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Date: Sun, 25 Apr 2021 08:54:44 +0000
From: portscout@FreeBSD.org
To: python@freebsd.org
Subject: FreeBSD ports you maintain which are out of date
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Dear port maintainer,
The portscout new distfile checker has detected that one or more of your
ports appears to be out of date. Please take the opportunity to check
each of the ports listed below, and if possible and appropriate,
submit/commit an update. If any ports have already been updated, you can
safely ignore the entry.
You will not be e-mailed again for any of the port/version combinations
below.
Full details can be found at the following URL:
http://portscout.freebsd.org/python@freebsd.org.html
Port | Current version | New version
------------------------------------------------+-----------------+------------
devel/py-pip | 20.3.4 | 21.1
------------------------------------------------+-----------------+------------
If any of the above results are invalid, please check the following page
for details on how to improve portscout's detection and selection of
distfiles on a per-port basis:
http://portscout.freebsd.org/info/portscout-portconfig.txt
Reported by: portscout!
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To: python@FreeBSD.org
Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Sun, 25 Apr 2021 11:23:22 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255237
--- Comment #2 from p5B2E9A8F@t-online.de ---
After py37-importlib-metadata-3.3.0_1 installed net-im/gajim is broken.
This is an ugly bug as it breaks peoples communication.=20
Please edit severity from "Affects Only Me" to an appropriate one.
Traceback (most recent call last):
File "/usr/local/lib/python3.7/site-packages/gajim/application.py", line =
232,
in _startup
from gajim.gui_interface import Interface
File "/usr/local/lib/python3.7/site-packages/gajim/gui_interface.py", line
63, in <module>
from gajim.groupchat_control import GroupchatControl
File "/usr/local/lib/python3.7/site-packages/gajim/groupchat_control.py",
line 75, in <module>
from gajim.gui.groupchat_settings import GroupChatSettings
File
"/usr/local/lib/python3.7/site-packages/gajim/gtk/groupchat_settings.py", l=
ine
23, in <module>
from .settings import SettingsBox
File "/usr/local/lib/python3.7/site-packages/gajim/gtk/settings.py", line=
23,
in <module>
from gajim.common import passwords
File "/usr/local/lib/python3.7/site-packages/gajim/common/passwords.py", =
line
33, in <module>
backends =3D keyring.backend.get_all_keyring()
File "/usr/local/lib/python3.7/site-packages/keyring/util/__init__.py", l=
ine
22, in wrapper
func.always_returns =3D func(*args, **kwargs)
File "/usr/local/lib/python3.7/site-packages/keyring/backend.py", line 21=
4,
in get_all_keyring
_load_plugins()
File "/usr/local/lib/python3.7/site-packages/keyring/backend.py", line 19=
8,
in _load_plugins
for ep in metadata.entry_points(group=3D'keyring.backends'):
TypeError: entry_points() got an unexpected keyword argument 'group'
--=20
You are receiving this mail because:
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Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Sun, 25 Apr 2021 15:07:31 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255237
Yuri Victorovich <yuri@freebsd.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Severity|Affects Only Me |Affects Many People
--=20
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Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Sun, 25 Apr 2021 15:45:05 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255237
Yuri Victorovich <yuri@freebsd.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Blocks| |255395
Referenced Bugs:
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255395
[Bug 255395] security/py-keyring: Is broken, missing dependencies
--=20
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Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Sun, 25 Apr 2021 15:51:08 +0000
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--- Comment #3 from Yuri Victorovich <yuri@freebsd.org> ---
devel/py-importlib-metadata is required to unbreak security/py-keyring, see
bug#255395
--=20
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Subject: [Bug 253815] lang/python38: switch default version of python from
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Date: Sun, 25 Apr 2021 17:56:33 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D253815
Antoine Brodin <antoine@FreeBSD.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Flags|exp-run? |exp-run+
Assignee|portmgr@FreeBSD.org |kai@FreeBSD.org
--- Comment #81 from Antoine Brodin <antoine@FreeBSD.org> ---
Exp-run looks fine
--=20
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Subject: [Bug 253815] lang/python38: switch default version of python from
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D253815
--- Comment #82 from commit-hook@FreeBSD.org ---
A commit in branch main references this bug:
URL:
https://cgit.FreeBSD.org/ports/commit/?id=3D210ee04dd3c3f2e82cd3130e412866a=
182066859
commit 210ee04dd3c3f2e82cd3130e412866a182066859
Author: Kai Knoblich <kai@FreeBSD.org>
AuthorDate: 2021-04-25 18:54:27 +0000
Commit: Kai Knoblich <kai@FreeBSD.org>
CommitDate: 2021-04-25 18:54:27 +0000
*: Add UPDATING entry of the Python 3.7 to 3.8 switchover
Add appropriately adapted upgrading instructions that have resulted
from the experience gained from the previous (Python 3.6 to 3.7)
switchover.
