turn on test.
* fix a bug.
* add test.
* fix.
* disable test.
* [DEMO] Add Pytorch demo for distributed sampler (#562 )
* update
* update
* update
* add sender
* update
* remove duplicate cpde
* [Test] Add gtest to project (#547 )
* add gtest module
* add gtest
* fix
* Update CMakeLists.txt
* Update README.md
* [Perf] lazily create msg_index. (#563 )
* lazily create msg_index.
* update test.
* [BUGFIX] fix bugs for running GCN on giant graphs. (#561 )
* load mxnet csr.
* enable load large csr.
* fix
* fix.
* fix int overflow.
* fix test.
* [BugFix] Fix error when bfs_level = 0 in Entity Classification with RGCN (#559 )
* [DEMO] Update demo of distributed sampler (#564 )
* update
* update
* update demo
* add network cpp test (#565 )
* Add unittest for C++ RPC (#566 )
* [CI] Fix CI for cpp test (#570 )
* fix CI for cpp test
* update port number
* [Docker] update docker image (#575 )
* update docker image
* specify lint version
* rm torch import from unified tests
* [Kernel][Scheduler][MXNet] Scheduler for DGL kernels and MXNet backend support (#541 )
* [Model] add multiprocessing training with sampling. (#484 )
* reorganize sampling code.
* add multi-process training.
* speed up gcn_cv
* fix graphsage_cv.
* add new API in graph store.
* update barrier impl.
* support both local and distributed training.
* fix multiprocess train.
* fix.
* fix barrier.
* add script for loading data.
* multiprocessing sampling.
* accel training.
* replace pull with spmv for speedup.
* nodeflow copy from parent with context.
* enable GPU.
* fix a bug in graph store.
* enable multi-GPU training.
* fix lint.
* add comments.
* rename to run_store_server.py
* fix gcn_cv.
* fix a minor bug in sampler.
* handle error better in graph store.
* improve graphsage_cv for distributed mode.
* update README.
* fix.
* update.
* [Tutorial] add sampling tutorial. (#522 )
* add sampling tutorial.
* add readme
* update author list.
* fix indent in the code.
* rename the file.
* update tutorial.
* fix the last API.
* update image.
* [BUGFIX] fix the problems in the sampling tutorial. (#523 )
* add index.
* update.
* update tutorial.
* fix gpu utest
* cuda utest runnable
* temp disable test nodeflow; unified test for kernel
* cuda test kernel done
* edge softmax module
* WIP
* Fixing typo in JTNN after interface change (#536 )
* mxnet backend support
* improve reduce grad
* add max to unittest backend
* fix kernel unittest
* [BugFix] Fix getting src and dst id of ALL edges in NodeFlow.apply_block (#515 )
* lint
* lint
* win build
* [Bug Fix] Fix inplace op at backend (#546 )
* Fix inplace operation
* fix line seprator
* [Feature] Add batch and unbatch for immutable graph (#539 )
* Add batch and unbatch for immutable graph
* fix line seprator
* fix lintr
* remove unnecessary include
* fix code review
* [BUGFix] Improve multi-processing training (#526 )
* fix.
* add comment.
* remove.
* temp fix.
* initialize for shared memory.
* fix graphsage.
* fix gcn.
* add more unit tests.
* add more tests.
* avoid creating shared-memory exclusively.
* redefine remote initializer.
* improve initializer.
* fix unit test.
* fix lint.
* fix lint.
* initialize data in the graph store server properly.
* fix test.
* fix test.
* fix test.
* small fix.
* add comments.
* cleanup server.
* test graph store with a random port.
* print.
* print to stderr.
* test1
* test2
* remove comment.
* adjust the initializer signature.
* try
* fix
* fix
* fix
* fix
* fix
* try
* test
* test
* test
* try
* try
* try
* test
* fix
* try gen_target
* fix gen_target
* fix msvc var_args expand issue
* fix
* [API] update graph store API. (#549 )
* add init_ndata and init_edata in DGLGraph.
* adjust SharedMemoryGraph API.
* print warning.
* fix comment.
* update example
* fix.
* fix examples.
* add unit tests.
* add comments.
