GitLab

* Several optimizations on DGL-KG:
1. Sorted positive edges for sampling which can reduce random
   memory access during positive sampling
2. Asynchronous node embedding update
3. Balanced Relation Partition that gives balanced number of
   edges in each partition. When there is no cross partition
   relation, relation embedding can be pin into GPU memory
4. tunable neg_sample_size instead of fixed neg_sample_size

* Fix test

* Fix test and eval.py

* Now TransR is OK

* Fix single GPU with mix_cpu_gpu

* Add app tests

* Fix test script

* fix mxnet

* Fix sample

* Add docstrings

* Fix

* Default value for num_workers

* Upd

* upd

* trying to refactor IndexSelect

* partial implementation

* add index select and assign for floats as well

* move to random choice source

* more updates

* fixes

* fixes

* more fixes

* adding python impl

* fixes

* unit test

* lint

* lint x2

* lint x3

* update metapath2vec

* debugging performance

* still debugging for performance

* tuning

* switching to succvec

* redo

* revert non-uniform sampler to use vector

* still not fast

* why does this crash with OpenMP???

* because there was a data race!!!

* add documentations and remove assign op

* lint

* lint x2

* lol what have i done

* lint x3

* fix and disable gpu testing

* bugfix

* generic random walk

* reorg the random walk source code

* Update randomwalks.h

* Update randomwalks_cpu.cc

* rename file

* move internal function to anonymous ns

* reorg & docstrings

* constant restart probability

* docstring fix

* more commit

* random walk with restart, tested

* some fixes

* switch to using NDArray for choice

* massive fix & docstring

* lint x?

* lint x??

* fix

* export symbols

* skip gpu test

* addresses comments

* replaces another VecToIdArray

* add randomwalks.h to include

* replace void * with template

* attach positive.

* add neg_deg_sample.

* add comment.

* add neg_deg_sample for eval.

* change the edge sampler.

* rename edge sampler in KG.

* allow specifying chunk size and negative sample size separately.

* fix bugs in KG.

* add check in sampler.

* add more checks.

* fix

* add comment.

* add comments.

* accel edge sampling.

* measure sampling time.

* attach positive.

* add neg_deg_sample.

* fix a minor bug.

* remove unnecessary code.

* Revert "add neg_deg_sample."

This reverts commit 45f3c08c87e33589563ca7e6a3ec91cb1239910e.

* Revert "attach positive."

This reverts commit 503d7821555b69b7ccfed55ce8b87ee24fff852d.
Co-authored-by: xiang song(charlie.song) <classicxsong@gmail.com>

* hot fix

* Fix docs

* Fix ArrayHeap float overflow bug

* Fix

* Clean some dead code

* Fix

* FIx

* Add some comments

* run test

current samplers only support working on CPU

* Add weight based edge sampler

* Can run, edge weight work.
TODO: test node weight

* Fix node weight sample

* Fix y

* Update doc

* Fix syntex

* Fix

* Fix GPU test for sampler

* Fix test

* Fix

* Refactor EdgeSampler to act as class object not function that it
can record its own private states.

* clean

* Fix

* Fix

* Fix run bug on kg app

* update

* update test

* test

* Simply python API and fix some C code

* Fix

* Fix

* Fix syntex

* Fix

* Update API description

* add replacement for edge sampler

* Now edge sampler support replacement and no-replacement

* Fix

* Fix

* change kg/app to use edge sampler with replacement config

* Update replacement algo

* Fix syntax

* Update

* Update
Co-authored-by: Da Zheng <zhengda1936@gmail.com>

* Add weight based edge sampler

* Can run, edge weight work.
TODO: test node weight

* Fix node weight sample

* Fix y

* Update doc

* Fix syntex

* Fix

* Fix GPU test for sampler

* Fix test

* Fix

* Refactor EdgeSampler to act as class object not function that it
can record its own private states.

* clean

* Fix

* Fix

* Fix run bug on kg app

* update

* update test

* test

* Simply python API and fix some C code

* Fix

* Fix

* Fix syntex

* Fix

* Update API description

* edge sampler return head nodes and tail nodes.

* edge subgraph.

* use VecToIdArray

* example.

* fix compile error.

* optimizer for sampling all negative edges.

* allow to disable checking false negative.

* fix lint.

* fix docstring.

* fix for comment.

* add comments.

* find the existence of negative edges.

* add comment.

* fix test.

* PBG negative edge sampler.

* add a positive edge to make it regular, handle last batch.

* exclude all positive edges in the parent graph.

* just uniformly sample negative nodes.

* fix lint.

* shuffle one-side nodes of positive edges.

* just uniformly sample negative nodes.

* change the data type.

* address comment.

* remove commented code.

* 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

* add edge sampler.

* add test and run.

* add negative sampling.

* remap the edge subgraph vid.

* negative graph excludes edges of positive edgs.

* remove print.

* avoid sampling NodeFlow when expand_factor or num_hops is 0.

* fix a bug when excluding nodes in negative graph.

* support multigraph.

* exclude positive edges.

* fix memory leak.

* return subgraph object directly.

* fix many problems.

* add comments.

* address comments

* nonuniform sampler

* unit test

* test on out neighbors

* error checks

* lint

* fix

* clarification

* use macro switcher

* use empty array for uniform sampling

* oops

* Revert "oops"

This reverts commit a11f9ae707aaeb67fb5921c887a17d3711d5b04a.

* Revert "use empty array for uniform sampling"

This reverts commit 8526ce4cade89f2c1b09a08aca8830375ebafb31.

* re-reverting

* use a method

* rng refactor

* fix bugs

* unit test

* remove setsize

* lint

* fix test

* use explicit instantiation instead of inlining

* stricter test

* use tvm solution

* moved python interface to dgl.random

* lint

* address comments

* make getthreadid an inline function

* 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

* WIP: array refactoring

* WIP: implementation

* wip

* most csr part

* WIP: on coo

* WIP: coo

* finish refactoring immutable graph

* compiled

* fix undefined ndarray copy bug; add COOToCSR when coo has no data array

* fix bug in COOToCSR

* fix bug in CSR constructor

* fix bug in in_edges(vid)

* fix OutEdges bug

* pass test_graph

* pass test_graph

* fix bug in CSR constructor

* fix bug in CSR constructor

* fix bug in CSR constructor

* fix stupid bug

* pass gpu test

* remove debug printout

* fix lint

* rm biparate grpah

* fix lint

* address comments

* fix bug in Clone

* cpp utests

* fix.

* add comments.

* fix sampler.

* update doc.

* fix.

* 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

* 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.

* 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

* 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

* 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

* 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

* 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

* 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

* fix.

* add check.

* fix assert.

* 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

* 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.