{bio}[foss/2021b] DeepCell v0.11.1 #15704

fizwit · 2022-06-16T18:02:40Z

(created using eb --new-pr)
requires PR #15551

fizwit · 2022-06-23T14:20:12Z

Dependency is in dev branch
EasyBuildError: 'Missing dependencies: TensorFlow/2.7.1-foss-2021b-CUDA-11.4.1
--from-pr #14990

Spektral --from-pr #15551 (open PR) held up by TensorFlow

fizwit · 2022-07-12T22:26:24Z

deps are merged

…asyconfigs into 20220616110207_new_pr_DeepCell0111

boegelbot · 2022-07-13T10:50:17Z

@fizwit: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/2662453634
Output from first failing test suite run:

ERROR: test_conflicts (test.easyconfigs.easyconfigs.EasyConfigTest)
Check whether any conflicts occur in software dependency graphs.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 325, in test_conflicts
    self.assertFalse(check_conflicts(self.ordered_specs, modules_tool(), check_inter_ec_conflicts=False),
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: spektral/1.1.0-foss-2021b-CUDA-11.4.1 (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_graph (test.easyconfigs.easyconfigs.EasyConfigTest)
Unit test that builds a full dependency graph.
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 312, in test_dep_graph
    dep_graph(fn, self.ordered_specs)
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: spektral/1.1.0-foss-2021b-CUDA-11.4.1 (no easyconfig file or existing module found)'

======================================================================
ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 811, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "test/easyconfigs/easyconfigs.py", line 277, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 215, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 461, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 324, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: spektral/1.1.0-foss-2021b-CUDA-11.4.1 (no easyconfig file or existing module found)'

----------------------------------------------------------------------
Ran 15040 tests in 879.218s

FAILED (errors=3)
ERROR: Not all tests were successful

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Please talk to my owner @boegel if you notice you me acting stupid),
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fizwit · 2022-08-25T21:59:51Z

waiting for dev merge of spektral-1.1.0-foss-2021b-CUDA-11.4.1.eb pr #15551

jfgrimm

As decided in issue #16330, we have deprecated the use of True to signify a system-toolchain dependency (#16384), in favour of the more intuitive SYSTEM template constant. Due to the change in the test suite, please run eb --sync-pr-with-develop 15704 and update the PR to use SYSTEM instead.

…asyconfigs into 20220616110207_new_pr_DeepCell0111

easybuild/easyconfigs/d/DeepCell/DeepCell-0.11.1-foss-2021b-CUDA-11.4.1.eb

boegelbot · 2023-04-25T10:26:15Z

@fizwit: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/4795902554
Output from first failing test suite run:

ERROR: test_dep_versions_per_toolchain_generation (test.easyconfigs.easyconfigs.EasyConfigTest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 854, in test_dep_versions_per_toolchain_generation
    for ec in self.ordered_specs:
  File "test/easyconfigs/easyconfigs.py", line 279, in ordered_specs
    EasyConfigTest.resolve_all_dependencies()
  File "test/easyconfigs/easyconfigs.py", line 217, in resolve_all_dependencies
    cls._parsed_easyconfigs, modules_tool(), retain_all_deps=True)
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 463, in resolve_dependencies
    raise_error_missing_deps(totally_missing, extra_msg="no easyconfig file or existing module found")
  File "/opt/hostedtoolcache/Python/2.7.18/x64/lib/python2.7/site-packages/easybuild/tools/robot.py", line 326, in raise_error_missing_deps
    raise EasyBuildError(error_msg)
EasyBuildError: 'Missing dependencies: spektral/1.1.0-foss-2021b-CUDA-11.4.1 (no easyconfig file or existing module found)'

======================================================================
FAIL: test__parse_easyconfig_DeepCell-0.11.1-foss-2021b-CUDA-11.4.1.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for easyconfig DeepCell-0.11.1-foss-2021b-CUDA-11.4.1.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1544, in innertest
    template_easyconfig_test(self, spec_path)
  File "test/easyconfigs/easyconfigs.py", line 1519, in template_easyconfig_test
    self.fail(error_msg)
AssertionError: use of `True` to indicate the system toolchain for dependency CUDA is deprecated, use the `SYSTEM` template constant instead

----------------------------------------------------------------------
Ran 16894 tests in 667.808s

FAILED (failures=1, errors=1)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

Use up to date toolchain for `CUDA` - `SYSTEM`

verdurin · 2023-05-30T14:27:08Z

@boegelbot please test @ generoso

boegelbot · 2023-05-30T14:30:13Z

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

PR test command 'EB_PR=15704 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_15704 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10881

Test results coming soon (I hope)...

