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[ci] prevent getting incompatible dask and distributed versions #4054

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merged 3 commits into from
Mar 9, 2021

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jameslamb
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Python CI jobs in several pull requests are failing right now. For example, see #4048 (comment) and https://dev.azure.com/lightgbm-ci/lightgbm-ci/_build/results?buildId=9396&view=logs&j=c28dceab-947a-5848-c21f-eef3695e5f11&t=fa158246-17e2-53d4-5936-86070edbaacf .

All of the Dask tests are failing with an error like this

E AttributeError: 'HighLevelGraph' object has no attribute 'dask_distributed_pack'

This error occurs when you try to use dask 2021.2.0 with distributed 2021.3.0. For more documentation on that, see dask/dask#7331.

Specifically, LightGBM's CI is hitting this error because it installs dask and distributed from the default anaconda channel, which is updated more slowly than conda-forge.

I see the following in the logs from one of the failed jobs.

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    ...
    dask-2021.2.0              |     pyhd3eb1b0_0           5 KB
    dask-core-2021.2.0         |     pyhd3eb1b0_0         643 KB
    ...
    distributed-2021.3.0       |   py39h06a4308_0         1.0 MB

This PR proposes installing dask and distributed from conda-forge, and putting an explicit version floor of 2021.3.0 on those libraries.

@jameslamb jameslamb marked this pull request as ready for review March 9, 2021 03:17
@jameslamb jameslamb removed the request for review from Laurae2 March 9, 2021 03:17
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Thanks for the prompt fix!
I'm OK with these changes as they are really needed to unblock our CI. However, I'd like to remind that mixing installations from different conda channels can be very messy and always leads to significant increasing of installation time and consumed memory.
ContinuumIO/anaconda-issues#11604 (comment)

.ci/test.sh Outdated Show resolved Hide resolved
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So we should revert migration to conda-forge right after the needed versions will be available on default conda channel.

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
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So we should revert migration to conda-forge right after the needed versions will be available on default conda channel.

ok

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several Azure jobs failed with what looks like infrastructure problems

##[error]We stopped hearing from agent lgbubb5e00004AJ. Verify the agent machine is running and has a healthy network connection. Anything that terminates an agent process, starves it for CPU, or blocks its network access can cause this error. For more information, see: https://go.microsoft.com/fwlink/?linkid=846610
Agent: lgbubb5e00004AJ
Started: Today at 9:20 AM
Duration: 51m 51s

https://dev.azure.com/lightgbm-ci/lightgbm-ci/_build/results?buildId=9406&view=logs&j=5ea309bb-dea2-5bcb-538b-5c76ecf159eb

Rebuilding by pushing an empty commit, so the logs are still there to go back and look at.

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I'm not sure what's happening, but I see 2 check-docs tasks. One is marked failed and one marked successful.

image

Weirdly, that failing one isn't blocking merge and it didn't cause Static Analysis / all-successful to fail. So maybe it is just a "ghost job" created accidentally by GitHub?

Since there was a successful one and since this PR is blocking other PRs, I'm going to merge this. But it's still very strange.

@jameslamb jameslamb merged commit 4e9c976 into master Mar 9, 2021
@jameslamb jameslamb deleted the fix/dask-ci-version branch March 9, 2021 17:20
@jameslamb jameslamb removed the blocking label Mar 9, 2021
StrikerRUS added a commit that referenced this pull request Mar 15, 2021
jameslamb pushed a commit that referenced this pull request Mar 16, 2021
StrikerRUS added a commit that referenced this pull request Mar 25, 2021
* [docs]Add alt text on images

* Update docs/GPU-Windows.rst

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Update docs/GPU-Windows.rst

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Apply suggestions from code review

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Apply suggestions from code review

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* Merge main branch commit updates (#1)

* [docs] Add alt text to image in Parameters-Tuning.rst (#4035)

* [docs] Add alt text to image in Parameters-Tuning.rst

Add alt text to Leaf-wise growth image, as part of #4028

* Update docs/Parameters-Tuning.rst

Co-authored-by: James Lamb <jaylamb20@gmail.com>

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* [ci] [R-package] upgrade to R 4.0.4 in CI (#4042)

* [docs] update description of deterministic parameter (#4027)

* update description of deterministic parameter to require using with force_row_wise or force_col_wise

* Update include/LightGBM/config.h

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* update docs

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [dask] Include support for init_score (#3950)

* include support for init_score

* use dataframe from init_score and test difference with and without init_score in local model

