52d4535b61
[Hetero][RFC] Heterogeneous graph Python interfaces & Message Passing ( #752 )
...
* moving heterograph index to another file
* node view
* python interfaces
* heterograph init
* bug fixes
* docstring for readonly
* more docstring
* unit tests & lint
* oops
* oops x2
* removed node/edge addition
* addressed comments
* lint
* rw on frames with one node/edge type
* homograph with underlying heterograph demo
* view is not necessary
* bugfix
* replace
* scheduler, builtins not working yet
* moving bipartite.h to header
* moving back bipartite to bipartite.h
* oops
* asbits and copyto for bipartite
* tested update_all and send_and_recv
* lightweight node & edge type retrieval
* oops
* sorry
* removing obsolete code
* oops
* lint
* various bug fixes & more tests
* UDF tests
* multiple type number_of_nodes and number_of_edges
* docstring fixes
* more tests
* going for dict in initialization
* lint
* updated api as per discussions
* lint
* bug
* bugfix
* moving back bipartite impl to cc
* note on views
* fix
2019-08-23 15:45:37 -04:00
02029dce9b
Sync initializers ( #772 )
2019-08-17 20:25:54 +08:00
17b60e1af0
[Bugfix] EdgeBatch.edges call attempts tuple item assignment ( #747 )
...
* upd
* fig edgebatch edges
* add test
* trigger
2019-08-11 04:07:41 +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
86f28d6553
[Misc] Provide a "return 1s instead of edge IDs" option in scipy adjacency matrix ( #730 )
...
* return 1 option in scipy adjacency matrix
* lint
* use dgl warning
* i'm an idiot
* lint x2
* rename
2019-07-29 21:40:09 +08:00
67dc11971f
[Refactor] Use object system for all CAPIs ( #716 )
...
* 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
* address comments
2019-07-23 12:47:05 -04:00
e16e895d53
[Doc] fix some document warnings ( #645 )
...
* fix doc
* fix some format and warnings
* fix
2019-06-11 13:41:41 -04:00
d6a9265d16
[Doc] docstring for node/edge removal APIs ( #639 )
2019-06-10 12:38:06 -04:00
411bcd7e6c
[BUGFIX] extand DGLGraph graph_data. ( #632 )
...
* enable tutorial test in CI.
* extand DGLGraph graph_data.
* update doc.
* Revert "enable tutorial test in CI."
This reverts commit cd774067180922bb6ae979bde4aecbffc61c8147.
* accept DGLGraph in graph store.
2019-06-09 17:22:04 -07:00
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
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
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
14af8402f0
[Perf] lazily create msg_index. ( #563 )
...
* lazily create msg_index.
* update test.
2019-05-24 13:41:03 -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
681e5217dd
[Refactor] Sampler code refactor ( #454 )
...
* refactored sampler code
* docstring
* fix tutorial
2019-03-18 10:41:35 -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
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
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
525bb61245
[Doc] Fix a typo ( #365 )
2019-01-25 10:41:37 -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
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
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
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
eafcb7e7f5
[Bugfix][MXNet] Fix edge order and builtin max bug in mx ( #247 )
...
* Fix edge order and builtin max bug in mx
* fix as requested
2018-12-05 01:32:54 -08:00
274e1082f5
[Doc] API doc string for many components ( #245 )
...
* builtin function docstring
* init docstring
* view docstring
* add init to index and fix
* node /edge feature
* Example -> Examples
* fix func hyperlink
* traversal
* fix
* from/to_networkx docstring
* minor
* fix duplicate label
* comment about tensor framework
* from scipy sparse matrix
* fix format errors
2018-12-04 17:52:00 -05:00
7cca500787
[Doc] Computing with DGLGraph ( #212 )
...
* Docs for graph computing
* Docs for graph computing
* Fix
* WIP
* update the docstring
2018-12-04 16:51:46 -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
5680f8dc13
[DOC] Documentation strings for graph mutation, queries, and subgraphing ( #207 )
...
* docstrings for graph mutation & queries
* [Doc] contrib.sampler. (#200 )
* subgraph docs
* updates
2018-12-02 14:41:25 -05:00
57daf9c9a6
[Graph] small fix on the all index ( #219 )
2018-12-02 13:39:04 -05:00
57b07fce92
[Model] Accelerate SSE ( #172 )
...
* lazy eval edge ids.
* parallelize node id lookup.
* fix a bug.
* use mxnet for index.
* use update_all in the subgraph training.
* sample neighbors.
* Revert "parallelize node id lookup."
This reverts commit e661f69bb06cb5a7c246f0e106f245e27800e220.
* update README.
* cache subgraphs.
* support all degrees.
* cache adj in CPU.
* fix a bug in sse.
* print.
* raise error on mutable graphs.
* measure train time per epoch.
* fix a bug in graph_index.
* remove readonly in DGLSubGraph.
* cache subgraph properly.
* accelerate getting adjacency.
* split infer.
* lazy eval edges.
* specify inference mode.
* update for new sampler.
* use new mxnet sampling api.
* fix indent.
* remove profiling code.
* remove mxnet from sampler.
* return a lambda function for graph edges.
* add docs for immutable subgraph.
* Revert "return a lambda function for graph edges."
This reverts commit 0de5d7f100e230c518a3fb8976a6227f474d09ee.
* get parent_eid.
2018-12-02 12:43:25 -05:00
53ea03ad82
[Doc] Fix doc bug and warning ( #213 )
...
* fix dgmg tutorial indentation
* bug in incidence_matrix docstring
* remove print
2018-12-01 18:58:56 -05:00
a0d0b1ea00
[Model] Fix + batched DGMG ( #175 )
...
* DGMG with batch size 1
* Fix
* Adjustment
* Fix
* Fix
* Fix
* Fix
* Fix has_node and __contains__
* Batched implementation for DGMG
* Remove redundant dependency
* Adjustment
* Fix
* Add comments
2018-11-29 00:13:30 +08:00
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
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
048f6d7a30
[GraphIndex] refactor graph caching ( #150 )
...
* refactor graph caching
* fix mx test
* fix typo
2018-11-13 22:12:38 -05:00
Quan (Andy) Gan