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Syncing forks #2

Merged
merged 159 commits into from
Jul 8, 2020
Merged

Syncing forks #2

merged 159 commits into from
Jul 8, 2020

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jinboci
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@jinboci jinboci commented Jul 8, 2020

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 $JIRA_ID refers to the relevant JIRA issue created (except PRs with tiny changes)
  • Changes are complete (i.e. I finished coding on this PR)
  • All changes have test coverage:
  • Unit tests are added for small changes to verify correctness (e.g. adding a new operator)
  • Nightly tests are added for complicated/long-running ones (e.g. changing distributed kvstore)
  • Build tests will be added for build configuration changes (e.g. adding a new build option with NCCL)
  • Code is well-documented:
  • For user-facing API changes, API doc string has been updated.
  • For new C++ functions in header files, their functionalities and arguments are documented.
  • For new examples, README.md is added to explain the what the example does, the source of the dataset, expected performance on test set and reference to the original paper if applicable
  • Check the API doc at https://mxnet-ci-doc.s3-accelerate.dualstack.amazonaws.com/PR-$PR_ID/$BUILD_ID/index.html
  • To the best of my 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

zhreshold and others added 30 commits May 7, 2020 10:34
@zhreshold
Gluon data 2.0: c++ dataloader and built-in image/bbox transforms (#1…
a0e6735 
…7841)

* c++ dataloader and built-in image/bbox

* update

* fix error

* fix import error

* fix ci build

* fix vs openmp loop type

* fix warning as error with sign/unsign comp

* sign/unsign comp

* update to pytest

* remove nose

* fix tear_down

* address comments

* thread safe dataset

* address comments

* address comments

* fix

* serial pytest for data download
@ChaiBapchya
Remove duplicate large_vector_test (#18259)
353c243
@jinboci
Fixing #16655 (#18257)
7f24823 
* fix the error message of reshape()

* Fixing issue #16655 reshape() error message

Co-authored-by: Ubuntu <ubuntu@ip-172-31-34-249.ap-northeast-1.compute.internal>
@Kh4L
Change include to relative in nvvm_to_onnx.cc (#18249)
21b187b 
Signed-off-by: Serge Panev <spanev@nvidia.com>
@samskalicky
fixed overwrite of args/aux variables (#18232)
68cb955 
* fixed overwrite of args/aux variables

* fixed spacing
fix when clicking version dropdown it jumps to top of the page (#18238)
33dfbf7
@yijunc
fix mixed type backward (#18250)
f00b9ab
@nickguletskii
Change LC_NUMERIC for CentOS CI jobs to verify locale invariance (#18097
eab068b 
)

* Load the user's locale before performing tests

* Change the locale for the CentOS CI jobs to weed out locale-related bugs

* Mark tests that fail due to the decimal point with xfail

* Run localedef when generating the CentOS CI image

* Cancel some Scala tests when C locale uses a non-standard decimal sep.

* Rename xfail helper to xfail_when_nonstandard_decimal_separator

* Fix scalastyle errors

* Disable more Python tests that fail due to locale-related issues

* Move assumeStandardDecimalSeparator into separate object to fix scaladoc

* Disable the "symbol pow" test when running with non-standard decimal sep

* Disable new tests that fail due to locale-related issues
@eric-haibin-lin
Fix interleave matmul doc (#18260)
de51058 
* fix doc

* fix doc

* fix axis

Co-authored-by: Lin <haibilin@a483e7be4c92.ant.amazon.com>
@leezu
CI: Update Android, ARM build and ARM test containers (#18264)
1d14bf3 
* Android build containers

* ARM build containers

* ARM test containers

* Fix naming scheme

* Set WORKDIR at correct location
@xidulu
[Numpy] Port nd.random.multinomial to npx.sample_categorical (#18272)
9d44086 
* port nd.multinomial to npx.sample_categorical

* move to npx.random
@zhreshold
Deprecate dataset transform= argument in gluon data API (#17852)
18b6e05
@ryanwentaoxu
[Numpy] New FFIs for Operator: squeeze, repeat, around, round, diagfl…
0523f09 
…at (#18263)

* FFI new feature

* Feature ffi x 5

* Fix pylint error

* Fix pylint error

* Fix around error

* repeat modified
@ChaiBapchya
Update unix gpu toolchain (#18186)
21899f8 
* update nvidiadocker command & remove cuda compat

* replace cu101 with cuda since compat is no longer to be used

* skip flaky tests

* get rid of ubuntu_build_cuda and point ubuntu_cu101 to base gpu instead of cuda compat

* Revert "skip flaky tests"

This reverts commit 1c720fa.