PR: 253815
UPDATING | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
--=20
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To: python@FreeBSD.org
Subject: [Bug 250379] www/py-cherrypy: fails to import with lang/python38 or
later
Date: Sun, 25 Apr 2021 19:00:03 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D250379
--- Comment #13 from commit-hook@FreeBSD.org ---
A commit in branch main references this bug:
URL:
https://cgit.FreeBSD.org/ports/commit/?id=3D7915fe9b3fce2721c82d041ebbe47cf=
0a47981c1
commit 7915fe9b3fce2721c82d041ebbe47cf0a47981c1
Author: Kai Knoblich <kai@FreeBSD.org>
AuthorDate: 2021-04-25 18:45:34 +0000
Commit: Kai Knoblich <kai@FreeBSD.org>
CommitDate: 2021-04-25 18:45:34 +0000
www/py-cherrypy: Fix runtime with Python 3.8 and onward
Backport patches from the 18.x release branch that uses the Python's
library "contextlib" instead of the external library "contextlib2".
The "contextlib2" library is a backported version which is required for
compatibility with Python 2.7 as the 17.x release of CherryPy is the
last one that has compatibility for Python 2.7.
Since the support for Python 2.7 has been removed in aa7a6c429ea6,
"contextlib2 is no longer needed for backward compatibility.
This is a transitional solution to fix the regression with Python 3.8
because an update to the 18.x release needs a bit more work and also
requires one or more new Python packages.
While I'm here:
* Sort variables according to the PHB and pet portclippy.
* Remove superfluous EXAMPLESDIR.
* Convert to newer options framework.
* Set NO_ARCH as there are no architecture specific files.
* Add "do-test" target to make future QA easier.
PR: 250379
Reported by: jbeich
Approved by: maintainer timeout (6+ months)
MFH: 2021Q2
www/py-cherrypy/Makefile | 43 ++++++++++++------=
----
.../files/patch-cherrypy_lib_sessions.py (new) | 27 ++++++++++++++
www/py-cherrypy/files/patch-setup.py (new) | 17 +++++++++
3 files changed, 68 insertions(+), 19 deletions(-)
--=20
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Subject: [Bug 253815] lang/python38: switch default version of python from
3.7 to 3.8
Date: Sun, 25 Apr 2021 19:00:04 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D253815
--- Comment #83 from commit-hook@FreeBSD.org ---
A commit in branch main references this bug:
URL:
https://cgit.FreeBSD.org/ports/commit/?id=3D6cd3db2d03cc544c5893e41dbbacd20=
00fcbd35a
commit 6cd3db2d03cc544c5893e41dbbacd2000fcbd35a
Author: Kai Knoblich <kai@FreeBSD.org>
AuthorDate: 2021-04-25 18:48:44 +0000
Commit: Kai Knoblich <kai@FreeBSD.org>
CommitDate: 2021-04-25 18:48:44 +0000
*: Switch default version of python and python3 from 3.7 to 3.8
PR: 253815
Reported by: VVD <vvd@unislabs.com>
Approved by: kai (python, maintainer)
Exp-run by: antoine
Mk/Uses/python.mk | 2 +-
Mk/bsd.default-versions.mk | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
--=20
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Subject: [Bug 253815] lang/python38: switch default version of python from
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Date: Sun, 25 Apr 2021 19:00:05 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D253815
--- Comment #84 from commit-hook@FreeBSD.org ---
A commit in branch main references this bug:
URL:
https://cgit.FreeBSD.org/ports/commit/?id=3D26d8faac23752e2fc666fb9aaf10366=
0c132360a
commit 26d8faac23752e2fc666fb9aaf103660c132360a
Author: Kai Knoblich <kai@FreeBSD.org>
AuthorDate: 2021-04-25 18:50:30 +0000
Commit: Kai Knoblich <kai@FreeBSD.org>
CommitDate: 2021-04-25 18:50:30 +0000
*: Bump a few ports after the Python 3.7 to 3.8 switchover
Bump the PORTREVISION of the following ports as the concurrent symlinks
change with a new default version of Python:
* devel/py-setuptools
* lang/cython
* math/py-numpy
This is a follow-up to 6cd3db2d03cc544c5893e41dbbacd2000fcbd35a .
