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Bug 1837012 - python-pyriemann fails to build with Python 3.9: joblib.externals.loky.process_executor.TerminatedWorkerError: A worker process managed by the executor was unexpectedly terminated
Summary: python-pyriemann fails to build with Python 3.9: joblib.externals.loky.proces...
Keywords:
Status: CLOSED ERRATA
Alias: None
Product: Fedora
Classification: Fedora
Component: python-pyriemann
Version: 33
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Aniket Pradhan
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard: AcceptedFreezeException
: 1841769 (view as bug list)
Depends On: 1831128 1871994
Blocks: F33FTBFS F33FailsToInstall F33BetaFreezeException PYTHON39
TreeView+ depends on / blocked
 
Reported: 2020-05-18 16:30 UTC by Miro Hrončok
Modified: 2020-09-14 23:43 UTC (History)
8 users (show)

Fixed In Version: python-pyriemann-0.2.6-5.fc33
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2020-09-14 23:43:55 UTC
Type: Bug
Embargoed:

Attachments (Terms of Use)

Description Miro Hrončok 2020-05-18 16:30:26 UTC 
python-pyriemann fails to build with Python 3.9.0a6.


======================================================================
ERROR: Test prediction of MDM
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/builddir/build/BUILD/pyRiemann-0.2.6/tests/test_classification.py", line 62, in test_MDM_predict
    mdm.fit(covset, labels)
  File "/builddir/build/BUILDROOT/python-pyriemann-0.2.6-1.fc33.x86_64/usr/lib/python3.9/site-packages/pyriemann/classification.py", line 124, in fit
    self.covmeans_ = Parallel(n_jobs=self.n_jobs)(
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 934, in __call__
    self.retrieve()
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 833, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/usr/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 521, in wrap_future_result
    return future.result(timeout=timeout)
  File "/usr/lib64/python3.9/concurrent/futures/_base.py", line 440, in result
    return self.__get_result()
  File "/usr/lib64/python3.9/concurrent/futures/_base.py", line 389, in __get_result
    raise self._exception
joblib.externals.loky.process_executor.TerminatedWorkerError: A worker process managed by the executor was unexpectedly terminated. This could be caused by a segmentation fault while calling the function or by an excessive memory usage causing the Operating System to kill the worker. The exit codes of the workers are {EXIT(1)}

======================================================================
ERROR: Test Kmeans
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.9/site-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/builddir/build/BUILD/pyRiemann-0.2.6/tests/test_clustering.py", line 45, in test_Kmeans_init
    km.fit(covset)
  File "/builddir/build/BUILDROOT/python-pyriemann-0.2.6-1.fc33.x86_64/usr/lib/python3.9/site-packages/pyriemann/clustering.py", line 160, in fit
    res = Parallel(n_jobs=self.n_jobs, verbose=0)(
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 934, in __call__
    self.retrieve()
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 833, in retrieve
    self._output.extend(job.get(timeout=self.timeout))
  File "/usr/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 521, in wrap_future_result
    return future.result(timeout=timeout)
  File "/usr/lib64/python3.9/concurrent/futures/_base.py", line 440, in result
    return self.__get_result()
  File "/usr/lib64/python3.9/concurrent/futures/_base.py", line 389, in __get_result
    raise self._exception
  File "/usr/lib/python3.9/site-packages/joblib/externals/loky/_base.py", line 625, in _invoke_callbacks
    callback(self)
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 309, in __call__
    self.parallel.dispatch_next()
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 731, in dispatch_next
    if not self.dispatch_one_batch(self._original_iterator):
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch
    self._dispatch(tasks)
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 716, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File "/usr/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 510, in apply_async
    future = self._workers.submit(SafeFunction(func))
  File "/usr/lib/python3.9/site-packages/joblib/externals/loky/reusable_executor.py", line 150, in submit
    return super(_ReusablePoolExecutor, self).submit(
  File "/usr/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py", line 1022, in submit
    raise self._flags.broken
joblib.externals.loky.process_executor.TerminatedWorkerError: A worker process managed by the executor was unexpectedly terminated. This could be caused by a segmentation fault while calling the function or by an excessive memory usage causing the Operating System to kill the worker. The exit codes of the workers are {EXIT(1), EXIT(1)}
-------------------- >> begin captured logging << --------------------
concurrent.futures: ERROR: exception calling callback for <Future at 0x7f1448018580 state=finished raised TerminatedWorkerError>
Traceback (most recent call last):
  File "/usr/lib/python3.9/site-packages/joblib/externals/loky/_base.py", line 625, in _invoke_callbacks
    callback(self)
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 309, in __call__
    self.parallel.dispatch_next()
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 731, in dispatch_next
    if not self.dispatch_one_batch(self._original_iterator):
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 759, in dispatch_one_batch
    self._dispatch(tasks)
  File "/usr/lib/python3.9/site-packages/joblib/parallel.py", line 716, in _dispatch
    job = self._backend.apply_async(batch, callback=cb)
  File "/usr/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 510, in apply_async
    future = self._workers.submit(SafeFunction(func))
  File "/usr/lib/python3.9/site-packages/joblib/externals/loky/reusable_executor.py", line 150, in submit
    return super(_ReusablePoolExecutor, self).submit(
  File "/usr/lib/python3.9/site-packages/joblib/externals/loky/process_executor.py", line 1022, in submit
    raise self._flags.broken
joblib.externals.loky.process_executor.TerminatedWorkerError: A worker process managed by the executor was unexpectedly terminated. This could be caused by a segmentation fault while calling the function or by an excessive memory usage causing the Operating System to kill the worker. The exit codes of the workers are {EXIT(1), EXIT(1)}
--------------------- >> end captured logging << ---------------------

----------------------------------------------------------------------
Ran 99 tests in 5.932s

FAILED (errors=2)

For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.9/fedora-rawhide-x86_64/01388166-python-pyriemann/

For all our attempts to build python-pyriemann with Python 3.9, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/package/python-pyriemann/

Testing and mass rebuild of packages is happening in copr. You can follow these instructions to test locally in mock if your package builds with Python 3.9:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/

Let us know here if you have any questions.