* [Refactor] Immutable graph index (#543 )
* WIP
* header
* WIP .cc
* WIP
* transpose
* wip
* immutable graph .h and .cc
* WIP: nodeflow.cc
* compile
* remove all tmp dl managed ctx; they caused refcount issue
* one simple test
* WIP: testing
* test_graph
* fix graph index
* fix bug in sampler; pass pytorch utest
* WIP on mxnet
* fix lint
* fix mxnet unittest w/ unfortunate workaround
* fix msvc
* fix lint
* SliceRows and test_nodeflow
* resolve reviews
* resolve reviews
* try fix win ci
* try fix win ci
* poke win ci again
* poke
* lazy multigraph flag; stackoverflow error
* revert node subgraph test
* lazy object
* try fix win build
* try fix win build
* poke ci
* fix build script
* fix compile
* add a todo
* fix reviews
* fix compile
* WIP
* WIP
* all demo use python-3 (#555 )
* ToImmutable and CopyTo
* [DEMO] Reproduce numbers of distributed training in AMLC giant graph paper (#556 )
* update
* update
* update
* update num_hops
* fix bug
* update
* report numbers of distributed training in AMLC giant graph paper
* [DEMO] Remove duplicate code for sampling (#557 )
* update
* update
* re-use single-machine code
* update
* use relative path
* update
* update
* update
* add __init__.py
* add __init__.py
* import sys, os
* fix typo
* update
* [Perf] Improve performance of graph store. (#554 )
* fix.
* use inplace.
* move to shared memory graph store.
* fix.
* add more unit tests.
* fix.
* fix test.
* fix test.
* disable test.
* fix.
* [BUGIFX] fix a bug in edge_ids (#560 )
* add test.
* fix compute.
* fix test.
* turn on test.
* fix a bug.
* add test.
* fix.
* disable test.
* DGLRetValue DGLContext conversion
* [DEMO] Add Pytorch demo for distributed sampler (#562 )
* update
* update
* update
* add sender
* update
* remove duplicate cpde
* [Test] Add gtest to project (#547 )
* add gtest module
* add gtest
* fix
* Update CMakeLists.txt
* Update README.md
* Add support to convert immutable graph to 32 bits
* [Perf] lazily create msg_index. (#563 )
* lazily create msg_index.
* update test.
* fix binary reduce following new minigun template
* enable both int64 and int32 kernels
* [BUGFIX] fix bugs for running GCN on giant graphs. (#561 )
* load mxnet csr.
* enable load large csr.
* fix
* fix.
* fix int overflow.
* fix test.
* new kernel interface done for CPU
* docstring
* rename & docstring
* copy reduce and backward
* [BugFix] Fix error when bfs_level = 0 in Entity Classification with RGCN (#559 )
* [DEMO] Update demo of distributed sampler (#564 )
* update
* update
* update demo
* adapt cuda kernels to the new interface
* add network cpp test (#565 )
* fix bug
* Add unittest for C++ RPC (#566 )
* [CI] Fix CI for cpp test (#570 )
* fix CI for cpp test
* update port number
* [Docker] update docker image (#575 )
* update docker image
* specify lint version
* rm torch import from unified tests
* remove pytorch-specific test_function
* fix unittest
* fix
* fix unittest backend bug in converting tensor to numpy array
* fix
* mxnet version
* [BUGFIX] fix for MXNet 1.5. (#552 )
* remove clone.
* turn on numpy compatible.
* Revert "remove clone."
This reverts commit 17bbf76ed72ff178df6b3f35addc428048672457.
* revert format changes
* fix mxnet api name
* revert mistakes in previous revert
* roll back CI to 20190523 build
* fix unittest
* disable test_shared_mem_store.py for now
* remove mxnet/test_specialization.py
* sync win64 test script
* fix lowercase
* missing backend in gpu unit test
* transpose to get forward graph
* pass update all
* add sanity check
* passing test_specialization.py
* fix and pass test_function
* fix check
* fix pytorch softmax
* mxnet kernels
* c++ lint
* pylint
* try
* win build
* fix
* win
* ci enable gpu build
* init submodule recursively
* backend docstring
* try
* test win dev
* doc string
* disable pytorch test_nn
* try to fix windows issue
* bug fixed, revert changes
* [Test] fix CI. (#586 )
* disable unit test in mxnet tutorial.
* retry socket connection.
* roll back to set_np_compat
* try to fix multi-processing test hangs when it fails.
* fix test.
* fix.
