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Reduce Auto3DSeg tests memory footprint and running time#5689

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wyli merged 11 commits intoProject-MONAI:devfrom
mingxin-zheng:fix-5604
Dec 9, 2022
Merged

Reduce Auto3DSeg tests memory footprint and running time#5689
wyli merged 11 commits intoProject-MONAI:devfrom
mingxin-zheng:fix-5604

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@mingxin-zheng mingxin-zheng commented Dec 8, 2022

Signed-off-by: Mingxin Zheng 18563433+mingxin-zheng@users.noreply.github.com

Fixes #5604

also fixes #5697 by 5b1865e

Description

  • Update the Auto3DSeg templates
    • SwinUNETR optionally uses pretrain weights
    • Fix bug when multiple GPUs are used in a tiny datasets, step_size will be zero.
  • Change image size in the test dataset from (64, 64, 64) to (24, 24, 24)
  • Change num_epochs from 2 to 1
  • Remove an unnecessary unit test in test_auto3dseg_hpo (check the algorithm can run in another folder, which is not very useful and may bring bugs in the future).

Types of changes

  • Non-breaking change (fix or new feature that would not break existing functionality).
  • Integration tests passed locally by running ./runtests.sh -f -u --net --coverage.
  • Quick tests passed locally by running ./runtests.sh --quick --unittests --disttests.

Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
Comment thread monai/apps/auto3dseg/bundle_gen.py Outdated
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wyli commented Dec 8, 2022

/integration-test

mingxin-zheng and others added 2 commits December 8, 2022 23:06
Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
@wyli wyli enabled auto-merge (squash) December 8, 2022 16:23
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wyli commented Dec 8, 2022

/build

wyli
wyli previously approved these changes Dec 8, 2022
@wyli wyli dismissed their stale review December 8, 2022 17:18

tests

@wyli wyli disabled auto-merge December 8, 2022 17:18
Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
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/integration-test

Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
Signed-off-by: Mingxin Zheng <18563433+mingxin-zheng@users.noreply.github.com>
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wyli commented Dec 9, 2022

/build

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The test quick-py3 (macOS-latest) gives the following error:

======================================================================
FAIL: test_sampling (tests.test_weighted_random_sampler_dist.DistributedWeightedRandomSamplerTest)

Traceback (most recent call last):
File "/Users/runner/work/MONAI/MONAI/tests/utils.py", line 521, in _wrapper
assert results.get(), "Distributed call failed."
AssertionError: Distributed call failed.


Ran 9971 tests in 3399.369s

FAILED (failures=1, skipped=896)

wyli added 2 commits December 9, 2022 08:39
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
Signed-off-by: Wenqi Li <wenqil@nvidia.com>
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wyli commented Dec 9, 2022

/build

@wyli wyli enabled auto-merge (squash) December 9, 2022 08:42
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wyli commented Dec 9, 2022

/build

@wyli wyli merged commit 4f584a9 into Project-MONAI:dev Dec 9, 2022
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quick-py3 (macOS-latest) gives error test_auto3dseg_hpo OOM frequently

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