d706298019
fix a bug. ( #646 )
2019-06-11 16:23:48 -07:00
fb9dcc51ff
[Feature] Add API to convert graph to bidirected graph ( #598 )
...
* to_bidirected
* to_bidirected
* Fix style
* Fix
* Update
* Fix
* Fix
* Update
* Add examples
2019-06-10 14:02:29 +08:00
fc7775a20f
Define node/edge Ids in NodeFlow more clearly ( #628 )
...
* add tests.
* distinguish layer-local nid and nodeflow nid.
* use numpy assert_array_equal and assert_allclose
* fix map_from_parent_nid
* fix test
* fix test.
* renmae remap.
* update doc.
* update doc.
* update doc.
* fix test.
* fix test.
2019-06-09 12:10:07 -07:00
dec8b49b5d
[Examples] Run all the examples ( #623 )
...
* all pytorch examples
* scan through mxnet examples
* change reddit data
* tweak numerical range for unittest
* fix ci
* fix ci
* fix
* add seed to workaround
2019-06-09 00:26:13 -04:00
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
993fd3f94b
[Enhancement] Add DGLGraph.to for PyTorch and MXNet backend ( #600 )
...
* add graph_to
* use backend copy_to
* add test
* fix test
* framework agnostic to() test
* disable pylint complaint
* add examples
* fix docstring
* formatting
* Format
* Update test_to_device.py
2019-06-08 16:21:29 +08:00
baa16231f3
[Feature] Remove nodes/edges. ( #599 )
...
* upd
* upd
* reformat
* upd
* upd
* add test
* fix arange
* fix slight bug
* upd
* trigger
* upd docs
* upd
* upd
* upd
* change subgraph to be raw data wrapper
* upd
* fix test
2019-06-08 13:44:36 +08:00
e7389d7c20
[BUGFIX] fix the order of the seed nodes in NodeFlow ( #626 )
...
* fix.
* add comments.
2019-06-07 18:18:51 -07:00
7ad0485ace
[BUGFIX] handle more negative layer id and block id. ( #606 )
...
* handle negative layer id and block id.
* add tests.
* fix.
* fix.
2019-06-07 15:04:38 -07:00
5ea7a2509e
Fix random BFS traversal failures ( #621 )
...
Essentially a redo of PR #612 which is erased by git merge somehow.
2019-06-08 00:16:29 +08:00
5da57663cc
[BUGFIX] fix sampler. ( #616 )
...
* fix sampler.
* update doc.
* fix.
2019-06-06 20:47:59 -07:00
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
da0c92a228
[BUGFix][Test] fix random bfs failure ( #612 )
2019-06-06 13:24:18 -04:00
21ff161db6
fix occasional assertion fail ( #611 )
2019-06-06 18:23:49 +08:00
84702916d3
[BugFix] Some negative layer_id/block_id are not converted to the actual one. ( #584 )
...
* [BugFix] Some negative layer_id/block_id are not converted to the actual one.
* Add some tests for negatives block/layer ids
2019-06-04 12:19:43 -07:00
01a4cc5b7b
[Graph] Add API to convert graph to simple graph ( #587 )
...
* to simple
* WIP: multigraph flag
* graph index refactor; pass basic testing
* graph index refactor; pass basic testing
* fix bug in to_simple; pass torch test
* fix mx utest
* fix example
* fix lint
* fix ci
* poke ci
* poke ci
* WIP
* poke ci
* poke ci
* poke ci
* change ci workspace
* poke ci
* poke ci
* poke ci
* poke ci
* delete ci
* use enum for multigraph flag
2019-06-01 23:32:46 -04:00
c64405b1f6
[Docker] update docker image ( #575 )
...
* update docker image
* specify lint version
* rm torch import from unified tests
2019-05-27 17:04:46 -04:00
8f378d90ad
[BUGFIX] fix bugs for running GCN on giant graphs. ( #561 )
...
* load mxnet csr.
* enable load large csr.
* fix
* fix.
* fix int overflow.
* fix test.
2019-05-25 11:09:33 -07:00
14af8402f0
[Perf] lazily create msg_index. ( #563 )
...
* lazily create msg_index.
* update test.