* doc string
* doc string and clean up
* missing field in ctypes
* fix node flow schedule and unit test
* rename
* pylint
* copy from parent default context
* fix unit test script
* fix
* demo bug in nodeflow gpu test
* [Kernel][Bugfix] fix nodeflow bug (#604 )
* fix nodeflow bug
* remove debug code
* add build gtest option
* fix cmake; fix graph index bug in spmv.py
* remove clone
* fix div rhs grad bug
* [Kernel] Support full builtin method, edge softmax and unit tests (#605 )
* add full builtin support
* unit test
* unit test backend
* edge softmax
* apply edge with builtin
* fix kernel unit test
* disable mxnet test_shared_mem_store
* gen builtin reduce
* enable mxnet gpu unittest
* revert some changes
* docstring
* add note for the hack
* [Kernel][Unittest][CI] Fix MXNet GPU CI (#607 )
* update docker image for MXNet GPU CI
* force all dgl graph input and output on CPU
* fix gpu unittest
* speedup compilation
* add some comments
* lint
* add more comments
* fix as requested
* add some comments
* comment
* lint
* lint
* update pylint
* fix as requested
* lint
* lint
* lint
* docstrings of python DGL kernel entries
* disable lint warnings on arguments in kernel.py
* fix docstring in scheduler
* fix some bug in unittest; try again
* Revert "Merge branch 'kernel' of github.com:zzhang-cn/dgl into kernel"
This reverts commit 1d2299e68b004182ea6130b088de1f1122b18a49, reversing
changes made to ddc97fbf1bec2b7815c0da7c74f7ecb2f428889b.
* Revert "fix some bug in unittest; try again"
This reverts commit ddc97fbf1bec2b7815c0da7c74f7ecb2f428889b.
* more comprehensive kernel test
* remove shape check in test_specialization
2019-06-06 15:47:55 -04:00
33b9c38389
[Bugfix] fix bug in pickling ( #456 )
...
* fix bug in pickling
* fix lint
2019-03-18 23:48:20 -04:00
565f0c88fc
[WIP] [NN] Refactor NN package ( #406 )
...
* refactor graph conv
* docs & tests
* fix lint
* fix lint
* fix lint
* fix lint script
* fix lint
* Update
* Style fix
* Fix style
* Fix style
* Fix gpu case
* Fix for gpu case
* Hotfix edgesoftmax docs
* Handle repeated features
* Add docstring
* Set default arguments
* Remove dropout from nn.conv
* Fix
* add util fn for renaming
* revert gcn_spmv.py
* mx folder
* fix wierd bug
* fix mx
* fix lint
2019-02-25 18:41:21 -05:00
e19cd62ecd
[Test] Unify tests for different backends ( #333 )
...
* test basics
* batched graph & filter, mxnet filter fix
* frame and function; bugfix
* test graph adj and inc matrices
* fixing start = 0 for mxnet
* test index
* inplace update & line graph
* multi send recv
* more tests
* oops
* more tests
* removing old test files; readonly graphs for mxnet still kept
* modifying test scripts
* adding a placeholder for pytorch to reserve directory
* torch 0.4.1 compat fixes
* moving backend out of compute to avoid nose detection
* tests guide
* mx sparse-to-dense/sparse-to-numpy is buggy
* oops
* contribution guide for unit tests
* printing incmat
* printing dlpack
* small push
* typo
* fixing duplicate entries that causes undefined behavior
* move equal comparison to backend
2019-01-05 23:32:33 -05:00
24bbdb745e
[Feature] Reversed Graph and Transform Module ( #331 )
...
* reverse a graph
* Reverse a graph
* Fix
* Revert "Fix"
This reverts commit 1728826b4f3a083b76dfc0fdecd2bbf943a971b2.
* Fix
* Fix
* Delete vcs.xml
* Delete Project_Default.xml
* Fix
* Fix
* Fix
* Remove outdated test
* Reorg transform and update reverse (#2 )
* Reorg transform and update reverse
* Fix doc and test
* Update test
* Resolve conflict
* CI oriented fix
* Remove outdated import
* Fix import
* Fix import
* define __all__ for wildcard imports
* Fix import
* Address circular imports
* Fix
* Fix test case
* Fix
* Fix
* Remove unused import
* Fix
* Fix
* Fix
2019-01-04 13:51:19 -05:00
4bd4d6e348
[Lint] Pylint ( #330 )
...
