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add graph_compact. #13436

Merged

eric-haibin-lin merged 7 commits into apache:master from zheng-da:graph_compact

Dec 1, 2018

Contributor

zheng-da commented Nov 28, 2018

Description

dgl_graph_compact works with csr_neighbor_uniform_sample and csr_neighbor_non_uniform_sample. These two sampling operators create CSR matrices with many empty rows. This operator compacts these CSR matrices.

Checklist

Essentials

Please feel free to remove inapplicable items for your PR.

The PR title starts with [MXNET-$JIRA_ID], where $JIRA_ID refers to the relevant JIRA issue created (except PRs with tiny changes)
Changes are complete (i.e. I finished coding on this PR)
All changes have test coverage:
Unit tests are added for small changes to verify correctness (e.g. adding a new operator)
Nightly tests are added for complicated/long-running ones (e.g. changing distributed kvstore)
Build tests will be added for build configuration changes (e.g. adding a new build option with NCCL)
Code is well-documented:
For user-facing API changes, API doc string has been updated.
For new C++ functions in header files, their functionalities and arguments are documented.
For new examples, README.md is added to explain the what the example does, the source of the dataset, expected performance on test set and reference to the original paper if applicable
Check the API doc at http://mxnet-ci-doc.s3-accelerate.dualstack.amazonaws.com/PR-$PR_ID/$BUILD_ID/index.html
To the my best knowledge, examples are either not affected by this change, or have been fixed to be compatible with this change

Changes

Feature1, tests, (and when applicable, API doc)
Feature2, tests, (and when applicable, API doc)

Comments

If this change is a backward incompatible change, why must this change be made.
Interesting edge cases to note here

zheng-da requested a review from anirudh2290 as a code owner

November 28, 2018 04:16

Contributor

vandanavk commented Nov 28, 2018

@mxnet-label-bot add [Operator, pr-awaiting-review]

marcoabreu added Operator pr-awaiting-review labels

zheng-da requested a review from szha as a code owner

November 29, 2018 08:28

zheng-da force-pushed the graph_compact branch from c1fc549 to cce728e Compare

November 30, 2018 02:45

eric-haibin-lin approved these changes

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eric-haibin-lin left a comment

LGTM pending doc enhancement

src/operator/contrib/dgl_graph.cc

+                return true;
+              }
+              NNVM_REGISTER_OP(_contrib_dgl_graph_compact)

Member

eric-haibin-lin Nov 30, 2018

Please also update ndarray/contrib.md and symbol/contrib.md

src/operator/contrib/dgl_graph.cc Outdated

+              csr_neighbor_uniform_sample and csr_neighbor_non_uniform_sample.
+              The CSR matrices generated by these two operators may have many empty
+              rows at the end. This operator removes these empty rows and empty columns.
+              Example::

Member

eric-haibin-lin Nov 30, 2018

Extra line

src/operator/contrib/dgl_graph.cc Outdated

+              NNVM_REGISTER_OP(_contrib_dgl_graph_compact)
+              .describe(R"code(This operator compacts a CSR matrix generated by
+              csr_neighbor_uniform_sample and csr_neighbor_non_uniform_sample.

Member

eric-haibin-lin Nov 30, 2018

I think the name csr_neighbor_uniform_sample has been changed

src/operator/contrib/dgl_graph.cc Outdated

+                subg_v = subgs[0]
+                subg = subgs[1]
+                compacts = mx.nd.contrib.dgl_graph_compact(subg, subg_v,
+                        graph_sizes=(subg_v[-1].asnumpy()[0]))

Member

eric-haibin-lin Nov 30, 2018

Can you also print the input/output if dgl_graph_compact?

src/operator/contrib/dgl_graph.cc Outdated

+                size_t num_elems = csr.aux_data(csr::kIdx).shape_.Size();
+                // The last element in vids is the actual number of vertices in the subgraph.
+                CHECK_EQ(vids.shape()[0], in_ptr_data.shape_[0]);
+                CHECK_EQ((size_t) row_ids[vids.shape()[0] - 1], graph_size);

Member

eric-haibin-lin Nov 30, 2018

nit nit: use static_cast

Member

eric-haibin-lin commented Nov 30, 2018

Please follow doc style in #13463

zheng-da added 6 commits

December 1, 2018 09:43


          add graph_compact.

