Pull this #1

SamanthaFeidFischer · 2018-11-17T09:40:00Z

Description

(Brief description on what this PR is about)

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

* opencv2-->opencv; deleted duplicate content * update troubleshooting info

* Fix exception handling bug * Trigger CI * Add test for exc handling * Trigger CI * Resolve conflicts

* fix bug in prelu * add unit test

* add mentions of the gluon toolkits and links to resources * fix nlp and cv text

* upgrade onnx * import helpers * upgrade version in ci * addressing comments * fix * test name changed * retrigger tests * adding comments

* char RNN tutorial * nit fixes

…che#12668) * document env. * update. * update. * retrigger

…12674) * update mshadow * bump

…e script (apache#12556) * Initial Commit for docker automation python * Fixes * change dir for tests * Fix more issues * fix docker tag command * cosmetic changes * update README * update test to fail on version mismatch * remove debug mode * Update README.md * Update README.md * update README * Add Licenses * Some review comments * Add Cuda80 and cuda92 dockerfiles and build steps * Add renamed and hence untracked files for cu90 * Update README * More ways to login * Update README with login options * Update README with links to test. test_mxnet link will work only after merge

* Rebase to align the latest changes on test_gluon.py * Referring the issue link to skip message * Retrigger the PRECI * Remove previous changes * Modify the cases trying to eliminate the errors on GPU * Resolving conflict * Further reduce the tensor size * minor changes * move to mkl * fix flaky case * Remove the test_mkldnn_gluon.py * Move the cases back to test_gluon.py

* Update contribute.md Fixed grammar * Update contribute.md Fixed Grammar

* added R LSTM examples * added tutorial to whitelist * fix encoding * added seed and fixed few formatting issues * addressed PR comments * formatting fixes' * nit fixes * fix epochs * fixed tutorial link

git-subtree-dir: julia git-subtree-mainline: c595f2d git-subtree-split: 224ae96

- enable Jenkins CI build for Julia - add license headers to Julia source code - update links for Julia README

* [MXNET-860] Use emplace where helpful * [MXNET-860] Add emplace as an error in clang-tidy

* [MXNET-860] Remove std::moves that have no affect * [MXNET-860] Check for unneeded moves as errors

…pache#12678) * Fix apache#12672 Problem is in using np.ascontiguousarray, which is buggy for zero-dimensional arrays (see numpy/numpy#5300 for details). Here I use the solution proposed by numpy team: switch to asarray with order='C'. Add some tests for this situation (for array() and for setitem too). * typo in tests

This PR removes some redundant build tasks and removes some slow tests to try and decrease the number of TravisCI timeouts that would otherwise occur on large PRs.

* Throw exception if MXSymbolInferShape fails. * scala-package/native/src/main/native/org_apache_mxnet_native_c_api.cc: (Java_org_apache_mxnet_LibInfo_mxSymbolInferShape): throw IllegalArgumentException with the content of MXGetError if call to MXSymbolInferShape fails. * Remove stray space. * Don't throw in JNI. checkCall in scala code will do the right thing with a nonzero exit status. * Don't repeat the memory free code. Just wrap the FillSymbolInferShape calls in `if (ret == 0) { ... }`. * Fix too-long line.

* fix. * add test. * retrigger

* Addressed doc issues * Update optimizer.py

* fixing gradcam * changed loading parameters code * fixing type conversions issue with previous versions of matplotlib * gradcam consolidation * creating directory structures in utils * changing location * empty commit

* Adding info_gan example * adjust paths of filenames * Update index.md * Update index.md * Update index.md * Update info_gan.md Added an image * Update info_gan.md Applied some fixes * Update info_gan.md Applied some fixes * Update info_gan.md Applied some fixes * Update info_gan.md * Updated index.md file * Updated index.md file * change links * Fixed typo * Delete Untitled.ipynb * Adding Vishaals comments * Adding Anirudh's comments * Fixed some bugs * Adding Anirudh's comments * some minor fixes

…che#13298)

* Fix Sphinx python docstring formatting error (apache#13021). Fixes apache#13021 * Update src/operator/nn/batch_norm.cc Co-Authored-By: frankfliu <frankfliu2000@gmail.com>

* update the doc for test_optimizer * add docstring for test_score

* update the README to solve the library cannot find problem * fix the broken format * remove redundancy and broken format * add .