* revert removal of ubuntu_build_cuda

* add linux gpu g4 node to all steps using g3 in unix-gpu pipeline
@eric-haibin-lin
add gelu doc (#18274)
8a5886a 
Co-authored-by: Lin <haibilin@a483e7be4c92.ant.amazon.com>
@leezu
Mark test_np_mixed_precision_binary_funcs flaky (#18290)
51844b2
@rondogency
Revert PR 17767 for fixing GPU memory usage regression (#18283)
47a38d1 
* Revert "Fix and optimize handling of vectorized memory accesses (#17767)"

This reverts commit 5542d03.

* add license to reverted file
@bgawrych
Fix LSTM and GRU layers gradient calculations (#18203)
b4c70eb 
* Fix input gradient calculation for bidirectional LSTM

For bidiractional LSTM with number of layers > 2 input gradient calculation was incorrect.
Reason of wrong calculations was overwriting y derivative (dy) tensor by
calculated x derivative (dx) tensor before right2left layer could use dy for own
gradient calculations.
Propsed fix uses additional space to avoid overwriting.

* Fix gradient calculation for GRU

For GRU with number of layers > 2 i2h_weight gradient for
layers in the middle (all except last and first) was incorrect.
Wrong caluculations were caused by assigning output pointer to
input instead of calculating new input pointer.

* Enable tests for GRU and LSTM gradients

* Fix comments

* Change loop iteration deduction

* Add more test cases for fused rnn layers
@acphile @leezu
Changes to mxnet.metric (#18083)
effbb8b 
* finish 5 changes

* move metric.py to gluon, replace mx.metric with mx.gluon.metric in python/mxnet/

* fix importError

* replace mx.metric with mx.gluon.metric in tests/python

* remove global support

* remove macro support

* rewrite BinaryAccuracy

* extend F1 to multiclass/multilabel

* add tests for new F1, remove global tests

* use mxnet.numpy instead of numpy

* fix sanity

* rewrite ce and ppl, improve some details

* use mxnet.numpy.float64

* remove sklearn

* remove reset_local() and get_global in other files

* fix test_mlp

* replace mx.metric with mx.gluon.metric in example

* fix context difference

* Disable -DUSE_TVM_OP on GPU builds

* Fix disable tvm op for gpu runs

* use label.ctx in metric.py; remove gluoncv dependency in test_cvnets

* fix sanity

* fix importError

* remove nose

Co-authored-by: Ubuntu <ubuntu@ip-172-31-12-243.us-east-2.compute.internal>
Co-authored-by: Leonard Lausen <lausen@amazon.com>
@rondogency
Mark CD quantization tests as xfail on , decimal separator locales (#…
6d5e471 
…18307)
@leezu
Reenable test_amp_conversion (#18292)
446ce14 
TVMOP feature is now disabled on GPU builds, which caused this test to fail previously
@leezu
xfail_when_nonstandard_decimal_separator for test_metric.py (#18312)
4d4cbd5
@leezu
Fix missing MKLDNN headers (#18310)
fec534a
@leezu
Fix memory leaks in Gluon (#18328)
3e676fc 
Fix leak of ndarray objects in the frontend due to reference cycle.
@leezu
Fix deferred compute mode for operators using new FFI (#18284)
37280e4
@eric-haibin-lin
Add a timeout to the storage profiler in case mem_counters_ is not ye…
09224c4 
…t initialized (#18306)

* avoid race condition in profiler init

* Update storage_profiler.h

Co-authored-by: Ubuntu <ubuntu@ip-172-31-61-76.ec2.internal>
@mseth10
fix native cd builds (#18337)
9482728
@szha
[CI] run operator tests with naive engine (#18252)
10b6b48 
* run operator tests with naive engine

* fix take tests

* update skip mark

* fix cuda error reset

* adjust tests

* disable parallel testing and naive engine for mkl/mkldnn #18244
@szha
[numpy] add dlpack functions to npx (#18342)
7ab326c 
* add dlpack functions to npx