PR: 253815
Approved by: kai (python, maintainer)
devel/py-setuptools/Makefile | 1 +
lang/cython/Makefile | 1 +
math/py-numpy/Makefile | 1 +
3 files changed, 3 insertions(+)
--=20
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Subject: [Bug 250379] www/py-cherrypy: fails to import with lang/python38 or
later
Date: Sun, 25 Apr 2021 19:14:25 +0000
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Kai Knoblich <kai@FreeBSD.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Flags| |merge-quarterly?
Status|Open |In Progress
--- Comment #14 from Kai Knoblich <kai@FreeBSD.org> ---
Thank you, Jan for the report and the reviewing of the earlier versions, an=
d to
James for creating the patches!
I plan to MFH'ing it in a few days, so I leave this bug open for now.
--=20
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Kai Knoblich <kai@FreeBSD.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Status|New |Closed
Resolution|--- |FIXED
Flags|maintainer-feedback?(python |maintainer-feedback+
|@FreeBSD.org) |
--- Comment #85 from Kai Knoblich <kai@FreeBSD.org> ---
All finished, thanks to VVD for reporting, many thanks to Antoine for the
multiple exp-runs and of course everyone else who was involved!
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To: python@FreeBSD.org
Subject: Problem reports for python@FreeBSD.org that need special attention
Date: Sun, 25 Apr 2021 21:00:08 +0000
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To view an individual PR, use:
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=(Bug Id).
The following is a listing of current problems submitted by FreeBSD users,
which need special attention. These represent problem reports covering
all versions including experimental development code and obsolete releases.
Status | Bug Id | Description
------------+-----------+---------------------------------------------------
Open | 205308 | devel/py-pip and devel/py-virtualenv don't aggree
Open | 240343 | x11-themes/plasma5-breeze-gtk: Fails to build if
Open | 242896 | lang/python*: Fail to package in poudriere (testp
Open | 251235 | net/py-urllib3: Update to 1.26.2
Open | 255013 | Mk/Uses/python.mk: Prepare infrastructure support
In Progress | 241416 | [NEW PORT] lang/python38
Open | 243937 | lang/python38: Fails to package in certain condit
Open | 224115 | devel/py-babel directory name != port name
New | 251626 | math/py-numpy: update to 1.19.4 (compatible with
New | 231555 | Mk/Uses/python.mk: Add USE_PYTHON=pytest
10 problems total for which you should take action.
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Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Mon, 26 Apr 2021 01:09:58 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255237
--- Comment #4 from Kubilay Kocak <koobs@FreeBSD.org> ---
(In reply to p5B2E9A8F from comment #2)
Please open a separate issue (regression) for this bug, this issue is for a
version update
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Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Mon, 26 Apr 2021 01:12:51 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255237
--- Comment #5 from Kubilay Kocak <koobs@FreeBSD.org> ---
(In reply to Yuri Victorovich from comment #3)
Can you clarify the issue dependency, an issue cant block a closed issue.
I'm guessing bug 255050 is the real blocked issue here as bug 255395 was cl=
osed
a dupe of it. Is that correct?
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Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Mon, 26 Apr 2021 01:18:12 +0000
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--- Comment #6 from Yuri Victorovich <yuri@freebsd.org> ---
(In reply to Kubilay Kocak from comment #5)
The closed one is a duplicate.
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Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Mon, 26 Apr 2021 01:19:40 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255237
--- Comment #7 from Kubilay Kocak <koobs@FreeBSD.org> ---
(In reply to Yuri Victorovich from comment #6)
Danke.
--=20
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Subject: [Bug 255237] devel/py-importlib-metadata: Update 3.3.0 -> 4.0.0
Date: Mon, 26 Apr 2021 02:31:57 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255237
--- Comment #8 from Steve Wills <swills@FreeBSD.org> ---
It seems to me, the problem is the update to py-keyring in 38825393978e, wh=
ich
lacked the dependency on importlib-metadata and was done without checking t=
he
version of importlib-metadata.
And further it seems that what should happen to solve that is that that com=
mit
to update py-keyring should be reverted and PORTEPOCH bumped on py-keyring,=
for
now.
Then, it should be re-done after importlib-metadata is updated, along with a
further change to add a dependency on importlib-metadata to the py-keyring
port.
But there's no need to MFH any of this, as the py-keyring update was done a=
fter
the branch was created.