* fix lint for graph_index.py
* pylint for base.py
* pylint for batched_graph.py
* pylint for frame.py; simplify and fix bugs in frame when index is slice type
* pylint for graph.py
* pylint for immutable_graph_index.py
* pylint for init.py
* pylint for rest files in root package
* pylint for _ffi package
* pylint for function package
* pylint for runtime package
* pylint for runtime.ir package
* add pylint to ci
* fix mx tests
* fix lint errors
* fix ci
* fix as requested
* fix lint
2019-01-01 15:15:41 -05:00
2664ed2dff
[Bugfix] Fix multiple send recv ( #320 )
...
* fix bug: frame append should check itself
* more test case
* fix multi-send-recv bug
* remv msg graph and clean up
* test cases
* more test case
* fix for batchedgraph
* fix bugs: converting from a graph with edges
* fix
* add more operators to utils.Index
* clear frame executor
* change message indicator to a graph level index
* fix test cases
* guard the case that mxnet does not support concat zero shape tensor
* fix bug: avoid convert full slice to numpy
* test multi-send-recv after conversion
* fix as request (partially)
* add dtype, ctx to full_1d
* add slice data to utils.Index
* fix
* more doc string
* fix as requested
2018-12-23 21:35:49 -05:00
75e2af7993
[CI] Jenkins on Windows builds ( #324 )
...
* Jenkins build & test on Windows
* oops
* still running nohup on Windows slaves
* ooops again
* squishing vcvars and cmake
* another try
* reverting back
* --user
* switching to msbuild
* made the graph size in cache testing bigger
* put commands into script files
* oooops
2018-12-22 00:39:29 -05:00
f35ac5443e
[Graph][Model] Cache adj & inc; MX GCN ( #307 )
...
* add cache to adj and incmat
* Fix bug in cached adj/inc
* mx gcn spmv runnable; acc debugging...
* fix bug in mx gcn that loss is not correctly calculated
* fix mx utest
* fix as requested
* use raw parameter tensors rather than dense layer
* fix dropout
* Add numbers in readme
2018-12-16 22:51:01 -05:00
e2926544b6
[Graph] Better string repr ( #311 )
2018-12-16 12:23:49 -05:00
597ac7f8b5
[Release] v0.1.3 ( #288 )
...
* 0.1.2 release
* oops
* more fixes on windows
* [Bugfix] fix download dir (#275 )
* fix download dir
* add doc for the env var
* windows 7 -> 10
* doc update
* [Bugfix] Fix conversion from networkx (#286 )
* fix from_nx when no edge id available
* add test cases
* more detailed tests
* more comments
* [Bugfix] Switch to sparse_coo_matrix for torch 1.0+ (#282 )
* switch to sparse_coo_matrix for torch 1.0+
* fix bug when the version is 0.4.1.post2
* change to distutils
2018-12-11 01:30:47 -05:00
2194b7dfa6
[Bugfix] edge order is not preserved when converting from edge list ( #262 )
2018-12-05 17:41:26 -05:00
21255b6528
[Bugfix] tolist and dependencies in dgl.data ( #239 )
...
* change Index.tolist -> Index.tonumpy; fix bug in traversal; remove dependencies in data
* fix import
* fix __all__ and some docstring
2018-12-05 12:20:59 -05:00
455ea48570
[Bugfix] Conversion between networkx and DGLGraph ( #244 )
...
* copy feature to networkx
* fix to_network for multi-graph
* test case for nx conversion
* iterate over Index returns plain int instead of numpy.int64
* fix from_network multi-edge bug
2018-12-04 16:19:11 -05:00
52ed09a392
[Bug] Fix inplace update ( #221 )
...
* inplace write row op and executor
* update scheduler and graph to use inplace write
* fix
* fix bug
* test case for inplace
* fix bugs for inplace apply node/edge
* fix comments
* th.allclose -> U.allclose
2018-12-02 19:14:39 -05:00
524e656dd6
[Bugfix] enable SPMV for multi-dimension node feature ( #178 )
...
* Support multi-dimension node feature in SPMV
* fix as requested
2018-11-26 11:12:28 -05:00
b1eeb93449
[Bugfix][Runtime] Zero degree behaviors ( #177 )
...