Details

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it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-05-30T14:34:52Z

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/32ef9b3c7e5f38a0b828b4314c1478ca for a full test report.

verdurin · 2023-05-30T14:46:06Z

@boegelbot please test @ jsc-zen2

boegelbot · 2023-05-30T14:47:09Z

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

PR test command 'EB_PR=15704 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_15704 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2675

Test results coming soon (I hope)...

Details

- notification for comment with ID 1568567964 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-05-30T14:50:00Z

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/b5e45e876024a91e7c44c1e87500e25b for a full test report.

verdurin · 2023-05-30T15:12:46Z

@fizwit I think we're ready to go, if you can add some comments to the patches, as noted above.

fizwit · 2023-05-30T20:23:09Z

@verdurin comments added, checksums updated

boegelbot · 2023-05-30T21:25:32Z

@fizwit: Tests failed in GitHub Actions, see https://github.com/easybuilders/easybuild-easyconfigs/actions/runs/5125919090
Output from first failing test suite run:

FAIL: test__parse_easyconfig_DeepCell-0.11.1-foss-2021b-CUDA-11.4.1.eb (test.easyconfigs.easyconfigs.EasyConfigTest)
Test for easyconfig DeepCell-0.11.1-foss-2021b-CUDA-11.4.1.eb
----------------------------------------------------------------------
Traceback (most recent call last):
  File "test/easyconfigs/easyconfigs.py", line 1544, in innertest
    template_easyconfig_test(self, spec_path)
  File "test/easyconfigs/easyconfigs.py", line 1519, in template_easyconfig_test
    self.fail(error_msg)
AssertionError: use of `True` to indicate the system toolchain for dependency CUDA is deprecated, use the `SYSTEM` template constant instead

----------------------------------------------------------------------
Ran 17131 tests in 673.495s

FAILED (failures=1)
ERROR: Not all tests were successful

bleep, bloop, I'm just a bot (boegelbot v20200716.01)
Please talk to my owner @boegel if you notice me acting stupid),
or submit a pull request to https://github.com/boegel/boegelbot fix the problem.

Use SYSTEM for CUDA

…asyconfigs into 20220616110207_new_pr_DeepCell0111

verdurin · 2023-06-01T15:59:20Z

@boegelbot please test @ generoso

boegelbot · 2023-06-01T16:00:10Z

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

PR test command 'EB_PR=15704 EB_ARGS= EB_CONTAINER= /opt/software/slurm/bin/sbatch --job-name test_PR_15704 --ntasks=4 ~/boegelbot/eb_from_pr_upload_generoso.sh' executed!

exit code: 0
output:

Submitted batch job 10887

Test results coming soon (I hope)...

Details

- notification for comment with ID 1572322543 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

verdurin · 2023-06-01T16:00:46Z

Test report by @verdurin
SUCCESS
Build succeeded for 1 out of 1 (1 easyconfigs in total)
easybuild-c7.novalocal - Linux CentOS Linux 7.9.2009, x86_64, Intel Xeon Processor (Skylake, IBRS), Python 3.6.8
See https://gist.github.com/verdurin/0babdcc7e423b91dbeb3ad62cb2335b8 for a full test report.

boegelbot · 2023-06-01T16:07:08Z

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

PR test command 'EB_PR=15704 EB_ARGS= /opt/software/slurm/bin/sbatch --mem-per-cpu=4000M --job-name test_PR_15704 --ntasks=8 ~/boegelbot/eb_from_pr_upload_jsc-zen2.sh' executed!

exit code: 0
output:

Submitted batch job 2680

Test results coming soon (I hope)...

Details

- notification for comment with ID 1572329842 processed

Message to humans: this is just bookkeeping information for me,
it is of no use to you (unless you think I have a bug, which I don't).

boegelbot · 2023-06-01T16:10:03Z

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/9e0670708a1d8c12989b81df63402ed1 for a full test report.

verdurin

Looks fine.