* improve tests

* further improve test

* fix comment
@eric-haibin-lin
[BUGFIX] Remove Profiler from the runtime feature list, since its alw…
7f5df07 
…ays built (#18308)

* remove Profiler from the runtime feature list, since its always built

* Update libinfo.cc

* Update RunTime.pm

Co-authored-by: Lin <haibilin@a483e7be4c92.ant.amazon.com>
leezu and others added 29 commits June 19, 2020 14:46
@leezu
cmake: x86 options only on x86 and remove manual specification on CI (#…
c1b96f5 
…18588)

Use CMAKE_SYSTEM_PROCESSOR to detect target architecture and make x86 related
options available only when compiling for x86. Remove the code turning these
options manually off on CI.

Remove ANDROID cmake option which was used to decide if -lpthread needs to be
specified explicitly (on most Linux systems) or not (on Android). Instead
auto-detect the behavior.
@eric-haibin-lin
Switch to cached op in the testing suite (#18579)
c1098aa 
* add default ctx to cachedop fwd

* add test

* perl fix

* initial commit

* update sparse tests

* add aux_states

* fix aux-state type

* fix some tests

* fix check symbolic forwrad/backward

* fix symbolic grad check

* arg_dict fixes

* support init ops

* support forward only graph

* fix check symbolic backward stype

* add missing file

* replace extension test bind

* replace bind with _bind

* simplify backward_mul implementation

* small fix

* drop contrib.sparseembedding

* remove simple_bind in test sparse ops

* use simple_bind

* replave simple bind in quantization

* fix aux index

* update amp simple_bind calls

* drop ifft

* fix a bug found in subgraph op

* add aux_array method

* replace symbols

* minor fix

* fix executor default context

* fix import

* bug fix for nd.where

* add subgraph test

* fix forward grad req

* fix batch dot dtype

* remove unused code

* fix slice dtype

* fix attach grad

* remove tests for non-existing sparse ops

* MXCachedOpGetOptimizedSymbol

* fix foreach test

* enhance err msg

* skip failed test

* add docs

* add docs

* fix lint

* fix lint, remove quantization

* fix lint

* fix lint

* fix lint

* fix build and import

* fix import

* fix perl call

* fix test

* remove perl binding

* remove reshape test

* fix profiler, trt

* remove tensorrt test

* remove quantization tests

* fix import

* fix conflcit

* fix lint

* skip buggy test

Co-authored-by: EC2 Default User <ec2-user@ip-172-31-81-80.ec2.internal>
Co-authored-by: Lin <haibilin@a483e7be4c92.ant.amazon.com>
@eric-haibin-lin
graph executor c api removal (#18598)
2fbec60 
* add default ctx to cachedop fwd

* add test

* perl fix

* initial commit

* update sparse tests

* add aux_states

* fix aux-state type

* fix some tests

* fix check symbolic forwrad/backward

* fix symbolic grad check

* arg_dict fixes

* support init ops

* support forward only graph

* fix check symbolic backward stype

* add missing file

* replace extension test bind

* replace bind with _bind

* simplify backward_mul implementation

* small fix

* drop contrib.sparseembedding

* remove simple_bind in test sparse ops

* use simple_bind

* replave simple bind in quantization

* fix aux index

* update amp simple_bind calls

* drop ifft

* fix a bug found in subgraph op

* add aux_array method

* replace symbols

* minor fix

* fix executor default context

* fix import

* bug fix for nd.where

* add subgraph test

* fix forward grad req

* fix batch dot dtype

* remove unused code

* fix slice dtype

* fix attach grad

* remove tests for non-existing sparse ops

* MXCachedOpGetOptimizedSymbol

* fix foreach test

* enhance err msg

* skip failed test

* add docs

* add docs

* fix lint

* fix lint, remove quantization

* fix lint

* fix lint

* fix lint

* fix build and import

* fix import

* remove scala, R, julia, perl bindings

* remove cpp, matlab bindings

* fix perl call

* fix test

* remove perl binding

* remove reshape test

* fix profiler, trt

* remove tensorrt test

* remove quantization tests

* fix import

* fix conflcit

* fix lint

* skip buggy test

* remove clojure

* remove executor c api

* remove amalgamation

* fix build

* move executor folder

* fix import

* fix lint

* fix cpp pcakge

* fix predict cpp

* fix cpp make

* remove jnilint

* remove cpp package tset

* remove julia test pipeline

* disable numpy tests

* disable compat test for delete

Co-authored-by: EC2 Default User <ec2-user@ip-172-31-81-80.ec2.internal>
Co-authored-by: Lin <haibilin@a483e7be4c92.ant.amazon.com>
@cool-RR
Use chain.from_iterable in artifact_repository.py (#18578)
56cfd9c
@ys2843
redirect api reference on v-master to v1.6 (#18607)
74fcb99 
* redirect api reference on v-master to v1.6