For reference:
https://github.com/jaraco/keyring/compare/18.0.1...v23.0.1#diff-fa602a8a75d=
c9dcc92261bac5f533c2a85e34fcceaff63b3a3a81d9acde2fc52R28
https://cgit.freebsd.org/ports/commit/?id=3D38825393978e4606227947eeefa0624=
54e449b3e
https://cgit.freebsd.org/ports/tree/security/py-keyring/Makefile?h=3D2021Q2
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Subject: devel/py-setuptools : orphaned packages?
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Hi There,
After today's update for devel/py-setuptools, it left me with a whole bunch
or orphaned packages.
py37-authres-1.2.0 ? orphaned: mail/py-authres
py37-dnspython-1.16.0 ? orphaned: dns/py-dnspython
py37-fail2ban-0.11.2 ? orphaned: security/py-fail2ban
py37-milter-1.0.4 ? orphaned: mail/py-milter
py37-pyinotify-0.9.6 ? orphaned: devel/py-pyinotify
py37-pyspf-2.0.14 ? orphaned: mail/py-pyspf
py37-setuptools-44.0.0 < needs updating (port has 44.0.0_1)
py37-spf-engine-2.9.2 ? orphaned: mail/py-spf-engine
Are we now required to update Python to version 3.8 to use the new version
of setuptools?
I did not see anything in UPDATING regarding this.
Thanks,
Ken
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Tue, 27 Apr 2021 18:41:24 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255445
Bug ID: 255445
Summary: lang/python 3.8/3.9 SIGSEV core dumps in libthr
TrueNAS
Product: Ports & Packages
Version: Latest
Hardware: amd64
OS: Any
Status: New
Keywords: crash
Severity: Affects Many People
Priority: ---
Component: Individual Port(s)
Assignee: python@FreeBSD.org
Reporter: yocalebo@gmail.com
Flags: maintainer-feedback?(python@FreeBSD.org)
Assignee: python@FreeBSD.org
Seeing many TrueNAS (previously FreeNAS) users dump core on the main
middlewared process (python) starting with our version 12.0 release.
Relevant OS information:
12.2-RELEASE-p6 FreeBSD 12.2-RELEASE-p6 f2858df162b(HEAD) TRUENAS amd64
Python versions that experience the core dump:
Python 3.8.7
Python 3.9.4
When initially researching this, I did find a regression with threading and
python 3.8 on freeBSD and was able to resolve that particular problem by
backporting the commits:
https://github.com/python/cpython/commit/4d96b4635aeff1b8ad41d41422ce808ce0=
b971c8
and
https://github.com/python/cpython/commit/9ad58acbe8b90b4d0f2d2e139e38bb5aa3=
2b7fb6.
The reason why I backported those commits is because all of the core dumps =
that
I've analyzed are panic'ing in the same spot (or very close to it). For
example, here are 2 backtraces showing null-ptr dereference.
Core was generated by `python3.8: middlewared'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0 cond_signal_common (cond=3D<optimized out>) at
/truenas-releng/freenas/_BE/os/lib/libthr/thread/thr_cond.c:457
warning: Source file is more recent than executable.
457 mp =3D td->mutex_obj;
[Current thread is 1 (LWP 100733)]
(gdb) list
452 _sleepq_unlock(cvp);
453 return (0);
454 }
455
456 td =3D _sleepq_first(sq);
457 mp =3D td->mutex_obj;
458 cvp->__has_user_waiters =3D _sleepq_remove(sq, td);
459 if (PMUTEX_OWNER_ID(mp) =3D=3D TID(curthread)) {
460 if (curthread->nwaiter_defer >=3D MAX_DEFER_WAITERS=
) {
461 _thr_wake_all(curthread->defer_waiters,=20
(gdb) p *td
Cannot access memory at address 0x0
and another one
Core was generated by `python3.8: middlewared'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0 cond_signal_common (cond=3D<optimized out>) at
/truenas-releng/freenas/_BE/os/lib/libthr/thread/thr_cond.c:459warning: Sou=
rce
file is more recent than executable.