7ceaaf4


          fix.

b52d5a8


          add doc.

29a5d17


          add tests for graph_compact.

c089024


          address comments.

2f7175f


          update docs.

ebbcb4a

zheng-da force-pushed the graph_compact branch from 8da1a24 to ebbcb4a Compare

December 1, 2018 02:38


          trigger CI

b72ec27

eric-haibin-lin merged commit 4cd3355 into apache:master

Contributor

aaronmarkham commented Dec 4, 2018

Hi guys, this PR breaks the docs. Specifically, I think I need to remove these from the Symbol Contrib API docs page:
isinf
isfinite
isnan
They don't correlate to any function in Symbol. NDArray has something for these though. Any issue with me submitting a PR to remove those lines?

aaronmarkham mentioned this pull request

Clean up some Sphinx warnings. #13539

Merged

3 tasks

Member

eric-haibin-lin commented Dec 4, 2018

@aaronmarkham good catch. No concern from my side. Thanks for pointing that out!

sergeykolychev pushed a commit that referenced this pull request


          Bumped minor version from 1.4.0 to 1.5.0 on master, updated License f…

40db619

…ile (#13478)

* updated to v1.5.0

* Bumped minor version from 1.4.0 to 1.5.0 on master

* added Anirudh as maintainer for R package

... adding something useful and re-trigger PR check

* Updated license file for clojure, onnx-tensorrt, gtest, R-package

* Get the correct include path in pip package (#13452)

* add find_include_path API

* address reviewer comment

* change return type from list to string

* add unit test

* address reviewer comment

* address reviewer comment

* address reviewer comment

* address reviewer comment

* fix include path problem in pip package

* add comment

* fix lint error

* address reviewer comment

* address reviewer comment

* Use ~/.ccache as default ccache directory so is not cache is not erased on reboot (#13431)

* Skip flaky test #13446 (#13480)

* Rewrite dataloader with process pool, improves responsiveness and reliability (#13447)

* fix recordio.py

* rewrite dataloader with pool

* fix batch as tuple

* fix prefetching

* fix pylint

* picklable function

* use pickle

* add missing commit

* Fix errors in docstrings for subgraph op; use code directive (#13463)

* [MXNET-1158] JVM Memory Management Documentation (#13105)

* update train_mnist

* Add documentation for JVM Memory Management

* update doc

* address nit picks

* address nit picks

* Grammar and clarity edits for memory management doc

* Edits for scala memory management

* Update memory-management.md

* Update memory-management.md

* Update memory-management.md

* capitalization fix

* Update row_sparse tutorial (#13414)

Update row_sparse tutorial

* Add resiliency to onnx export code (#13426)

* Added resiliency to onnx export code

- With previous infer-shape implementation, if input shape was list instead of tuple or if extra non-existent parameters were provided, the code would still work. The fixes in this commit make sure that behavior is restored to prevent any compatibility issues with existing export code.

* Fixed name of net in unittest

* Fix pylint

* [MXNET-1185] Support large array in several operators (part 1) (#13418)

* fix a few operators with large arrays (# of elements)

* fix bug in broadcast_div and add tests

* address reviewer comment

* add unit test

* add empty line

* retrigger CI

* [MXNET-1210 ] Gluon Audio - Example (#13325)

* Initialized the example

* Addressed PR comments, about existing synset.txt file - no overwrite

* RST - docstring issues fixed

* added README

* Addressed PR comments

* Addressed PR comments, checking Divide by 0

* Raising error if format is not supported.

