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3053 release *_dist.py tests memory to avoid OOM #3537

Merged
merged 12 commits into from
Dec 24, 2021
Merged

3053 release *_dist.py tests memory to avoid OOM #3537

merged 12 commits into from
Dec 24, 2021

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wyli
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@wyli wyli commented Dec 22, 2021 •
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Fixes #3053

Description

to address the OOM issue when running tests:

  • DistCall now releases any potential gpu memory cache.
  • this PR moves the *_dist.py test cases out of unit tests, runtests.sh --disttests now becomes the only method to trigger distributed tests, and it runs each test case independently.

Status

Ready

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Breaking change (fix or new feature that would cause existing functionality to change).
  • New tests added to cover the changes.
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests.
  • In-line docstrings updated.
  • Documentation updated, tested make html command in the docs/ folder.

wyli added 4 commits December 22, 2021 10:45
@wyli
adds min. memory testing utils
3fbc4fa 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
include valueerror for robust outcome
af43e08 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
ensure float
2e29c74 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli
msg improvements
87146f6 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli requested review from ericspod, Nic-Ma and rijobro December 22, 2021 10:57
@wyli wyli marked this pull request as draft December 22, 2021 13:28
@wyli wyli force-pushed the 3053-skip-test-when-nomemory branch from b5d8a7e to a9991c0 Compare December 22, 2021 17:04
@wyli wyli force-pushed the 3053-skip-test-when-nomemory branch from f1f2af3 to 5f44fd1 Compare December 22, 2021 22:49
@wyli
separate disttests
da02476 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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wyli commented Dec 23, 2021 •
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update the tests with a few improvements:

  • *_dist.py tests now check the memory availability first (get memory by device id is via nvidia-smi, but CUDA_VISIBILE_DEVICES might hide the real id, so this is not useful.)
  • DistCall now releases any potential gpu memory cache
  • looks like the python unittest runner is not compatible with the distributed test cases because the memory is not released across test cases, so I move the *_dist.py test cases out of unit tests.

wyli
wyli commented Dec 23, 2021
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@wyli
update based on comments
f31e9d3 
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
@wyli wyli force-pushed the 3053-skip-test-when-nomemory branch from 06a5195 to f31e9d3 Compare December 23, 2021 14:10
@wyli wyli marked this pull request as ready for review December 23, 2021 15:06
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wyli commented Dec 23, 2021

/build

@wyli wyli changed the title 3053 skip test - insufficient memory 3053 release *_dist.py tests memory to avoid OOM Dec 23, 2021
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wyli commented Dec 23, 2021

/build

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wyli commented Dec 23, 2021

/build

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wyli commented Dec 23, 2021

/build

Nic-Ma
Nic-Ma approved these changes Dec 23, 2021
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Looks good to me.
@IsaacYangSLA @madil90 Could you please help double confirm?

Thanks in advance.

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wyli commented Dec 24, 2021

/build

@wyli wyli enabled auto-merge (squash) December 24, 2021 09:21
@wyli wyli merged commit 7f23f38 into Project-MONAI:dev Dec 24, 2021
@wyli wyli deleted the 3053-skip-test-when-nomemory branch December 24, 2021 10:05
wyli added a commit that referenced this pull request Jan 4, 2022
@wyli
3053 release *_dist.py tests memory to avoid OOM (#3537)
f5f460d 
* adds min. memory testing utils

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* include valueerror for robust outcome

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* ensure float

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* msg improvements

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update threshold

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* remove ref

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* separate disttests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Can-Zhao added a commit that referenced this pull request Jan 5, 2022
@Can-Zhao @drbeh
@Nic-Ma @wyli @monai-bot @yiheng-wang-nv @rijobro @ebrahimebrahim @ericspod @pre-commit-ci
rebase dev and add box utils (#3586)
dd74c59 
* 3415 Update WSIReader (#3417)

* Update WSIReader level/location/size calculation

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* Update location downsampling

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* Update tests and add a new test case

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* Update few names and logics

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* Fix the dependency issue

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* Check for imagecodecs + tifffile

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* Remove new test case that uses too much memory

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* Add new case and ignore level=0 for TiffFile

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* Address comments

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* update create_file_basename (#3436)

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* Update TiffFile backend in WSIReader (#3438)

* Update TiffFile backend to read only the entire image

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* 3429 Enhance the scalar write logic of TensorBoardStatsHandler (#3431)

* [DLMED] extract write logic

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* [DLMED] update according to comments

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* [DLMED] update according to comments

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* 3430 support dataframes and streams in CSVDataset (#3440)

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* [DLMED] enhance CSV iterable dataset

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* 3293 Remove extra deep supervision modules of DynUNet (#3427)

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* update based on comments

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* improve error message if reader nott available (#3457)

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* deprecate reduction (#3464)

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* 3444 Add DatasetFunc (#3456)

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* [DLMED] update rtol for CI

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* Add missing components to API doc (#3468)

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* [DLMED] add missing components

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* [DLMED] fix test

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* 3466 3467 Add `channel_wise` and correct doc-string (#3469)

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* [DLMED] fix typo

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* [DLMED] remove cls (#3475)

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* [DLMED] update according to comments

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* fix link error (#3488)

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* 3465 Support string as dtype (#3478)

* [DLMED] support string dtype

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* [DLMED] fix typo

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* [DLMED] enhance dtype in ToCupy

