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{bio}[foss/2021a] BMTK v1.0.8#18863

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bedroge merged 2 commits intoeasybuilders:developfrom
stevenvdb:20230925164357_new_pr_BMTK108
Sep 27, 2023
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{bio}[foss/2021a] BMTK v1.0.8#18863
bedroge merged 2 commits intoeasybuilders:developfrom
stevenvdb:20230925164357_new_pr_BMTK108

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@stevenvdb stevenvdb commented Sep 25, 2023

(created using eb --new-pr)

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boegelbot commented Sep 25, 2023

@stevenvdb: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/6300990425
Output from first failing test suite run:

FAIL: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 332, in test_conflicts
    "No conflicts detected")
AssertionError: True is not false : No conflicts detected

======================================================================
FAIL: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/runner/work/easybuild-easyconfigs/easybuild-easyconfigs/test/easyconfigs/easyconfigs.py", line 898, in test_dep_versions_per_toolchain_generation
    self.assertFalse(multi_dep_vars, error_msg)
AssertionError: ['typing-extensions'] is not false : No multi-variant deps found for '^.*-(?P<tc_gen>20(1[89]|[2-9][0-9])[ab]).*\.eb$' easyconfigs:

found 2 variants of 'typing-extensions' dependency in easyconfigs using '2021a' toolchain generation
* version: 3.10.0.0; versionsuffix:  as dep for {'torchvision-0.11.3-foss-2021a.eb', 'Detectron2-0.6-foss-2021a.eb', 'sfftk-0.7.4-foss-2021a.eb', 'jax-0.3.9-foss-2021a.eb', 'dm-haiku-0.0.9-foss-2021a-CUDA-11.3.1.eb', 'rising-0.2.2-foss-2021a.eb', 'deepmedic-0.8.2-foss-2021a-CUDA-11.3.1.eb', 'bokeh-2.4.1-foss-2021a.eb', 'colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb', 'toil-5.8.0-foss-2021a.eb', 'cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb', 'AlphaFold-2.1.2-foss-2021a.eb', 'AlphaFold-2.2.2-foss-2021a-CUDA-11.3.1.eb', 'Megalodon-2.5.0-foss-2021a.eb', 'HD-BET-20220318-foss-2021a-CUDA-11.3.1.eb', 'flair-NLP-0.11.3-foss-2021a.eb', 'ont-remora-1.0.0-foss-2021a.eb', 'Albumentations-1.1.0-foss-2021a-CUDA-11.3.1.eb', 'cwltool-3.1.20221008225030-foss-2021a.eb', 'Megalodon-2.5.0-foss-2021a-CUDA-11.3.1.eb', 'deepmedic-0.8.2-foss-2021a.eb', 'PyTorch-1.11.0-foss-2021a-CUDA-11.3.1.eb', 'jax-0.2.24-foss-2021a.eb', 'topaz-0.2.5-foss-2021a-CUDA-11.3.1.eb', 'scArches-0.5.6-foss-2021a.eb', 'PyTorch-1.10.0-foss-2021a.eb', 'PyTorch-Lightning-1.5.9-foss-2021a.eb', 'Detectron2-0.6-foss-2021a-CUDA-11.3.1.eb', 'Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.11.0.eb', 'MONAI-0.8.0-foss-2021a.eb', 'TensorFlow-2.6.0-foss-2021a-CUDA-11.3.1.eb', 'imgaug-0.4.0-foss-2021a.eb', 'CLEASE-0.10.6-intel-2021a.eb', 'rising-0.2.2-foss-2021a-CUDA-11.3.1.eb', 'ont-remora-0.1.2-foss-2021a.eb', 'ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb', 'ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb', 'scib-metrics-0.3.3-foss-2021a.eb', 'TensorFlow-2.4.4-foss-2021a.eb', 'scikit-image-0.18.3-foss-2021a.eb', 'Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.6.0.eb', 'FastFold-20220729-foss-2021a-CUDA-11.3.1.eb', 'TensorFlow-2.6.0-foss-2021a.eb', 'histolab-0.4.1-foss-2021a.eb', 'torchdata-0.3.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb', 'n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb', 'cwltool-3.1.20221018083734-foss-2021a.eb', 'Horovod-0.28.1-foss-2021a-CUDA-11.3.1-PyTorch-1.12.1.eb', 'ONNX-1.11.0-foss-2021a.eb', 'neptune-client-0.16.2-foss-2021a.eb', 'torchvision-0.11.1-foss-2021a.eb', 'smooth-topk-1.0-20210817-foss-2021a.eb', 'torchvision-0.12.0-foss-2021a-PyTorch-1.11.0-CUDA-11.3.1.eb', 'scArches-0.5.6-foss-2021a-CUDA-11.3.1.eb', 'BMTK-1.0.8-foss-2021a.eb', 'medaka-1.5.0-foss-2021a.eb', 'PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb', 'skorch-0.11.0-foss-2021a-PyTorch-1.10.0.eb', 'torchvision-0.11.1-foss-2021a-CUDA-11.3.1.eb', 'skorch-0.11.0-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb', 'TensorFlow-2.5.3-foss-2021a.eb', 'ont-remora-0.1.2-foss-2021a-CUDA-11.3.1.eb', 'PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb', 'Transformers-4.20.1-foss-2021a.eb', 'topaz-0.2.5-foss-2021a.eb', 'AlphaFold-2.1.2-foss-2021a-CUDA-11.3.1.eb', 'flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb', 'CellRank-1.4.0-foss-2021a.eb', 'DeepMod2-0.0.1-foss-2021a.eb', 'PyTorch-Ignite-0.4.9-foss-2021a-CUDA-11.3.1.eb', 'OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb', 'Ray-project-1.13.0-foss-2021a.eb', 'eht-imaging-1.2.2-foss-2021a.eb', 'Horovod-0.22.1-foss-2021a-CUDA-11.3.1-TensorFlow-2.5.3.eb', 'dask-2021.9.1-foss-2021a.eb', 'Horovod-0.23.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb', 'batchgenerators-0.25-foss-2021a.eb', 'ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb', 'smooth-topk-1.0-20210817-foss-2021a-CUDA-11.3.1.eb', 'jax-0.3.9-foss-2021a-CUDA-11.3.1.eb', 'torchvision-0.11.3-foss-2021a-CUDA-11.3.1.eb', 'HD-BET-20220318-foss-2021a.eb', 'AlphaFold-2.2.2-foss-2021a.eb', 'OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb', 'imgaug-0.4.0-foss-2021a-CUDA-11.3.1.eb', 'arosics-1.7.6-foss-2021a.eb', 'Horovod-0.25.0-foss-2021a-CUDA-11.3.1-PyTorch-1.10.0.eb', 'DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb', 'TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb', 'PyTorch-1.12.1-foss-2021a.eb', 'GPyTorch-1.9.1-foss-2021a-CUDA-11.3.1.eb', 'jax-0.2.24-foss-2021a-CUDA-11.3.1.eb', 'ESM-2-2.0.0-foss-2021a.eb', 'DGL-0.9.1-foss-2021a-CUDA-11.3.1.eb', 'Braindecode-0.7-foss-2021a-PyTorch-1.10.0.eb', 'TensorFlow-2.5.3-foss-2021a-CUDA-11.3.1.eb', 'Cogent-8.0.0-foss-2021a.eb', 'PyTorch-Lightning-1.5.9-foss-2021a-CUDA-11.3.1.eb', 'redis-py-4.3.1-foss-2021a.eb', 'FMPy-0.3.2-foss-2021a.eb', 'ONNX-Runtime-1.10.0-foss-2021a.eb', 'cryoDRGN-1.0.0-beta-foss-2021a-CUDA-11.3.1.eb', 'PyImageJ-1.3.1-foss-2021a.eb', 'Braindecode-0.7-foss-2021a-PyTorch-1.10.0-CUDA-11.3.1.eb', 'scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb', 'PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb', 'MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb', 'cryoDRGN-0.3.5-foss-2021a-CUDA-11.3.1.eb', 'scvi-tools-0.16.4-foss-2021a.eb', 'scikit-allel-1.3.3-foss-2021a.eb'}
* version: 4.4.0; versionsuffix:  as dep for {'BMTK-1.0.8-foss-2021a.eb'}