Python 3.9 will be included in Fedora 33. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.9.
A build failure prevents us from testing all dependent packages (transitive [Build]Requires), so if this package is required a lot, it's important for us to get it fixed soon.
We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.
Comment 1 Miro Hrončok 2020-05-25 13:02:37 UTC 
This comment is mass posted to all bugs blocking the Python 3.9 tracker, sorry if it is not 100 % relevant. When in doubt, please ask.


The Python 3.9 rebuild is in progress in a Koji side tag.

If you fix this bug, please don't rebuild the package in regular rawhide, but do it in the side tag with:

    $ fedpkg build --target=f33-python

The rebuild is progressing slowly and it is possible this package won't have all the required build dependencies yet. If that's the case, please just leave the fix committed and pushed and we will eventually rebuild it for you.

You are not asked to go and try rebuild all the missing dependencies yourself. If you know there is a bootstrap loop in the dependencies, let me know and we can untangle it together.

If you want to test your fix or reproduce the failure, you can still use the Copr repo mentioned in the initial comment of this bug: https://copr.fedorainfracloud.org/coprs/g/python/python3.9/
Comment 2 Miro Hrončok 2020-05-29 07:12:17 UTC 
Python 3.9 update: The f33-python side tag is currently being merged.

New builds in f33-python are no longer possible, but python3 is not yet updated to Python 3.9 in rawhide. You can check when Python is Python 3.9 with:

    $ koji wait-repo f33-build --build python3.9-3.9.0~b1-3.fc3

And build the packages normally after that.
Comment 3 Tomáš Hrnčiar 2020-06-11 09:56:06 UTC 
*** Bug 1841769 has been marked as a duplicate of this bug. ***
Comment 4 Igor Raits 2020-06-18 12:54:19 UTC 
Hello,

This is the first reminder (step 3 from https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/#_package_removal_for_long_standing_ftbfs_and_fti_bugs).

If you know about this problem and are planning on fixing it, please acknowledge so by setting the bug status to ASSIGNED. If you don't have time to maintain this package, consider orphaning it, so maintainers of dependent packages realize the problem.
Comment 5 Igor Raits 2020-07-09 20:37:19 UTC 
Hello,

This is the second reminder (step 4 from https://docs.fedoraproject.org/en-US/fesco/Fails_to_build_from_source_Fails_to_install/#_package_removal_for_long_standing_ftbfs_and_fti_bugs).

If you know about this problem and are planning on fixing it, please acknowledge so by setting the bug status to ASSIGNED. If you don't have time to maintain this package, consider orphaning it, so maintainers of dependent packages realize the problem.
Comment 6 Ankur Sinha (FranciscoD) 2020-07-10 10:06:04 UTC 
On my radar.
Comment 7 Ben Cotton 2020-08-11 13:31:53 UTC 
This bug appears to have been reported against 'rawhide' during the Fedora 33 development cycle.
Changing version to 33.
Comment 8 Miro Hrončok 2020-08-22 10:30:59 UTC 
Hello. This comment is mass posted to all 16 bugzillas for packages that failed to rebuild with Python 3.9 (and, in most cases, also fail to install on Fedora 33 and 34). Apologies if some of the suggestions or questions don't apply 100%.

Fedora 33 Beta Freeze starts next week on Tuesday, 2020-08-25. I haven't spammed this bugzilla because it is in ASSIGNED, or I've seen upstream has been notified.

Please consider what to do here. Is this failure critical? For example, can a test be temporarily skipped to make this package build? Is it possible to fix or workaround the failure before Fedora 33 Beta? Or before Fedora 33 Final? If not, would it make sense to retire the package (even temporarily) before the release to unblock updates from Fedora 31 or Fedora 32?

In case you need any assistance with a Python-related problem with the build, don't hesitate to let me know and I'll try to have a look.

Thank you!
Comment 9 Charalampos Stratakis 2020-09-07 17:37:01 UTC 
https://src.fedoraproject.org/rpms/python-joblib/pull-request/2 should fix the issue with pyriemann
Comment 10 Fedora Update System 2020-09-10 17:43:53 UTC 
FEDORA-2020-4f07527b3e has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-4f07527b3e
Comment 11 Fedora Update System 2020-09-10 17:43:55 UTC 
FEDORA-2020-4f07527b3e has been submitted as an update to Fedora 33. https://bodhi.fedoraproject.org/updates/FEDORA-2020-4f07527b3e
Comment 12 Fedora Blocker Bugs Application 2020-09-10 17:44:45 UTC 
Proposed as a Freeze Exception for 33-beta by Fedora user churchyard using the blocker tracking app because:

 The package does not install without the proposed update.
Comment 13 Kamil Páral 2020-09-14 14:22:02 UTC 
Accepted as a Beta freeze exception:
https://pagure.io/fedora-qa/blocker-review/issue/79
Comment 14 Fedora Update System 2020-09-14 23:43:55 UTC 
FEDORA-2020-4f07527b3e has been pushed to the Fedora 33 stable repository.
If problem still persists, please make note of it in this bug report.
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