* revert refactoring

* initial docs. test between distributed models with and without init_score

* remove ranker from tests

* test value for root node and change docs

* comma

* re-include parametrize

* fix incorrect merge

* use single init_score and the booster_ attribute

* use np.float64 instead of float

* [ci] ignore untitle Jupyter notebooks in .gitignore (#4047)

* [ci] prevent getting incompatible dask and distributed versions (#4054)

* [ci] prevent getting incompatible dask and distributed versions

* Update .ci/test.sh

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* empty commit

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [ci] fix R CMD CHECK note about example timings (fixes #4049) (#4055)

* [ci] fix R CMD CHECK note about example timings (fixes #4049)

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* empty commit

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [ci] add CMake + R 3.6 test back (fixes #3469) (#4053)

* [ci] add CMake + R 3.6 test back (fixes #3469)

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Update .ci/test_r_package_windows.ps1

* -Wait and remove rtools40

* empty commit

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [dask] include multiclass-classification task in tests (#4048)

* include multiclass-classification task and task_to_model_factory dicts

* define centers coordinates. flatten init_scores within each partition for multiclass-classification

* include issue comment and fix linting error

* Update index.rst (#4029)

Add alt text to logo image

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* [dask] raise more informative error for duplicates in 'machines' (fixes #4057) (#4059)

* [dask] raise more informative error for duplicates in 'machines'

* uncomment

* avoid test failure

* Revert "avoid test failure"

This reverts commit 9442bdf.

* [dask] add tutorial documentation (fixes #3814, fixes #3838) (#4030)

* [dask] add tutorial documentation (fixes #3814, fixes #3838)

* add notes on saving the model

* quick start examples

* add examples

* fix timeouts in examples

* remove notebook

* fill out prediction section

* table of contents

* add line back

* linting

* isort

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* move examples under python-guide

* remove unused pickle import

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* set 'pending' commit status for R Solaris optional workflow (#4061)

* [docs] add Yu Shi to repo maintainers (#4060)

* Update FAQ.rst

* Update CODEOWNERS

* set is_linear_ to false when it is absent from the model file (fix #3778) (#4056)

* Add CMake option to enable sanitizers and build gtest (#3555)

* Add CMake option to enable sanitizer

* Set up gtest

* Address reviewer's feedback

* Address reviewer's feedback

* Update CMakeLists.txt

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* added type hint (#4070)

* [ci] run Dask examples on CI (#4064)

* Update Parallel-Learning-Guide.rst

* Update test.sh

* fix path

* address review comments

* [python-package] add type hints on Booster.set_network() (#4068)

* [python-package] add type hints on Booster.set_network()

* change behavior

* [python-package] Some mypy fixes (#3916)

* Some mypy fixes

* address James' comments

* Re-introduce pass in empty classes

* Update compat.py

Remove extra lines

* [dask] [ci] fix flaky network-setup test (#4071)

* [tests][dask] simplify code in Dask tests (#4075)

* simplify Dask tests code

* enable CI

* disable CI

* Revert "[ci] prevent getting incompatible dask and distributed versions (#4054)" (#4076)

This reverts commit 4e9c976.

* Fix parsing of non-finite values (#3942)

* Fix index out-of-range exception generated by BaggingHelper on small datasets.

Prior to this change, the line "score_t threshold = tmp_gradients[top_k - 1];" would generate an exception, since tmp_gradients would be empty when the cnt input value to the function is zero.

* Update goss.hpp

* Update goss.hpp

* Add API method LGBM_BoosterPredictForMats which runs prediction on a data set given as of array of pointers to rows (as opposed to existing method LGBM_BoosterPredictForMat which requires data given as contiguous array)

* Fix incorrect upstream merge

* Add link to LightGBM.NET

* Fix indenting to 2 spaces

* Dummy edit to trigger CI

* Dummy edit to trigger CI

* remove duplicate functions from merge

* Fix parsing of non-finite values.  Current implementation silently returns zero when input string is "inf", "-inf", or "nan" when compiled with VS2017, so instead just explicitly check for these values and fail if there is no match.  No attempt to optimise string allocations in this implementation since it is usually rarely invoked.

* Dummy commit to trigger CI

* Also handle -nan in double parsing method

* Update include/LightGBM/utils/common.h

Remove trailing whitespace to pass linting tests

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

Co-authored-by: matthew-peacock <matthew.peacock@whiteoakam.com>
Co-authored-by: Guolin Ke <guolin.ke@outlook.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

* [dask] remove unused imports from typing (#4079)

* Range check for DCG position discount lookup (#4069)

* Add check to prevent out of index lookup in the position discount table. Add debug logging to report number of queries found in the data.

