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Bug 1825464 - petsc4py fails to build with Python 3.9: openmpi: undefined symbol: ScalePermstructInit
Summary: petsc4py fails to build with Python 3.9: openmpi: undefined symbol: ScalePerm...
Keywords:
Status: CLOSED NOTABUG
Alias: None
Product: Fedora
Classification: Fedora
Component: petsc4py
Version: rawhide
Hardware: Unspecified
OS: Unspecified
unspecified
unspecified
Target Milestone: ---
Assignee: Antonio T. (sagitter)
QA Contact: Fedora Extras Quality Assurance
URL:
Whiteboard:
Depends On:
Blocks: PYTHON39
TreeView+ depends on / blocked
 
Reported: 2020-04-18 09:51 UTC by Miro Hrončok
Modified: 2020-04-18 11:50 UTC (History)
4 users (show)

Fixed In Version:
Doc Type: If docs needed, set a value
Doc Text:
Clone Of:
Environment:
Last Closed: 2020-04-18 11:50:21 UTC
Type: Bug
Embargoed:


Attachments (Terms of Use)

Description Miro Hrončok 2020-04-18 09:51:46 UTC
petsc4py fails to build with Python 3.9.0a5.

+ /usr/bin/python3 setup.py test
running test
Traceback (most recent call last):
  File "/builddir/build/BUILD/petsc4py-3.13.0/petsc4py-openmpi/setup.py", line 270, in <module>
    main()
  File "/builddir/build/BUILD/petsc4py-3.13.0/petsc4py-openmpi/setup.py", line 267, in main
    run_setup()
  File "/builddir/build/BUILD/petsc4py-3.13.0/petsc4py-openmpi/setup.py", line 119, in run_setup
    setup(packages     = ['petsc4py',
  File "/usr/lib/python3.9/site-packages/setuptools/__init__.py", line 144, in setup
    return distutils.core.setup(**attrs)
  File "/usr/lib64/python3.9/distutils/core.py", line 148, in setup
    dist.run_commands()
  File "/usr/lib64/python3.9/distutils/dist.py", line 966, in run_commands
    self.run_command(cmd)
  File "/usr/lib64/python3.9/distutils/dist.py", line 985, in run_command
    cmd_obj.run()
  File "/builddir/build/BUILD/petsc4py-3.13.0/petsc4py-openmpi/setup.py", line 258, in run_testsuite
    err = main(args)
  File "test/runtests.py", line 203, in main
    package = import_package(options, pkgname)
  File "test/runtests.py", line 85, in import_package
    package.init(args, arch=options.arch)
  File "build/lib.linux-x86_64-3.9/petsc4py/__init__.py", line 42, in init
    PETSc = petsc4py.lib.ImportPETSc(arch)
  File "build/lib.linux-x86_64-3.9/petsc4py/lib/__init__.py", line 29, in ImportPETSc
    return Import('petsc4py', 'PETSc', path, arch)
  File "build/lib.linux-x86_64-3.9/petsc4py/lib/__init__.py", line 73, in Import
    module = import_module(pkg, name, path, arch)
  File "build/lib.linux-x86_64-3.9/petsc4py/lib/__init__.py", line 58, in import_module
    with f: return imp.load_module(fullname, f, fn, info)
  File "/usr/lib64/python3.9/imp.py", line 242, in load_module
    return load_dynamic(name, filename, file)
  File "/usr/lib64/python3.9/imp.py", line 342, in load_dynamic
    return _load(spec)
  File "<frozen importlib._bootstrap>", line 711, in _load
  File "<frozen importlib._bootstrap>", line 666, in _load_unlocked
  File "<frozen importlib._bootstrap>", line 565, in module_from_spec
  File "<frozen importlib._bootstrap_external>", line 1108, in create_module
  File "<frozen importlib._bootstrap>", line 228, in _call_with_frames_removed
ImportError: /usr/lib64/openmpi/lib/libHYPRE.so.2.1: undefined symbol: ScalePermstructInit


Maybe something si wrong with openmpi?


For the build logs, see:
https://copr-be.cloud.fedoraproject.org/results/@python/python3.9/fedora-rawhide-x86_64/01334757-petsc4py/

For all our attempts to build petsc4py with Python 3.9, see:
https://copr.fedorainfracloud.org/coprs/g/python/python3.9/package/petsc4py/

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 Antonio T. (sagitter) 2020-04-18 10:25:15 UTC
Hypre-2.18.1 is not ready for superlu_dist-6.3.1
Re-base Copr package database with latest releases.

Comment 2 Miro Hrončok 2020-04-18 10:57:08 UTC
> Re-base Copr package database with latest releases.

Neither hypre nor superlu_dist is included in our copr. I'll hit rebuild of openmpi, than petsc4py.

Comment 3 Antonio T. (sagitter) 2020-04-18 11:22:11 UTC
It's need to build with this superlu_dist release (required by Hypre):

* Mon Apr 13 2020 Dave Love <loveshack> - 1:6.1.1-3
- Introduce epoch and revert incompatible change to 6.3.1

Comment 5 Miro Hrončok 2020-04-18 11:50:21 UTC
Sorry for the noise.


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