2019-05-24 13:41:03 -07:00
ce27ebbbd0
[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.
2019-05-23 15:25:38 -07:00
605b51857e
[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
2019-05-21 14:28:06 -04:00
b2b8be25bb
[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.
2019-05-21 03:27:05 -07:00
4b761571b2
[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
2019-05-20 11:08:43 -04:00
d533e9ba62
[BugFix] Fix getting src and dst id of ALL edges in NodeFlow.apply_block ( #515 )
2019-05-16 18:08:43 -07:00
fe7d5e9b8b
[Sampler] Change Distributed Sampler API ( #499 )
...
* Change Distributed Sampler API
* fix lint
* fix lint
* update demo
* update
* update
* update
* update demo
* update demo
2019-04-22 09:41:47 +08:00
b89dcce16c
[RPC] Refactoring networking APIs ( #496 )
...
* Refactoring network API
* update demo
* update
* update demo
* update demo
* add num_sender
* update
* fix lint
* fix lint
* fix lint
* update
2019-04-16 16:33:29 +08:00
bfdd1eaa44
[Feature] Create shared memory graph store. ( #468 )
...
* accelerate gcn_ns.
* add timing.
* run infer with whole graph.
* distributed gcn_ns.
* reconstruct gcn_ns.
* minor fix.
* change graphsage_cv for numa.
* fix #OMP threads.
* accelerate graphsage_cv.
* fix a weird bug.
* add profiler in graphsage_cv.
* accelerate graphsage_cv.
manually aggregate neighbors' embeddings with pull.
* load csr directly in gcn_ns_sc.
* parallel sort for graph index.
* Revert "parallel sort for graph index."
This reverts commit 86fe2c7117fe5e56b0d481b39849c258b166945b.
* run gcn_ns_sc on GPUs.
* acc gcn_cv_sc.
* change gcn_cv for numa.
* fix gcn_cv to use numa and gpu.
* improve graphsage_cv to use numa and gpu.
* improve gcn_ns.
* improve graphsage_cv.
* init shared memory graph store.
* fix.
* enable init ndata.
* improve tests.
* add bidirectional communication.
* link to rt.
* fix compilation error.
* fix shared memory init.
* use MessageQueue for inter-process communication.
* reconstruct immutable graph csr.
* fix gcn.
* load csr to shared memory.
* fix minor bugs.
* add comments.
* refactor SharedMemory.
* fix bugs in ImmutableGraph.
* create CSR graph from shared memory.
* add more test for loading a csr graph.
* terminate graph store properly.
* allow initializing ndata in the graph store server.
* use RPC for inter-process communication.
* a script for loading a graph.
* allow customizing port.
* list all ndata and edata.
* support dtype.
* reorganize SharedMemoryGraphStore.
* fix ndata shape.
* reconstruct gcn_ns.
* print info.
* set omp in gcn_ns.
* reset sampling examples.
* fix lint.
* fix lint.
* reset gcn.
* disable shared memory in windows.
* fix.
* fix.
* reset changes.
* revert nodeflow changes.
* fix cmake.
* fix test.
* fix test.
* fix test.
* fix test.
* add comments.
* fix test.
* move vector out.
* fix lint.
* fix lint.
* move SharedMemory.
* update cmake.
* update comment.
* fix comments.
* Revert "update cmake."
This reverts commit 592445e37077f70a6e3f2e5245f9a3d086b04f3b.
* update cmake.
* add comments.
* rename.
* change the comment.
* fix a bug.
* rename.
* add comments.
* add comments.
* add init_edata.
* rewrite memory alloc.
* move vector to CSR.
* fix.
* init data.
* Revert "init data."
This reverts commit 2b217b9553911b7dd84a9f1d9b68430b5aa18e23.
* init data.
* init new columns correctly.
2019-04-08 12:09:02 -07:00
5d494c6207
[RPC] add C++ RPC infrastructure and distributed sampler ( #465 )
...