* update readme on module prediction * fix typo * update url * improve grammar * update link

* [MXNET-984] Add Java NDArray and introduce Java Operator Builder class (apache#12816) * clean history and add commit * add lint header * bypass the java unittest when make the package * clean up redundant test * clean spacing issue * revert the change * clean up * cleanup the JMacros * adding line escape * revert some changes and fix scala style * fixes regarding to Naveen's comment * Java Inference api and SSD example (apache#12830) * New Java inference API and SSD example * Adding license to java files and fixing SSD example * Fixing SSD example to point to ObjectDetector instead of ImageClassifier * Make scripts for object detector independent to os and hw cpu/gpu * Added API Docs to Java Inference API. Small fixes for PR * Cosmetic updates for API DOCS requested during PR * Attempt to fix the CI Javafx compiler issue * Migrate from Javafx to apache commons for Pair implementation * Removing javafx from pom file * Fixes to appease the ScalaStyle deity * Minor fix in SSD script and Readme * Added ObjectDetectorOutput which is a POJO for Object Detector to simplify the return type * Removing Apache Commons Immutable Pair * Adding license to new file * Minor style fixes * minor style fix * Updating to be in scala style and not explicitly declare some unnecessary variables * NativeResource Management in Scala (apache#12647) (apache#12883) * add Generic MXNetHandle trait and MXNetHandlePhantomRef class that will be used by all MXNetObjects * Generic Handle with AutoCloseable * add NativeResource and NativeResourceManager with Periodic GC calling * use NativeResource trait in NDArray, Symbol and Executor * add run train mnist script * create a Generic ResourceScope that can collect all NativeResources to dispose at the end * modify NativeResource and ResourceScope, extend NativeResource in NDArray, Symbol and Executor * remove GCExecutor * deRegister PhantomReferences by when calling dispose() * add Finalizer(temporary) to NativeResource * refactor NativeResource.dispose() method * update NativeResource/add Unit Test for NativeResource * updates to NativeResource/NativeResourceRef and unit tests to NativeResource * remove redundant code added because of the object equality that was needed * add ResourceScope * Fix NativeResource to not remove from Scope, add Unit Tests to ResourceScope * cleanup log/print debug statements * use TreeSet inplace of ArrayBuffer to speedup removal of resources from ResourceScope Fix Executor dispose and make KVStore a NativeResource * fix segfault that was happening because of NDArray creation on the fly in Optimizer * Add comments for dispose(param:Boolean) * Added unit tests for Resource Scope in Java (apache#12955) * Bumping down minimum java support from 8 to 7 (apache#12965) * [MXNET-984] Java NDArray Documentation Generation (apache#12835) * cherry pick javaDoc changes * update NDArray changes * refactoring change and merge all docGen in a single place * clean the scalastyle * take on Piyush nit * drop the comments * First pass at adding JavaDocs for new java api classes (apache#12963) * First pass at adding JavaDocs for new java api classes * Fix a scalastyle issue * Updating JavaDoc based on feedback * [MXNET-1160] add Java build/run example (apache#12969) * add example * clean up nit * find the pain point * add java tut into whitelist * Trigger CI * add java demo and split scala demo * address the comments * change the examples * fix the wrong configuration * Maven Surefire bug workaround (apache#13097) * use ResourceScope in Model/Trainer/FeedForward.scala (apache#12882) (apache#13164) * use ResourceScope in Model/Trainer/FeedForward.scala * add moveToOuterScope public method to move resources to a outerScope if it exists * fix memory leak in FeedForward.scala by making it a native resource and disposing argparams, auxParams in dispose() method * [MXNET-1187] Added Tutorial for Java under mxnet.io/docs/tutorials (apache#13183) * Added tutorial for Java installation on IntelliJ for mxnet.io website * Added correct image resources * Removed spurious quotes * Added java tutorial to whitelisting * Added community download edition link to intelliJ section * [MXNET-1202] Change Builder class into a better way (apache#13159) * applying changes for Builder functions * simplify the code structure * update docgen * follow Naveen's suggestion * apply comments to Param * clean up param build * change on the comments * add one description line * [MXNET-1041] Add Java benchmark (apache#13095) * add java benchmark * applied changes based on Piyush comments * applies Andrew's change * fix clojure test issue * update the statistic names * follow Naveen's instruction * [MXNET-918] [Introduce Random module / Refact code generation (apache#13038)][Cherry pick] (apache#13242) * [MXNET-918] Introduce Random module / Refact code generation (apache#13038) * refactor code gen * remove xxxAPIMacroBase (overkill) * CI errors / scala-style * PR review comments * clean up the duplicated code * add comments * Fixed missing break statement (apache#13257) * Java Benchmark failure (apache#13258) * patch fix * update ignore * rename getContext to bindToDevice * Update JavaBenchmark.java * Addressing PR feedback for merging Java API into master (apache#13277) * Addressing PR feedback for merging Java API into master * Changed constructors to package private instead of private * clean up the NDArray follow the comments (apache#13281) * [MXNET-1181] Added command line alternative to IntelliJ in install instructions (apache#13267) * Added command line alternative to IntelliJ * Removed the duplicate file * Fixed typos * Fixed minor command issue * add defaults and clean up the tests (apache#13295) * [MXNET-1187] Added Java SSD Inference Tutorial for website (apache#13201) * Added Java SSD Inference Tutorial for website * Added whitelisting to SSD tutorial * Address PR feedback * Marking intelliJ as optional * [MXNET-1182] Predictor example (apache#13237) * add initial commit * push back predictor * name fix and bug fix * update readme and script to run * minor fix * minor fix * fix on doc * update predictor * Reducing the length of setup tutorial (apache#13306)