459 if (PMUTEX_OWNER_ID(mp) =3D=3D TID(curthread)) {
[Current thread is 1 (LWP 101105)]
(gdb) list
454 }
455
456 td =3D _sleepq_first(sq);
457 mp =3D td->mutex_obj;
458 cvp->__has_user_waiters =3D _sleepq_remove(sq, td);
459 if (PMUTEX_OWNER_ID(mp) =3D=3D TID(curthread)) {
460 if (curthread->nwaiter_defer >=3D MAX_DEFER_WAITERS=
) {
461 _thr_wake_all(curthread->defer_waiters,
462 curthread->nwaiter_defer);
463 curthread->nwaiter_defer =3D 0;
(gdb) p *mp
Cannot access memory at address 0x0
I'm trying to instrument a program to "stress" test threading (tearing down=
and
recreating etc etc) but I've been unsuccessful at tickling this particular
problem. The end-users that have seen this core dump sometimes go 1month +
without a problem. Hoping someone more knowledgeable can at least give me a
pointer or help me figure this one out. I have access to my VM that has all=
the
relevant core dumps available so if someone needs remote access to it to "p=
oke"
around, please let me know. You can reach me at caleb [at] ixsystems.com
--=20
You are receiving this mail because:
You are the assignee for the bug.=
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From: bugzilla-noreply@freebsd.org
To: python@FreeBSD.org
Subject: maintainer-feedback requested: [Bug 255445] lang/python 3.8/3.9
SIGSEV core dumps in libthr TrueNAS
Date: Tue, 27 Apr 2021 18:41:24 +0000
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Bugzilla Automation <bugzilla@FreeBSD.org> has asked freebsd-python (Nobody)
<python@FreeBSD.org> for maintainer-feedback:
Bug 255445: lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255445
--- Description ---
Seeing many TrueNAS (previously FreeNAS) users dump core on the main
middlewared process (python) starting with our version 12.0 release.
Relevant OS information:
12.2-RELEASE-p6 FreeBSD 12.2-RELEASE-p6 f2858df162b(HEAD) TRUENAS amd64
Python versions that experience the core dump:
Python 3.8.7
Python 3.9.4
When initially researching this, I did find a regression with threading and
python 3.8 on freeBSD and was able to resolve that particular problem by
backporting the commits:
https://github.com/python/cpython/commit/4d96b4635aeff1b8ad41d41422ce808ce0=
b971
c8
and
https://github.com/python/cpython/commit/9ad58acbe8b90b4d0f2d2e139e38bb5aa3=
2b7f
b6.
The reason why I backported those commits is because all of the core dumps =
that
I've analyzed are panic'ing in the same spot (or very close to it). For
example, here are 2 backtraces showing null-ptr dereference.
Core was generated by `python3.8: middlewared'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0 cond_signal_common (cond=3D<optimized out>) at
/truenas-releng/freenas/_BE/os/lib/libthr/thread/thr_cond.c:457
warning: Source file is more recent than executable.
457 mp =3D td->mutex_obj;
[Current thread is 1 (LWP 100733)]
(gdb) list
452 _sleepq_unlock(cvp);
453 return (0);
454 }
455
456 td =3D _sleepq_first(sq);
457 mp =3D td->mutex_obj;
458 cvp->__has_user_waiters =3D _sleepq_remove(sq, td);
459 if (PMUTEX_OWNER_ID(mp) =3D=3D TID(curthread)) {
460 if (curthread->nwaiter_defer >=3D MAX_DEFER_WAITERS) {
461 _thr_wake_all(curthread->defer_waiters,=20
(gdb) p *td
Cannot access memory at address 0x0
and another one
Core was generated by `python3.8: middlewared'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0 cond_signal_common (cond=3D<optimized out>) at
/truenas-releng/freenas/_BE/os/lib/libthr/thread/thr_cond.c:459warning: Sou=
rce
file is more recent than executable.
459 if (PMUTEX_OWNER_ID(mp) =3D=3D TID(curthread)) {
[Current thread is 1 (LWP 101105)]
(gdb) list
454 }
455
456 td =3D _sleepq_first(sq);
457 mp =3D td->mutex_obj;
458 cvp->__has_user_waiters =3D _sleepq_remove(sq, td);
459 if (PMUTEX_OWNER_ID(mp) =3D=3D TID(curthread)) {
460 if (curthread->nwaiter_defer >=3D MAX_DEFER_WAITERS) {
461 _thr_wake_all(curthread->defer_waiters,
462 curthread->nwaiter_defer);
463 curthread->nwaiter_defer =3D 0;
(gdb) p *mp
Cannot access memory at address 0x0
I'm trying to instrument a program to "stress" test threading (tearing down=
and
recreating etc etc) but I've been unsuccessful at tickling this particular
problem. The end-users that have seen this core dump sometimes go 1month +
without a problem. Hoping someone more knowledgeable can at least give me a
pointer or help me figure this one out. I have access to my VM that has all=
the
relevant core dumps available so if someone needs remote access to it to "p=
oke"
around, please let me know. You can reach me at caleb [at] ixsystems.com
From owner-freebsd-python@freebsd.org Tue Apr 27 19:01:57 2021
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From: bugzilla-noreply@freebsd.org
To: python@FreeBSD.org
Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Tue, 27 Apr 2021 19:01:56 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255445
Li-Wen Hsu <lwhsu@FreeBSD.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |lwhsu@FreeBSD.org
Status|New |Open
--- Comment #1 from Li-Wen Hsu <lwhsu@FreeBSD.org> ---
(In reply to yocalebo@gmail.com from comment #0)
Thanks for reporting this. To narrow down the cause and to verify the fix. =
Do
you think it's possible to:
- Have a minimal test case to reproduce the issue.