----------------------------------------------------------------------
Ran 18118 tests in 916.028s

FAILED (failures=2)
ERROR: Not all tests were successful

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@bedroge bedroge added the new label Sep 26, 2023
@bedroge bedroge added this to the 4.x milestone Sep 26, 2023
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bedroge commented Sep 26, 2023

@boegelbot please test @ generoso

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bedroge commented Sep 26, 2023

Test report by @bedroge
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
bob-Latitude-5300 - Linux Ubuntu 22.04, x86_64, Intel(R) Core(TM) i7-8665U CPU @ 1.90GHz, Python 3.10.12
See https://gist.github.com/bedroge/85ba5a803a191cf0154444dc13da1deb for a full test report.

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boegelbot commented Sep 26, 2023

@bedroge: Request for testing this PR well received on login1

PR test command 'EB_PR=18863 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --job-name test_PR_18863 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 11783

Test results coming soon (I hope)...

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boegelbot commented Sep 26, 2023

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
cns1 - Linux Rocky Linux 8.5, x86_64, Intel(R) Xeon(R) CPU E5-2667 v3 @ 3.20GHz (haswell), Python 3.6.8
See https://gist.github.com/boegelbot/886bd25f1df45a021a371c777f43d9bb for a full test report.

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bedroge commented Sep 26, 2023

@boegelbot please test @ jsc-zen2

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boegelbot commented Sep 26, 2023

@bedroge: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18863 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18863 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 3433

Test results coming soon (I hope)...

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bedroge commented Sep 27, 2023

@boegelbot please test @ jsc-zen2

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boegelbot commented Sep 27, 2023

@bedroge: Request for testing this PR well received on jsczen2l1.int.jsc-zen2.easybuild-test.cluster

PR test command 'EB_PR=18863 EB_ARGS= EB_REPO=easybuild-easyconfigs /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_18863 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

  • exit code: 0
  • output:
Submitted batch job 3435

Test results coming soon (I hope)...

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boegelbot commented Sep 27, 2023

Test report by @boegelbot
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
jsczen2c1.int.jsc-zen2.easybuild-test.cluster - Linux Rocky Linux 8.5, x86_64, AMD EPYC 7742 64-Core Processor (zen2), Python 3.6.8
See https://gist.github.com/boegelbot/152789eb531874f160661d06b84ee41d for a full test report.

bedroge
bedroge approved these changes Sep 27, 2023
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Looks good to me.

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bedroge commented Sep 27, 2023

Going in, thanks @stevenvdb!

@bedroge bedroge merged commit 0fe42a0 into easybuilders:develop Sep 27, 2023
@bedroge bedroge modified the milestones: 4.x, next release (4.8.2?) Sep 27, 2023
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