* update R docs
@mk-61
Allow input reordering duing Gluon / CachedOp graph transformations (#…
4b86c32 
…17949)

* Initial commit of input reordering in Gluon

* Add test for Gluon input reorder

* Fix backward in CachedOp for input reordering

* Fix test_input_reorder for backward pass

* Fix merge error in NaiveCachedOp

* Include correct header for std::iota

Co-authored-by: Vladimir Cherepanov <vcherepanov@nvidia.com>
@acphile
Update tutorials (#18609)
acf2d27 
Update docs according to new Block APIs (#18413)
@RuRo
use new mxnet.gluon.block APIs (#18601)
1fcc7ea
@leezu
Update disclaimer wording (#18616)
3f555f8
@szhengac
add epsilon to adamax (#18532)
e4c93e3 
Co-authored-by: Ubuntu <ubuntu@ip-172-31-92-136.ec2.internal>
@ys2843
add version check on installation guide (#18587)
c9dcdd1
@ys2843
fix julia api redirect (#18613)
ecbda07
@ys2843
fix contrib interleaved_matmul_selfatt_valatt not render correctly (#…
8ee4600 
…18621)
@szhengac
Add LANS optimizer (#18620)
d6c3578 
* add lans optimizer

* fix

* fix

Co-authored-by: Zheng <shzheng@a483e789dd93.ant.amazon.com>
@ciyongch
Enhance license checker to cover multiple license header and md files (…
b12abbf 
…#18633)
@szha
Remove mention of nightly in pypi (#18635)
becb9ca
@access2rohit
Improve performance of broadcast_axis on CPU (#17882)
638622f 
* adding comments explaining code optimizations

* fixing broadcast_axis kernel to int32

* fixing slice_axis kernel to int32

* combining CPU and GPU implementation method signatures and cleaned up
code

* adding new broadcast_axis to np_matmul

Co-authored-by: Rohit Kumar Srivastava <srivastava.141@buckeyemail.osu.edu>
@xiaoxia42 @hzfan
[Numpy] FFI: tril_indices (#18546)
2158106 
* add numpy tril_indices ffi

* Update src/api/operator/numpy/np_matrix_op.cc

Co-authored-by: Haozheng Fan <hzfan9@outlook.com>

Co-authored-by: Haozheng Fan <hzfan9@outlook.com>
@anko-intel
Fix BatchNorm backward synchronization (#18644)
37bed6e 
* Add test for BatchNorm running variables synchronization

* Fix BatchNorm backward synchronization

It fixes issue #18610
@bgawrych
Fix softmax, logsoftmax failed on empty ndarray (#18602)
9a122ca 
* Fix failing empty array (log_)softmax

* Modify test for npx (log_)softmax
@TaoLv
update to onednn v1.4 (#18273)
a8c8dea
@ys2843
Clipboard refactor (#18605)
0c8b6b2 
* refactor clipboard

* make lang getter more extensible

* trigger ci
@leezu
build.py --no-pull (#18589)
d1b2cd9 
Add --no-pull option which disables overwriting the local docker cache based on CI docker cache. It is useful when locally changing Dockerfiles.
@leezu
Mark test_get_symbol as garbage_expected (#18595)
c519e0e
@Yiyan66
[numpy] FFI flip, rollaxis, stack (#18614)
d1b0a09 
* flip

* rollaxis

* stack

* fixed

* retrigger ci

Co-authored-by: Ubuntu <ubuntu@ip-172-31-18-97.us-east-2.compute.internal>
@Yiyan66
[numpy] Fix less/greater bug with scalar input (#18642)
6462887 
* fix ffi