- Test it on vanilla FreeBSD, here it is 12.2-RELEASE, it will be nice if it
can be also tested on 13.0-RELEASE and -CURRENT.
I know that debugging threading issues are hard and you're trying to do the
first item, but we firstly need to reproduce this on an unmodified FreeBSD.
Also you mentioned back porting the two commits, does it help?
--=20
You are receiving this mail because:
You are the assignee for the bug.=
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To: python@FreeBSD.org
Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Tue, 27 Apr 2021 19:22:03 +0000
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--- Comment #2 from yocalebo@gmail.com <yocalebo@gmail.com> ---
(In reply to Li-Wen Hsu from comment #1)
Hi Li-Wen Hsu, thanks for the feedback. I will definitely use stock GENERIC
freeBSD 12.2 kernel. The hard part is instrumenting a program that causes t=
he
SIGSEV :(.
I can, however, confirm that stock 12.2 has a regression with threads on
py3.8.7. You can use this script to test it.
from multiprocessing.pool import ThreadPool
from datetime import datetime
class Broken(object):
def __init__(self):
self.pool =3D ThreadPool()
def __del__(self):
self.pool.close()
self.pool.join()
ohno =3D Broken()
date =3D datetime.now()
print(str(date), ohno)
Running that 52 times caused an indefinite hang ~19.2% of the time. After
cherry-picking the 2 commits I linked above, I confirmed that it resolved t=
he
"hangs". It never did reproduce a core dump.
Anyways, I'll keep trying to write a program that tickles the problem. If y=
ou
or anyone has any ideas reading this, I'm all ears at this point and will
happily try anything at this point :)
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Tue, 27 Apr 2021 19:29:53 +0000
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--- Comment #3 from Li-Wen Hsu <lwhsu@FreeBSD.org> ---
(In reply to yocalebo@gmail.com from comment #2)
> Running that 52 times caused an indefinite hang ~19.2% of the time. After=
cherry-picking the 2 commits I linked above, I confirmed that it resolved =
the "hangs". It never did reproduce a core dump.
If this is the case, I think we need to backport this to current python 3.8
(and 3.9?) ports. Have this been done in the upstream? We can do it locally
but we also need to check it them won't cause other regressions. It would be
nice to work with the upstream to reduce the possible regressions, and let =
the
next version of 3.8 includes the fix.
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Tue, 27 Apr 2021 19:37:32 +0000
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--- Comment #4 from yocalebo@gmail.com <yocalebo@gmail.com> ---
(In reply to Li-Wen Hsu from comment #3)
Upstream python 3.9 includes these patches by default already, they were ne=
ver
backported to 3.8. I'm fairly confident there are no regressions because:
1. they were commited to upstream python for version 3.9
2. as of yesterday, there are 21,736 users running py3.8.7 with those 2
backported commits and we've seen no further reports of regressions.
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Tue, 27 Apr 2021 19:41:30 +0000
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--- Comment #5 from Li-Wen Hsu <lwhsu@FreeBSD.org> ---
(In reply to yocalebo@gmail.com from comment #4)
Thanks for the numbers and it sounds we should have those patches included.=
Do
you think you can ask if they also want to backport to 3.8, or do you mean =
they
have been asked but don't want to do so?
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255445
--- Comment #6 from yocalebo@gmail.com <yocalebo@gmail.com> ---
(In reply to Li-Wen Hsu from comment #5)
Unfortunately, I'm not sure why they did not include the threading patch in
python 3.8. I suspect because the use-case is relatively small (daemon=3DTr=
ue
threads and how they're destroyed/cleaned up by the calling thread) and they
were very late in the "release" process for pushing out 3.8?? I'm not sure,
hard to know.
--=20
You are receiving this mail because:
You are the assignee for the bug.=
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On 27/04/2021 5:05 am, Ken wrote:
> Hi There,
>
> After today's update for devel/py-setuptools, it left me with a whole bunch
> or orphaned packages.