* Change debug logging location so that we can print the data file name as well.

* Revert "Change debug logging location so that we can print the data file name as well."

This reverts commit 3981b34.

* Add data file name to debug logging.

* Move log line to a place where it is output even when query IDs are read from a separate file.

* Also add the out-of-range check to rank metrics.

* Perform check after number of queries is initialized.

* Update

* [ci] upgrade R CI scripts to work on Ubuntu 20.04 (#4084)

* [ci] install additional LaTeX packages in R CI jobs

* update autoconf version

* bump upper limit on package size to 100

* [SWIG] Add streaming data support + cpp tests (#3997)

* [feature] Add ChunkedArray to SWIG

* Add ChunkedArray
* Add ChunkedArray_API_extensions.i
* Add SWIG class wrappers

* Address some review comments

* Fix linting issues

* Move test to tests/test_ChunkedArray_manually.cpp

* Add test note

* Move ChunkedArray to include/LightGBM/utils/

* Declare more explicit types of ChunkedArray in the SWIG API.

* Port ChunkedArray tests to googletest

* Please C++ linter

* Address StrikerRUS' review comments

* Update SWIG doc & disable ChunkedArray<int64_t>

* Use CHECK_EQ instead of assert

* Change include order (linting)

* Rename ChunkedArray -> chunked_array files

* Change header guards

* Address last comments from StrikerRUS

* store all CMake files in one place (#4087)

* v3.2.0 release (#3872)

* Update VERSION.txt

* update appveyor.yml and configure

* fix Appveyor builds

Co-authored-by: James Lamb <jaylamb20@gmail.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: StrikerRUS <nekit94-12@hotmail.com>

* [ci] Bump version for development (#4094)

* Update .appveyor.yml

* Update cran-comments.md

* Update VERSION.txt

* update configure

Co-authored-by: James Lamb <jaylamb20@gmail.com>

* [ci] fix flaky Azure Pipelines jobs (#4095)

* Update test.sh

* Update setup.sh

* Update .vsts-ci.yml

* Update test.sh

* Update setup.sh

* Update .vsts-ci.yml

* Update setup.sh

* Update setup.sh

Co-authored-by: Subham Agrawal <34346812+subhamagrawal7@users.noreply.github.com>
Co-authored-by: James Lamb <jaylamb20@gmail.com>
Co-authored-by: shiyu1994 <shiyu_k1994@qq.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: jmoralez <jmoralz92@gmail.com>
Co-authored-by: marcelonieva7 <72712805+marcelonieva7@users.noreply.github.com>
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
Co-authored-by: Deddy Jobson <dedjob@hotmail.com>
Co-authored-by: Alberto Ferreira <AlbertoEAF@users.noreply.github.com>
Co-authored-by: mjmckp <mjmckp@users.noreply.github.com>
Co-authored-by: matthew-peacock <matthew.peacock@whiteoakam.com>
Co-authored-by: Guolin Ke <guolin.ke@outlook.com>
Co-authored-by: ashok-ponnuswami-msft <57648631+ashok-ponnuswami-msft@users.noreply.github.com>
Co-authored-by: StrikerRUS <nekit94-12@hotmail.com>

* Apply suggestions from code review

Co-authored-by: Nikita Titov <nekit94-08@mail.ru>

Co-authored-by: James Lamb <jaylamb20@gmail.com>
Co-authored-by: Subham Agrawal <34346812+subhamagrawal7@users.noreply.github.com>
Co-authored-by: shiyu1994 <shiyu_k1994@qq.com>
Co-authored-by: Nikita Titov <nekit94-08@mail.ru>
Co-authored-by: jmoralez <jmoralz92@gmail.com>
Co-authored-by: marcelonieva7 <72712805+marcelonieva7@users.noreply.github.com>
Co-authored-by: Philip Hyunsu Cho <chohyu01@cs.washington.edu>
Co-authored-by: Deddy Jobson <dedjob@hotmail.com>
Co-authored-by: Alberto Ferreira <AlbertoEAF@users.noreply.github.com>
Co-authored-by: mjmckp <mjmckp@users.noreply.github.com>
Co-authored-by: matthew-peacock <matthew.peacock@whiteoakam.com>
Co-authored-by: Guolin Ke <guolin.ke@outlook.com>
Co-authored-by: ashok-ponnuswami-msft <57648631+ashok-ponnuswami-msft@users.noreply.github.com>
Co-authored-by: StrikerRUS <nekit94-12@hotmail.com>
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