…asyconfigs into 20220616110207_new_pr_DeepCell0111

boegel · 2025-06-16T15:18:05Z

@boegelbot please test @ jsc-zen3-a100
CORE_CNT=16

boegelbot · 2025-06-16T15:20:11Z

@boegel: Request for testing this PR well received on jsczen3l1.int.jsc-zen3.fz-juelich.de

PR test command 'if [[ develop != 'develop' ]]; then EB_BRANCH=develop ./easybuild_develop.sh 2> /dev/null 1>&2; EB_PREFIX=/home/boegelbot/easybuild/develop source init_env_easybuild_develop.sh; fi; EB_PR=15704 EB_ARGS= EB_CONTAINER= EB_REPO=easybuild-easyconfigs EB_BRANCH=develop /opt/software/slurm/bin/sbatch --job-name test_PR_15704 --ntasks="16" --partition=jsczen3g --gres=gpu:1 ~/boegelbot/eb_from_pr_upload_jsc-zen3.sh' executed!

exit code: 0
output:

Submitted batch job 6782

Test results coming soon (I hope)...

Details

- notification for comment with ID 2977060673 processed

Message to humans: this is just bookkeeping information for me,
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boegelbot · 2025-06-16T15:20:57Z

Test report by @boegelbot
FAILED
Build succeeded for 0 out of 4 (1 easyconfigs in total)
jsczen3g1.int.jsc-zen3.fz-juelich.de - Linux Rocky Linux 9.5, x86_64, AMD EPYC-Milan Processor (zen3), 1 x NVIDIA NVIDIA A100 80GB PCIe, 555.42.06, Python 3.9.21
See https://gist.github.com/boegelbot/b8d18a257e5e7a5da6a44874d072a26b for a full test report.

boegel · 2025-06-16T15:26:39Z

I gave this a chance, but since it doesn't work at first attempt, I'll go ahead and close this...

Closing this since foss/2021b is deprecated or no longer supported, see https://docs.easybuild.io/policies/toolchains

Sorry for not getting back to this @fizwit

If this is still relevant, please consider opening a new pull request using a more recent toolchain

DeepCell 0.11.1

380e58b

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Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

72024bc

…asyconfigs into 20220616110207_new_pr_DeepCell0111

jfgrimm reviewed Oct 17, 2022

View reviewed changes

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

0a91e73

…asyconfigs into 20220616110207_new_pr_DeepCell0111

verdurin requested changes Apr 25, 2023

View reviewed changes

easybuild/easyconfigs/d/DeepCell/DeepCell-0.11.1-foss-2021b-CUDA-11.4.1.eb Show resolved Hide resolved

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Update DeepCell-0.11.1-foss-2021b-CUDA-11.4.1.eb

0101469

Use up to date toolchain for `CUDA` - `SYSTEM`

comment patches

076e835

verdurin and others added 3 commits May 31, 2023 10:21

Update DeepCell-0.11.1-foss-2021b-CUDA-11.4.1.eb

e8bd089

Use SYSTEM for CUDA

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

2d234cd

…asyconfigs into 20220616110207_new_pr_DeepCell0111

fix CUDA dependency specification

dc1aeed

verdurin closed this Jun 1, 2023

verdurin reopened this Jun 1, 2023

verdurin approved these changes Jun 1, 2023

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verdurin added this to the next release (4.7.3?) milestone Jun 1, 2023

verdurin added the new label Jun 1, 2023

boegel modified the milestones: 4.8.0, release after 4.8.0 Jul 6, 2023

boegel modified the milestones: 4.8.1, release after 4.8.1 Sep 9, 2023

boegel modified the milestones: next release (4.8.2), release after 4.8.2 Oct 27, 2023

boegel modified the milestones: next release (4.9.0), release after 4.9.0 Dec 29, 2023

boegel modified the milestones: 4.9.1, release after 4.9.1 Apr 3, 2024

boegel modified the milestones: 4.9.2, release after 4.9.2 Jun 8, 2024

boegel modified the milestones: 4.9.3, release after 4.9.3 Sep 11, 2024

boegel modified the milestones: release after 4.9.4, release after 5.0.0 Mar 18, 2025

boegel modified the milestones: next release (5.1.0), 5.x May 23, 2025

boegel changed the title ~~DeepCell 0.11.1~~ {bio}[foss/2021b] DeepCell v0.11.1 Jun 16, 2025

Merge branch 'develop' of https://github.com/easybuilders/easybuild-e…

733dad1

…asyconfigs into 20220616110207_new_pr_DeepCell0111

boegel closed this Jun 16, 2025

{bio}[foss/2021b] DeepCell v0.11.1 #15704

{bio}[foss/2021b] DeepCell v0.11.1 #15704

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