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* [DLMED] update to 0.4.7 (#3483)

Signed-off-by: Nic Ma <nma@nvidia.com>

* Improve NVTX Range Naming (#3484)

* Update to not include number for the name of the first range

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* Update CuCIM and TorchVision wrappers to include name

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* Update nvtx range to append undelying class for wrapper tranforms

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* Add new test cases to cover changes

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* Update cucim and torchvision check

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* 3471 3491 Add example images for intensity transforms (#3494)

* [DLMED] add missing images

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix 3471

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix AsDiscrete

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* Make bending energy loss invariant to resolution (#3493)

* make bending energy loss invariant to resolution

fixes #3485

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>

* set BendingEnergyLoss default normalize to False

Maybe it's more important that the default behavior match usage of the
term "bending energy" elsewhere, rather than that it be the most
convenient behavior.

Signed-off-by: Ebrahim Ebrahim <ebrahim.ebrahim@kitware.com>

* Removes redundant casting -- ensure tuple (#3495)

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 3498 Correct `kwargs` arg for `convert_to_torchscript` (#3499)

* [DLMED] correct kwargs

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* [DLMED] fix grammar

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* update tests with 1.10.1 (#3500)

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* 3501 Add dict version SavitzkyGolaySmoothd (#3502)

* [DLMED] add SavitzkyGolaySmoothd

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* [DLMED] fix typo

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* [DLMED] update according to comments

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* remove file (#3507)

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* avoid 60.0.0 (#3514)

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* [DLMED] add 6 new transform images (#3512)

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* support of reversed indexing (#3508)

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* Adding Torchscript utility functions (#3138)

* Adding Torchscript utility functions

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* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* [MONAI] python code formatting

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for more information, see https://pre-commit.ci

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* 3517 Refine AddCoordinateChannels transform (#3524)

* [DLMED] change to utility transforms

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* [DLMED] enhance args

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* 3521 Copyright header update (#3522)

* adds missing item

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* update the contributing guide

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* update copyright headers

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* 3521 - adds a util to check the licence info (#3523)

* util to check the licence info

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* update flags

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* update based on comments

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* 3350 Remove PyTorch 1.5.x related logic and mark versions for all new APIs (#3526)

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* 3533 Update PyTorch docker to 21.12 (#3534)

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* 3531 Add args to subclass of CacheDataset (#3532)

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* 3525 Fix invertible issue in OneOf compose (#3530)

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* 3535 - drop python 36 support (#3536)

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* 3552 - runtest.sh defaults to no build/install (#3555)

* runtest.sh defaults to no build/install

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* following test case conventions for multiprocessing

- adding `_dist` to multiprocessing test cases
- decouple multiprocessing LMDB tests from `test_lmdbdataset`

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* exclude lmdbdataset tests in min_tests

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* Remove apply_same_field (#3556)

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* [DLMED] fix mypy errors (#3562)

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* 3559 Enhance `DatasetSummary` for several points (#3560)

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* [DLMED] enhance data type

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix pickle issue

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Wenqi Li <wenqil@nvidia.com>

* add box util in monai/data

* add box util in monai/data

* [pre-commit.ci] pre-commit suggestions (#3568)

updates:
- [github.com/pre-commit/pre-commit-hooks: v4.0.1 → v4.1.0](pre-commit/pre-commit-hooks@v4.0.1...v4.1.0)
- [github.com/asottile/pyupgrade: v2.29.0 → v2.31.0](asottile/pyupgrade@v2.29.0...v2.31.0)
- [github.com/asottile/yesqa: v1.2.3 → v1.3.0](asottile/yesqa@v1.2.3...v1.3.0)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* 3565 - adds metadata when loading dicom series (#3566)

* adds metadata when loading dicom series

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes timed tests

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* update based on comments

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 3580 - create codeql-analysis.yml (#3579)

* Create codeql-analysis.yml

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* build cpp

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes Multiplication result converted to larger type

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* fixes url parsing

Signed-off-by: Wenqi Li <wenqil@nvidia.com>

* 498 Add logger_handler to LrScheduleHandler (#3570)

* [DLMED] add log handler

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI tests

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix CI test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] test CI

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix logging

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] temp test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix wrong unit test

Signed-off-by: Nic Ma <nma@nvidia.com>

* [DLMED] fix wrong test cases

Signed-off-by: Nic Ma <nma@nvidia.com>

Co-authored-by: Behrooz <3968947+drbeh@users.noreply.github.com>
Co-authored-by: Nic Ma <nma@nvidia.com>
Co-authored-by: Wenqi Li <wenqil@nvidia.com>
Co-authored-by: monai-bot <monai.miccai2019@gmail.com>
Co-authored-by: Yiheng Wang <68361391+yiheng-wang-nv@users.noreply.github.com>
Co-authored-by: Richard Brown <33289025+rijobro@users.noreply.github.com>
Co-authored-by: Ebrahim Ebrahim <ebrahim.mt@gmail.com>
Co-authored-by: Eric Kerfoot <17726042+ericspod@users.noreply.github.com>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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Reviewers

@Nic-Ma Nic-Ma Nic-Ma approved these changes

@ericspod ericspod Awaiting requested review from ericspod

@rijobro rijobro Awaiting requested review from rijobro

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Distributed unit test fails regularly
2 participants
@wyli @Nic-Ma