* fix recv nodes are all 0deg; fix hybriddict does not through keyerror properly
* fallback to apply_nodes when all nodes are 0deg; WIP on pull spmv 0deg
* new 0deg behavior
* new 0deg behavior
* update mx utest for pull-0deg
* fix mx
* fix mx
* get rid of unnecessary sort-n-unique
2018-11-25 22:33:08 -05:00
4dfe7547e8
Fix num_rows bug in batched_graph ( #169 )
2018-11-23 02:49:59 +08:00
23e2e83b5e
[API] change the signature of node/edge filter ( #166 )
...
* change the signature of node/edge filter
* upd filter
2018-11-22 13:00:36 -05:00
deb653f8dc
[Runtime] Scheduler and Executor ( #140 )
...
* executor api
* draft executor interface
* WIP
* revert changes to avoid conflict with api change
* core scheduling logic
* WIP: build graph adj
* incidence matrix for in edges
* support incidence matrix for partial recv nodes
* improve
* build adjmat in scheduler
* graph store
* get degree bucketing schedule
* connect to c++ degree bucketing
* conceptual executor creation code
* executor comments
* fix
* more executor comments
* WIP: full send_and_recv schedule
* most schedulers
* simplify scheduler
* executors
* runtime
* builtin function base class
* adj indices and shape
* completely refactor scheduler
* rename and move bundled out to function.py
* use_edge_feature in msg func
* rewrite scheduler
* node edge executor
* connect with graph api
* handle zero degree
* misc
* fix test cases
* fix a good many bugs...
* remove old scheduler
* push and pull
* fix send recv
* c++ lint
* fix batched send recv
* hot fix for mxnet
* typo
* write back executor
* apply node edge
* clean up, doc string
* fix as requested
* refactor
* fix
* WIP
* WIP
* ir draft
* more on ir
* WIP: spmv schedule
* WIP
* recv schedule
* refactor
* WIP
* snr degree bucketing
* snr scheduler
* move prog to graph.py; rename
* unittest for send/recv
* remove some legacy codes
* WIP: update_all
* pass test_basics
* passed all current utests
* more utests; fix mx utest
* WIP: fixing zero deg initial value
* some tests
* fix 0deg problem
* fix mx
* fix mx
* some notes
* fix as requested
2018-11-22 12:15:50 -05:00
0ec1a492b3
[Frame] change num rows behavior ( #163 )
...
* move initializer to column scheme; change num rows behavior
* poke mx ci
* fix mx utest in append
* fix bug in add edges
* utest for updating partial rows
* fix bug in from_networkx and from_scipy_matrix
* revert per-col initializer change
* fix pickle utest
2018-11-21 11:50:46 -05:00
e515f5311b
[Frame] supporting partial row on first column and individual column initializers ( #160 )
...
addresses issue #156
2018-11-19 18:18:36 -05:00
79a510252b
Pickling support ( #155 )
...
* pickling support
* resorting to suggested way of pickling
* custom attribute pickling check
* working around a weird pytorch pickling bug
* including partial frame case
* pickling everything now
* fix as requested
2018-11-16 17:19:20 -05:00
05f464f824
[Bugfix] fix args with incontiguous node and edge tensor ( #153 )
2018-11-15 10:55:15 -05:00
048f6d7a30
[GraphIndex] refactor graph caching ( #150 )
...
* refactor graph caching
* fix mx test
* fix typo
2018-11-13 22:12:38 -05:00
a95459e3a2
[CI] Improved CI ( #141 )
...
* change ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* update ci
* nx package
* update ci
* update ci
* update ci
* fix
* mx dockerfile by zhengda
* python3.6->3.5
* update ci image
* add tutorial test
* fix ci
* fix ssl problem
* minor change
* small fix on traversal utest
* fix syntax
* add matplotlib in image
* fix
* update ci
* update ci
2018-11-12 01:06:05 -05:00
7cbb83db9f
better bfs edge test ( #142 )
2018-11-11 23:09:39 -05:00
d6c80e0cf7
[API] bfs with edges ( #132 )
...
* bfs with edges
* dfs toy test case
* clean up
* style fix
* bugfix
* updating docs for bfs_edges and readouts
2018-11-11 17:19:55 -05:00
66676a548d
[Bugfix] Fix bug in bfs and topo ( #135 )
...
* Fix bug in bfs and topo
* remove legacy codes
2018-11-10 20:34:17 -05:00
Zihao Ye