* enabling test_dropout after fixing flaky issue * adding a check for positive seed

…3210)

* fixing gradcam * changed loading parameters code * fixing type conversions issue with previous versions of matplotlib * gradcam consolidation * creating directory structures in utils * changing location * empty commit * fix file lock issue * fix link * removing other commits * remove commit

* Updated Instructions for Label Bot * Updated instructions for mxnet-label-bot * Including myself as a contributor * Clarified usage of label bot * Fixed typos and instructions/examples have been made more clear * Added link for available labels

…11047) * fix mkldnn pooling to support full convention * backward with full convention * fix * add pooling test for full convention * add function for computing padding size * fix unit test * only support max-pooling * fix pooling bwd * address review comment

* add centos build for Scala * migrate the build portion to docker * update build script and chmod +x * address Jenkins change * allow CentOS provide all depdencies

aaronmarkham and others added 30 commits September 25, 2018 15:42

Change dependencies documentation opencv2-->opencv (apache#12654)

3042825

* opencv2-->opencv; deleted duplicate content * update troubleshooting info

fix bug, issue 12613 (apache#12614)

d4e202a

[MXNET-780] Fix exception handling bug (apache#12051)

34d9e10

* Fix exception handling bug * Trigger CI * Add test for exc handling * Trigger CI * Resolve conflicts

fix bug in prelu , issue 12061 (apache#12660)

40e3d9c

* fix bug in prelu * add unit test

add mentions of the gluon toolkits and links to resources (apache#12667)

0d29aec

* add mentions of the gluon toolkits and links to resources * fix nlp and cv text

Remove fixed seed for test_ctc_loss (apache#12686)

82c96f5

remove apachecon promo (apache#12695)

62d8fac

Onnx version update from 1.2.1 to 1.3 in CI (apache#12633)

1ae3217

* upgrade onnx * import helpers * upgrade version in ci * addressing comments * fix * test name changed * retrigger tests * adding comments

[MXNET-833] [R] Char-level RNN tutorial fix (apache#12670)

ca81535

* char RNN tutorial * nit fixes

Add documents for two new environment variables for memory pool. (apa…

9ce5792

…che#12668) * document env. * update. * update. * retrigger

update mshadow for omp acceleration when nvcc is not present (apache#…

c92a202

…12674) * update mshadow * bump

fix for test order (apache#12358)

4da3001

Enable test_gluon.test_export (apache#12688)

094661d

Update contribute.md (apache#12685)

454ec3c

* Update contribute.md Fixed grammar * Update contribute.md Fixed Grammar

Update proposal_target.py (apache#12709)

c595f2d

[MXNET-637] Multidimensional LSTM example for MXNetR (apache#12664)

6fb81af

* added R LSTM examples * added tutorial to whitelist * fix encoding * added seed and fixed few formatting issues * addressed PR comments * formatting fixes' * nit fixes * fix epochs * fixed tutorial link