>
> py37-authres-1.2.0 ? orphaned: mail/py-authres
> py37-dnspython-1.16.0 ? orphaned: dns/py-dnspython
> py37-fail2ban-0.11.2 ? orphaned: security/py-fail2ban
> py37-milter-1.0.4 ? orphaned: mail/py-milter
> py37-pyinotify-0.9.6 ? orphaned: devel/py-pyinotify
> py37-pyspf-2.0.14 ? orphaned: mail/py-pyspf
> py37-setuptools-44.0.0 < needs updating (port has 44.0.0_1)
> py37-spf-engine-2.9.2 ? orphaned: mail/py-spf-engine
>
> Are we now required to update Python to version 3.8 to use the new version
> of setuptools?
The *default* version (DEFAULT_VERSIONS [1]) of Python was switched from
3.7 to 3.8 in:
https://cgit.freebsd.org/ports/commit/?id=6cd3db2d03cc544c5893e41dbbacd2000fcbd35a
/usr/ports/UPDATING entry 20210426 [2] contains the instructions for
people for either updating from 3.7 to 3.8, or to remain on 3.7,
fulfilling the purpose of DEFAULT_VERSIONS, user choice among multiple
available version.
[1] https://wiki.freebsd.org/Ports/DEFAULT_VERSIONS
[2]
https://cgit.freebsd.org/ports/commit/?id=210ee04dd3c3f2e82cd3130e412866a182066859
> I did not see anything in UPDATING regarding this.
>
> Thanks,
> Ken
> _______________________________________________
> freebsd-python@freebsd.org mailing list
> https://lists.freebsd.org/mailman/listinfo/freebsd-python
> To unsubscribe, send any mail to "freebsd-python-unsubscribe@freebsd.org"
>
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255445
--- Comment #7 from Kubilay Kocak <koobs@FreeBSD.org> ---
(In reply to yocalebo@gmail.com from comment #4)
Upstream has a latest minor and back 2 minors merge policy. If you can iden=
tify
the issues and/or PR's associated with those two missing merge commits, I c=
an
take care of liaising with upstream to get them merged in the long term
Thank you for the excellent report, assessment and upstream research.
--=20
You are receiving this mail because:
You are the assignee for the bug.=
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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--- Comment #8 from Kubilay Kocak <koobs@FreeBSD.org> ---
(In reply to yocalebo@gmail.com from comment #6)
I run FreeBSD 12.x and CURRENT for upstream Cpython, which tests all non EoL
branches (latest-and-back-2-versions), so I'm surprised with this report. T=
his
would appear to hint at something else contributing to the issue.
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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Kubilay Kocak <koobs@FreeBSD.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |victor.stinner@gmail.com
Keywords| |needs-patch, needs-qa
Flags| |maintainer-feedback?(victor
| |.stinner@gmail.com)
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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--- Comment #9 from yocalebo@gmail.com <yocalebo@gmail.com> ---
(In reply to Kubilay Kocak from comment #7)
Hi Kubilay, thanks for adding Victor Stinner to this. Victor will more than
likely be able to give a more definitive reason on why those 2 commits did =
not
get backported to python3.8 since Victor is the author of those commits :)
Anyways, I have the upstream python bugs for those 2 commits:
https://github.com/python/cpython/commit/9ad58acbe8b90b4d0f2d2e139e38bb5aa3=
2b7fb6
links to https://bugs.python.org/issue19466
https://github.com/python/cpython/commit/4d96b4635aeff1b8ad41d41422ce808ce0=
b971c8
links to https://bugs.python.org/issue39511
Without those 2 commits, if you take the python script I posted earlier and
simply run a while true loop in the shell repeatedly calling it, you will
notice that it will eventually hang indefinitely. With the 2 commits, the w=
hile
true loop runs forever as expected.
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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--- Comment #10 from yocalebo@gmail.com <yocalebo@gmail.com> ---
(In reply to Kubilay Kocak from comment #8)
I was quite surprised at the regression with py3.8 as well. But that was be=
fore
I started looking at some of the changes from py3.7 to 3.8. Some of the cha=
nges
are very intrusive. For example, here is a quote from one of the release no=
te
entries.
"The ``PyGC_Head`` struct has changed completely. All code that touched the
struct member should be rewritten. (See :issue:`33597`.)"
That struct is the main struct for pythons garbage collection object (AFAIC=
T),
and I understand that it's a very "low-level" change and shouldn't effect t=
oo
much etc etc, but seems strange to me for something (for what I perceive to=
be)
such an intrusive change for a minor release.