* add C++ rpc infrastructure and distributed sampler
* update
* update lint
* update lint
* update lint
* update
* update
* update
* updare
* update
* update
* update
* update serialize and unittest
* update serialize
* lint
* update
* update
* update
* update
* update
* update
* update unittest
* put Finalize() to __del__
* update unittest
* update
* delete buffer in Finalize
* update unittest
* update unittest
* update unittest
* update unittest
* update
* update
* fix small bug
* windows socket impl
* update API
* fix bug in serialize
* fix bug in serialzie
* set parent graph
* update
* update
* update
* update
* update
* update
* fix lint
* fix lint
* fix
* fix windows compilation error
* fix windows error
* change API to lower-case
* update test
* fix typo
* update
* add SamplerPool
* add SamplerPool
* update
* update test
* update
* update
* update
* update
* add example
* update
* update
2019-03-29 16:48:45 +08:00
6066fee935
[Model][Feature] PinSage & Random Walk with Restart ( #453 )
...
* random walk traces generation
* remove outdated comments
* oops put in the wrong place
* explicit inline
* moving rand_r to util
* pinsage-like model on movielens
* the code runs now
* support cuda
* using readonly graph
* moving random walk to public function
* per-thread seed and openmp support
* pinsage-like model on movielens
* the code runs now
* support cuda
* using readonly graph
* using C random walk
* removing profile decorators
* param initialization
* no grad
* leaky relu fixes everything
* train and save
* WIP
* WIP
* WIP
* seems to work
* evaluation output
* swapping order of val/test and train
* debug
* hyperparam tuning
* prior/training dataset split changes
* random walk reorg
* random walk with restart
* signed comparison fix
* migrating random walk to nodeflow
* Revert "migrating random walk to nodeflow"
This reverts commit f2565347cced7c912a58a529b257c033d9f375b7.
* add README and remove dataset
* new endpoint
* lint
* lint x2
* oops forgot test
* including bpr - better for baseline
* addressing fixes
* throwing random walks out from SamplerOp class
* forgot to move RandomWalk; why did this even work?
* removing legacy garbage
* add todo
* address comments
* stupid bug fix
* call ndarrayvector converter to handle traces
2019-03-29 13:01:18 +08:00
33b9c38389
[Bugfix] fix bug in pickling ( #456 )
...
* fix bug in pickling
* fix lint
2019-03-18 23:48:20 -04:00
eb1acecd0d
[BugFix] Handle case when calling send with builtin message function ( #449 )
...
* fix send with builtin bug
* test cases
* remove todo comment
2019-03-13 14:49:50 -04:00
d1d580ecc1
[feature & bugfix] adjacency_matrix_scipy, wrong order of edges in immutable graph. ( #437 )
...
* fix rgcn tutorial
* small fix
* upd
* findedge/s
* upd
* upd
* upd
* upd
* add test
* remove redundancy
* upd
* upd
* upd
* upd
* add edge_subgraph
* explicit cast
* add test immutable subg
* reformat
* reformat
* fix bug
* upd
* hotfix
* subgraph docs
* fix adj mat
* fix edges() order
* add test
* revert
* upd
* fix
* upd
2019-03-12 23:57:13 -04:00
8651be54c2
[Perf] Accelerate block_compute when all nodes are invoked. ( #434 )
...
* refactor.
* accelerate update_all in nodeflow.
* fix.
* refactor.
* fix lint.
* fix lint.
* reorganize.
* reorg.
* remove.
* add doc.
* impl block_incidence_matrix
* fix lint.
* fix.
* simple fix.
* fix test.
* fix interface.
* fix eid.
* fix comments.
2019-03-07 13:39:39 -08:00
ca2a7e1ca1
[Refactor] Nodeflow, sampling, CAPI ( #430 )
...
* enable cython
* add helper function and data structure for void_p vector return
* move sampler from graph index to contrib.sampling
* WIP
* WIP
* refactor layer sampling
* pass tests
* fix lint
* fix graphsage
* remove comments
* pickle test
* fix comments
* update dev guide for cython build
2019-03-05 14:07:22 -05:00
fb4246e564
[Feature]Uniform layer-wise sampler ( #416 )
...