Add 'julia/' from commit '224ae962db8ae252ce1ac317c6d4a2cfe67a7d77'

06e1d36

git-subtree-dir: julia git-subtree-mainline: c595f2d git-subtree-split: 224ae96

import Julia binding

9f8425b

- enable Jenkins CI build for Julia - add license headers to Julia source code - update links for Julia README

Fix static / dynamic linking of gperftools and jemalloc (apache#12714)

42cc960

Disable test batchnorm slice (apache#12716)

5c86143

[MXNET-860] Use emplace where helpful (apache#12694)

bcd24f8

* [MXNET-860] Use emplace where helpful * [MXNET-860] Add emplace as an error in clang-tidy

[MXNET-953] Correct ASAN cflags flag (apache#12659)

811618a

[MXNET-860] Remove std::moves that have no affect (apache#12730)

ebe6ea8

* [MXNET-860] Remove std::moves that have no affect * [MXNET-860] Check for unneeded moves as errors

add FListInputNames attribute to softmax_cross_entropy (apache#12701)

01dd703

[MXNET-908] Speed up travis builds to avoid timeouts (apache#12706)

e41faf0

This PR removes some redundant build tasks and removes some slow tests to try and decrease the number of TravisCI timeouts that would otherwise occur on large PRs.

Merge branch 'pr-10149' import Julia binding

931555c

zheng-da and others added 29 commits November 15, 2018 12:56

Fix a bug in index_copy (apache#13218)

e7f9770

* fix. * add test. * retrigger

Addressed doc issues (apache#13165)

0259254

* Addressed doc issues * Update optimizer.py

Force APT cache update before executing install (apache#13285)

226f9cb

[Example] Gradcam consolidation in tutorial (apache#13255)

8ac7fb9

* fixing gradcam * changed loading parameters code * fixing type conversions issue with previous versions of matplotlib * gradcam consolidation * creating directory structures in utils * changing location * empty commit

Remove obsolete memory cost example (apache#13235)

c78f89f

stop gap fix to let website builds through; scaladoc fix pending (apa…

d73e4df

…che#13298)

Fix Sphinx errors in box_nms (apache#13261)

5369605

Fix Sphinx errors (apache#13252)

be5bac3

Sphinx errors in Gluon (apache#13275)

20a23ef

Fix Sphinx python docstring formatting error. (apache#13194)

21fc3af

* Fix Sphinx python docstring formatting error (apache#13021). Fixes apache#13021 * Update src/operator/nn/batch_norm.cc Co-Authored-By: frankfliu <frankfliu2000@gmail.com>

Visualization doc fix. Added notes for shortform (apache#13291)

5af975e

Addressed "dumplicate object reference" issues (apache#13214)

6ae5b65

Update basic_layers.py (apache#13299)

efff66b

add url and license to clojure package project (apache#13304)

2983185

[Example] Add docstring for test optimizer and test score (apache#13286)

d3f5340

* update the doc for test_optimizer * add docstring for test_score

[Example] Update cpp example README (apache#13280)

2775006

* update the README to solve the library cannot find problem * fix the broken format * remove redundancy and broken format * add .

[Example]update NER example readme on module prediction (apache#13184)

96a2a09

* update readme on module prediction * fix typo * update url * improve grammar * update link

enabling test_dropout after fixing flaky issue (apache#13276)

70f4e2c

* enabling test_dropout after fixing flaky issue * adding a check for positive seed

fix the flag (apache#13293)

46e870b

Made fixes to sparse.py and sparse.md (apache#13305)

1aa6a38

Fix descriptions in scaladocs for macro ndarray/sybmol APIs (apache#1…

dfeb6b0

…3210)

[MXNET-1213] add Cent OS build for Scala (apache#13279)

f87db9e

* add centos build for Scala * migrate the build portion to docker * update build script and chmod +x * address Jenkins change * allow CentOS provide all depdencies

fix file lock issue (apache#13296)

98830d5

modify code for working in gpu context. (apache#13302)

64657c2

SamanthaFeidFischer merged commit beed912 into enable-comment-report Nov 17, 2018

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Pull this #1

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SamanthaFeidFischer commented Nov 17, 2018

Pull this #1

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SamanthaFeidFischer commented Nov 17, 2018

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