* fix less/greater error

* back

* submodule

* fixed

Co-authored-by: Ubuntu <ubuntu@ip-172-31-8-94.us-east-2.compute.internal>
@ys2843
User Feedback Widget (#18639)
54c0155 
* user feedback widget implementation

* add user feedback widget to python docs site

* update margin

* add apache license

* one more license

* turn off feedback widget on python site

* update copy

* format

* add event value field

* turn on widget on Python site
@xidulu
Gluon.probability (#18403)
b4b8b80 
* package created

* mvn WIP

* normal wip, to be tested

* update

* docstring added, normal mostly done

* add test file

* Bernoulli WIP

* bernoulli wip

* bernoulli doc done

* dense variational WIP

* add kl infra

* implement normal kl method

* refactor kl

* add not implemented handling, rename kl_storage

* add  abstract method and Categorical class

* rewrite logit2prob prob2logit for multiclass support

* normal broadcast_to implemented

* categorical mostly done

* update distributions/utils.py

* add dot ahead of import

* fix normal F

* bernoulli, normal brief tests implemented

* add hybridize tests

* transformation infras done

* affine transformation, implemented tested

* add tests cases

* add sum_right_most

* fix get F bug

* compose transform implemented, tested

* fix

* add event_dim

* fetch mvn from upstremm

* clean code, implement normal cdf and tests

* constraint in bernoulli done

* fix constraint

* finish half normal

* add cached_property

* add test on cached_property

* add more features to distribution and constratins

* change constraint

* fix bernoulli

* add independent

* add independent tests

* update naming of cached_property

* revert

* add constraints

* add Cat

* add Stack for imperative mode

* add Stack for imperative mode

* add bernoulli entropy

* categorical WIP

* categorical sampling implemented

* finish categorical log_prob, sampling

* enumerate_support finished

* polish StochasticBlock, add test

* add test for stochastic sequential

* clean loss list in __call__

* fix affine, implement sigmoid, softmax

* add gumbel, relaxed bernoulli

* relaxed one-hot sampling implemented

* gamma done

* gamma, dirichlet implemented

* beta done

* gumbel softmax log-likelihood implemented

* refactor tests, implement exponential, fix compose transform

* weibull implemented, transformed distribution cdf icdf added

* pareto implemented

* uniform wip

* uniform done

* rewrite lgamma, implement chi2

* fix chi2 scale

* F distributiion done

* t implemented

* fix tiny problem

* cauchy done

* add half cauchy

* multinomial done, tests to be added

* add multinomial test

* MVN done, tests todo

* mvn polished

* fix a few precison issues

* add erf, erfinv unified api and learnable transform

* fix mvn attribute check

* MVN done

* poisson done

* hack poisson for size support

* geometric finished

* negative binomial done

* binomial done

* implement some kl

* add more kl

* refactor kl test

* add more kl

* binomial kl todo

* change constraint logical op implement

* implement gamma entropy

* finish beta dirchlet entropy

* finishi all entropy

* kl finished

* add constraint test

* domain map done

* remove bayesian dense

* fix tiny problems

* add kl uniform normal

* add kl tests

* acquire patch from upstream

* add some doc

* finish doc

* refactor kl test(WIP)

* add more kl, fix float32 underflow issue

* make sampling more stable

* handle inconsistent mode

* replace boolean idx with np.where

* fix file name

* add more doc

* add constraint check

* add half_normal/cauchy pdf cdf support check

* fix import problem

* change nosetest to pytest

* remove buggy lines

* change alias register path

* attempt to fix ci

* fix lint, change a few tests

* fix lint

* modify hybrid sequential

* fix lint

* change import order

* add test gluon probability v2

* fix hybridize flag

* change implementation of stochastic block

* fix lint

* fix comments

* fix block

* modify domain map

* add raises for improper add_loss

* add raises for improper add_loss

* add extra cases

* change collectLoss decorator to mandatory

* skip stochastic block tests

* remove test cases

* put gpu tests back

* add test_gluon_stochastic_block back

* remove export test

* put a test back

* tiny refactor

* add memory leak flag

* small changes

Co-authored-by: Zheng <shzheng@a483e789dd93.ant.amazon.com>
@ys2843
fix broken installation widget - remove empty entries (#18661)
348ab4d
@jinboci jinboci merged commit cf87b37 into jinboci:master Jul 8, 2020
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