* migrate to node-flow
* uniform layer sampler test cases
* more test cases
* documentations
* fix lint errors
* fix lint errors
* fix lint errors
* iota
* add asnumpy
* requested changes
* fix indptr error
* fix lint errors
* requested changes & fix lint errors
* fix lint errors
* fix LayerSampler unit test
2019-03-02 16:37:18 -08:00
bea07b41b3
[Sampler] fix the API of neighbor sampler. ( #407 )
...
* don't return aux_info.
* fix sampler test.
* fix sse.
* fix.
* add comment.
2019-02-28 13:45:21 -08:00
7e30382e4f
[Model][MXNet] neighbor sampling & skip connection & control variate & graphsage ( #322 )
...
* neighbor sampling draft
* val/test acc
* control variate draft
* control variate
* update
* fix new_history
* maintain aggregated history while updating new history
* preprocess the first layer, change push to pull
* update
* fix subg_degree
* nodeflow
* clear
* readme
* doc and unittest for self loop
* address comments
* rename
* update
* fix
* Update node_flow.py
* Update node_flow.py
2019-02-28 13:29:51 -08:00
724aa0caf0
[Feature] FindEdge/FindEdges for Immutable Graph ( #404 )
...
* fix rgcn tutorial
* small fix
* upd
* findedge/s
* upd
* upd
* upd
* upd
* add test
* remove redundancy
* upd
* upd
* upd
* upd
* add edge_subgraph
* explicit cast
* add test immutable subg
* reformat
* reformat
* fix bug
* upd
2019-02-27 15:32:32 +08:00
bfe3e9d64a
[Feature] Add switch readonly state interface ( #389 )
...
* fix rgcn tutorial
* small fix
* add switch readonly state interface
* remove trailing ws
* fix
* fix
* change signature
* change signature
* remove trailing ws
* upd
* upd interface
* upd
* rm trailing ws
* reformat
* trailing space
* upd
2019-02-20 18:51:56 -05:00
2e1cbd5d68
[Feature] Random walk traces generation ( #392 )
...
* random walk traces generation
* remove outdated comments
* oops put in the wrong place
* explicit inline
* moving rand_r to util
* moving random walk to public function
* per-thread seed and openmp support
* type cast styles
2019-02-20 10:41:59 -05:00
f370e628cd
[Feature] add NodeFlow API ( #361 )
...
* sample layer subgraphs.
* fix.
* fix.
* add layered subgraph.
* fix lint.
* fix.
* fix tutorial.
* fix.
* remove copy_to_parent.
* add num_layers
* move sampling code to sampler.cc
* fix.
* move subgraph construction out.
* Revert "move subgraph construction out."
This reverts commit 24b3d13b0d8ed5f91847ea75a7674ee8f7d45cff.
* change to NodeFlow.
* use NodeFlow in Python.
* use NodeFlowIndex.
* add node_mapping and edge_mapping.
* remove unnecessary code in SSE tutorial.
* Revert "remove unnecessary code in SSE tutorial."
This reverts commit 093f0413d5fa2e63ca5f80c46c80a126a9fb720c.
* fix tutorial.
* move to node_flow.
* update gcn cv updater.
* import NodeFlow.
* update.
* add demo code for vanilla control variate sampler.
* update.
* update.
* add neighbor sampling.
* return flow offsets.
* update node_flow.
* add test.
* fix sampler.
* fix graph index.
* fix a bug in sampler.
* fix map_to_layer_nid and map_to_flow_eid.
* fix apply_flow.
* remove model code.
* implement flow_compute.
* fix a bug.
* reverse the csr physically.
* add mini-batch test.
* add mini batch test.
* update flow_compute.
* add prop_flows
* run on specific nodes.
* test copy
* fix a bug in creating frame in NodeFlow.
* add init gcn_cv_updater.
* fix a minor bug.
* fix gcn_cv_updater.
* fix a bug.
* fix a bug in NodeFlow.
* use new h in gcn_cv_updater.
* add layer_in_degree and layer_out_degree.
* fix gcn_cv_updater for gpu.
* temp fix in NodeFlow for diff context.
* allow enabling/disabling copy back.
* add with-updater option.
* fix a bug in computing degree.
* add with-cv option.
* rename and add comments.
* fix lint complain.
* fix lint.
* avoid assert.
* remove assert.
* fix.
* fix.
* fix.
* fix.