* changed a line for ndarray of labels

* Trigger CI

* Trigger CI

* PR comments addressed around skip_header argument

* Addressed PR comments around librosa import

* PR Comments

* Passing lazy=lazy from argument

* Added PR comments, labels to README.MD

* Trigger CI

* Addressing PR Comments in README

* Modified README.md

* Added example under audio folder

* Retrigger CI

* Retrigger CI

* ONNX export: Instance normalization, Shape (#12920)

* ONNX import/export: Make backend_rep common

* ONNX export: Instance Normalization

* ONNX export: Shape operator

* Clarify dependency on OpenCV in CNN Visualization tutorial. (#13495)

* clarify ops faq regarding docs strings (#13492)

* Add graph_compact operator. (#13436)

* add graph_compact.

* fix.

* add doc.

* add tests for graph_compact.

* address comments.

* update docs.

* trigger CI

* Deprecate Jenkinsfile (#13474)

* update github location for sampled_block.py (#13508)

Updated to /~https://github.com/dmlc/gluon-nlp/blob/master/src/gluonnlp/model/sampled_block.py

* #13453 [Clojure] - Add Spec Validations to the Optimizer namespace (#13499)

* ONNX export: Logical operators (#12852)

* Fix cmake options parsing in dev_menu (#13458)

Add GPU+MKLDNN unittests to dev_menu

* Revert "Manually track num_max_thread (#12380)" (#13501)

This reverts commit 7541021.

* Feature/mkldnn static 2 (#13503)

* build mkldnn as static lib

* update makefile to statically build mkldnn

* build static mkldnn

* fix static name

* fix static name

* update static for mac

* rename mkldnn dep in ci

* remove moving mkldnn dynamic lib

* remove commented code

* remove mkldnn dnaymic for unitest

* force static for mkldnn lib

* remove dynamic mkldnn bind

* only link windows

* add mkldnn.mk

* try force linking

* remove mkldnn dynanmic check

* remove test mkldnn install

* fix spacing

* fix index

* add artifacts

* add comment about windows

* remove static

* update makefile

* fix toctree Sphinx errors (#13489)

* fix toctree errors

* nudging file for CI

* Disabled flaky test test_gluon_data.test_recordimage_dataset_with_data_loader_multiworker (#13527)

* [MXNET-1234] Fix shape inference problems in Activation backward (#13409)

* Provide a failing test for ReLU activation shape inference bug

* Fix Activation backward shape inference

fixes: #13333

* Add softsign Activation to test_gluon.py

* Use activation in GPU if we are using CUDNN and not MKLDNN as it's happening right now

* Don't disable MKLDNN

zheng-da deleted the graph_compact branch

December 5, 2018 18:38

zhaoyao73 pushed a commit to zhaoyao73/incubator-mxnet that referenced this pull request


          Add graph_compact operator. (apache#13436)

eae4215

* add graph_compact.

* fix.

* add doc.

* add tests for graph_compact.

* address comments.

* update docs.

* trigger CI

zhaoyao73 pushed a commit to zhaoyao73/incubator-mxnet that referenced this pull request


          Bumped minor version from 1.4.0 to 1.5.0 on master, updated License f…

1dcb085

…ile (apache#13478)

* updated to v1.5.0

* Bumped minor version from 1.4.0 to 1.5.0 on master

* added Anirudh as maintainer for R package

... adding something useful and re-trigger PR check

* Updated license file for clojure, onnx-tensorrt, gtest, R-package

* Get the correct include path in pip package (apache#13452)

* add find_include_path API

* address reviewer comment

* change return type from list to string

* add unit test

* address reviewer comment

* address reviewer comment

* address reviewer comment

* address reviewer comment

* fix include path problem in pip package

* add comment

* fix lint error

* address reviewer comment

* address reviewer comment

* Use ~/.ccache as default ccache directory so is not cache is not erased on reboot (apache#13431)

* Skip flaky test apache#13446 (apache#13480)

* Rewrite dataloader with process pool, improves responsiveness and reliability (apache#13447)

* fix recordio.py

* rewrite dataloader with pool

* fix batch as tuple

* fix prefetching

* fix pylint

* picklable function

* use pickle

* add missing commit

* Fix errors in docstrings for subgraph op; use code directive (apache#13463)