* fix the methods in NodeFlow.
* fix lint.
* update SSE.
* remove gcn_cv_updater.
* correct comments for the schedulers.
* update comment.
* add map_to_nodeflow_nid
* address comment.
* remove duplicated test.
* fix int.
* fix comments.
* fix lint
* fix.
* replace subgraph with NodeFlow.
* move view.
* address comments.
* fix lint.
* fix lint.
* remove static_cast.
* fix docstring.
* fix comments.
* break SampleSubgraph.
* move neighbor sampling to sampler.cc
* fix comments.
* rename.
* split neighbor_list.
* address comments.
* fix.
* remove TODO.
2019-02-19 15:49:28 -08:00
220a1e68fb
[BUG] Fixing bug in pickling readonly graphs ( #397 )
...
* fixing bug in pickling readonly graphs
* multigraph test coverage
* fixing lint (??????)
* another lint
* is_readonly interface
2019-02-19 00:14:11 -05:00
5b9147c464
[Feature] Edge Group Apply API ( #358 )
...
* add rtfd
* rrr
* update
* change env
* temp fix
* update
* fix
* fix
* add
* conf
* Move file_pattern from Makefile to conf.py
* remove yml
* fix
* fix
* fix
* fix
* remove yml
* remove yml
* add doc docker
* add dgl install script
* change name
* change dockerfile
* fix
* name
* add
* fix
* fix
* fix
* fix
* fix docker
* delete sphinx.py for doc-build backend
* Add softmax to test backend
* Add group apply function and tests
* Delete unnecessary file
* Update comments and test
* Fix lint
* remove unused bucketing code
* group apply edge bucketing code
* gen degree bucket schedule for group apply edge
* schedule and graph code
* fix compiling
* fix
* fix lint
* naming
* harder test case
* fix comments
* more comments
* tweak function name
2019-02-03 11:14:52 -05:00
abf12fc757
[Data] Synthetic dataset for graph classificaiton ( #364 )
...
* minigc dataset
* more comments
* sphinx
2019-01-25 10:47:47 -05:00
929742b588
[Feature] Reimplement Immutable graph index in DGL ( #342 )
...
* init.
* it's compiled.
* add immutable graph constructor.
* add immutable graph API.
* fix.
* impl get adjacency matrix.
* fix.
* fix graph_index from scipy matrix.
* add neighbor sampling.
* remap vertex ids.
* fix.
* move sampler test.
* fix tests.
* add comments
* remove mxnet-specific immutable graph.
* fix.
* fix lint.
* fix.
* try to fix windows compile error.
* fix.
* fix.
* add test.
* unify Graph and ImmutableGraph.
* fix bugs.
* fix compile.
* move immutable graph.
* fix.
* remove print.
* fix lint.
* fix
* fix lint.
* fix lint.
* fix test.
* fix comments.
* merge GraphIndex and ImmutableGraphIndex.
* temp fix.
* impl GetAdj.
* fix lint
* fix.
* fix.
* fix.
* fix.
* fix.
* use csr only for readonly graph.
* Revert "use csr only for readonly graph."
This reverts commit 8e24bb033af8504531b22849de5b7567b168e0d5.
* remove code.
* fix.
* fix.
* fix.
* fix.
* fix.
* fix.
* address comments.
* fix for comments.
* fix comments.
* revert.
* move test_graph_index to compute.
* fix.
* fix.
* impl GetAdj for coo.
* fix.
* fix tests.
* address comments.
* address comments.
* fix comment.
* address comments.
* use lambda.
* other comments.
* address comments.
* modify the semantics of edges.
* fix order.
* use DGLIdIter
* fix.
* remove NotImplemented.
* revert some code.
2019-01-17 09:59:53 +08:00
3a868eb04b
[Feature] Max readout and consecutive labeling for networkx ( #341 )
...
* Max readout and consecutive labeling
* Delete test_readout.py
* Delete test_basics.py
* Test case and fix
* Recover accidentally removed file
* Fix import order
* Fix test case
* Fix
* Fix
* Fix
* Fix
* Fix
* revert
* Fix
* Fix
* Fix
2019-01-10 12:58:05 -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
Da Zheng