* [MXNET-1158] JVM Memory Management Documentation (apache#13105)

* update train_mnist

* Add documentation for JVM Memory Management

* update doc

* address nit picks

* address nit picks

* Grammar and clarity edits for memory management doc

* Edits for scala memory management

* Update memory-management.md

* Update memory-management.md

* Update memory-management.md

* capitalization fix

* Update row_sparse tutorial (apache#13414)

Update row_sparse tutorial

* Add resiliency to onnx export code (apache#13426)

* Added resiliency to onnx export code

- With previous infer-shape implementation, if input shape was list instead of tuple or if extra non-existent parameters were provided, the code would still work. The fixes in this commit make sure that behavior is restored to prevent any compatibility issues with existing export code.

* Fixed name of net in unittest

* Fix pylint

* [MXNET-1185] Support large array in several operators (part 1) (apache#13418)

* fix a few operators with large arrays (# of elements)

* fix bug in broadcast_div and add tests

* address reviewer comment

* add unit test

* add empty line

* retrigger CI

* [MXNET-1210 ] Gluon Audio - Example (apache#13325)

* Initialized the example

* Addressed PR comments, about existing synset.txt file - no overwrite

* RST - docstring issues fixed

* added README

* Addressed PR comments

* Addressed PR comments, checking Divide by 0

* Raising error if format is not supported.

* changed a line for ndarray of labels

* Trigger CI

* Trigger CI

* PR comments addressed around skip_header argument

* Addressed PR comments around librosa import

* PR Comments

* Passing lazy=lazy from argument

* Added PR comments, labels to README.MD

* Trigger CI

* Addressing PR Comments in README

* Modified README.md

* Added example under audio folder

* Retrigger CI

* Retrigger CI

* ONNX export: Instance normalization, Shape (apache#12920)

* ONNX import/export: Make backend_rep common

* ONNX export: Instance Normalization

* ONNX export: Shape operator

* Clarify dependency on OpenCV in CNN Visualization tutorial. (apache#13495)

* clarify ops faq regarding docs strings (apache#13492)

* Add graph_compact operator. (apache#13436)

* add graph_compact.

* fix.

* add doc.

* add tests for graph_compact.

* address comments.

* update docs.

* trigger CI

* Deprecate Jenkinsfile (apache#13474)

* update github location for sampled_block.py (apache#13508)

Updated to /~https://github.com/dmlc/gluon-nlp/blob/master/src/gluonnlp/model/sampled_block.py

* apache#13453 [Clojure] - Add Spec Validations to the Optimizer namespace (apache#13499)

* ONNX export: Logical operators (apache#12852)

* Fix cmake options parsing in dev_menu (apache#13458)

Add GPU+MKLDNN unittests to dev_menu

* Revert "Manually track num_max_thread (apache#12380)" (apache#13501)

This reverts commit 7541021.

* Feature/mkldnn static 2 (apache#13503)

* build mkldnn as static lib

* update makefile to statically build mkldnn

* build static mkldnn

* fix static name

* fix static name

* update static for mac

* rename mkldnn dep in ci

* remove moving mkldnn dynamic lib

* remove commented code

* remove mkldnn dnaymic for unitest

* force static for mkldnn lib

* remove dynamic mkldnn bind

* only link windows

* add mkldnn.mk

* try force linking

* remove mkldnn dynanmic check

* remove test mkldnn install

* fix spacing

* fix index

* add artifacts

* add comment about windows

* remove static

* update makefile

* fix toctree Sphinx errors (apache#13489)

* fix toctree errors

* nudging file for CI

* Disabled flaky test test_gluon_data.test_recordimage_dataset_with_data_loader_multiworker (apache#13527)

* [MXNET-1234] Fix shape inference problems in Activation backward (apache#13409)

* Provide a failing test for ReLU activation shape inference bug

* Fix Activation backward shape inference

fixes: apache#13333

* Add softsign Activation to test_gluon.py

* Use activation in GPU if we are using CUDNN and not MKLDNN as it's happening right now

* Don't disable MKLDNN

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