But I will admit, I do not follow the release process for python very close=
ly
and this very well could be par for the course. :)
--=20
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255445
--- Comment #11 from yocalebo@gmail.com <yocalebo@gmail.com> ---
Update on the matter. I was able to analyze a python3.9.4 core dump and I've
narrowed the fact down that the thread on CPU that crashed is in
concurrent.future._base.Executor class.
Core was generated by `python3.9: middlewared'.
Program terminated with signal SIGSEGV, Segmentation fault.
#0 pymalloc_alloc (ctx=3D<optimized out>, nbytes=3D56) at Objects/obmalloc=
.c:1621
warning: Source file is more recent than executable.
1621 if (UNLIKELY((pool->freeblock =3D *(block **)bp) =3D=3D NUL=
L)) {
[Current thread is 1 (LWP 100893)]
(gdb) info locals
size =3D 3
pool =3D 0x83757b000
bp =3D 0x0
(gdb) py-bt
Traceback (most recent call first):
File "/usr/local/lib/python3.9/xml/etree/ElementPath.py", line 282, in se=
lect
yield elem
File "/usr/local/lib/python3.9/xml/etree/ElementPath.py", line 389, in fi=
nd
return next(iterfind(elem, path, namespaces), None)
File
"/usr/local/lib/python3.9/site-packages/middlewared/plugins/disk_/disk_info=
_freebsd.py",
line 96, in label_to_disk
part =3D
geom.class_by_name('PART').xml.find(f'.//provider[name=3D"{dev}"]/../name')
File "/usr/local/lib/python3.9/site-packages/middlewared/main.py", line 1=
521,
in call_sync
)
File "/usr/local/lib/python3.9/site-packages/middlewared/plugins/pool.py",
line 416, in transform_topology
disk =3D self.middleware.call_sync('disk.label_to_disk', *args)
File "/usr/local/lib/python3.9/site-packages/middlewared/plugins/pool.py",
line 435, in transform_topology
x[i] =3D self.transform_topology(x[i], dict(options, geom_scan=3DFalse))
File "/usr/local/lib/python3.9/site-packages/middlewared/plugins/pool.py",
line 432, in transform_topology
x[key] =3D self.transform_topology(x[key], dict(options, geom_scan=3DFa=
lse))
File "/usr/local/lib/python3.9/site-packages/middlewared/plugins/pool.py",
line 435, in transform_topology
x[i] =3D self.transform_topology(x[i], dict(options, geom_scan=3DFalse))
File "/usr/local/lib/python3.9/site-packages/middlewared/plugins/pool.py",
line 432, in transform_topology
x[key] =3D self.transform_topology(x[key], dict(options, geom_scan=3DFa=
lse))
File "/usr/local/lib/python3.9/site-packages/middlewared/plugins/pool.py",
line 469, in pool_extend
'topology': self.transform_topology(zpool['groups']),
File
"/usr/local/lib/python3.9/site-packages/middlewared/utils/io_thread_pool_ex=
ecutor.py",
line 25, in run
result =3D self.fn(*self.args, **self.kwargs)
File
"/usr/local/lib/python3.9/site-packages/middlewared/utils/io_thread_pool_ex=
ecutor.py",
line 308, in _target
File "/usr/local/lib/python3.9/threading.py", line 892, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/lib/python3.9/threading.py", line 954, in _bootstrap_inn=
er
self.run()
File "/usr/local/lib/python3.9/threading.py", line 912, in _bootstrap
self._bootstrap_inner()
--=20
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To: python@FreeBSD.org
Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Thu, 29 Apr 2021 16:18:12 +0000
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Kai Knoblich <kai@FreeBSD.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
CC| |kai@FreeBSD.org
--- Comment #12 from Kai Knoblich <kai@FreeBSD.org> ---
Created attachment 224534
--> https://bugs.freebsd.org/bugzilla/attachment.cgi?id=3D224534&action=
=3Dedit
python38-fix-threading-v1.patch
At the outset: Thanks for the report and the detailed descriptions.
The threading issue with Python 3.8 (tested with 3.8.9 from the Ports tree)=
can
be reproduced via the script from comment #2. Following vanilla releases of
FreeBSD were tested:
- 11.4-RELEASE-p9 [amd64/i386]
- 12.2-RELEASE-p6 [amd64/i386]
- 13.0-RELEASE-p0 [amd64]
- 14.0-CURRENT main-n246037-ca6e1fa3ce8 [amd64]
If the attached patch is used, which contains the two backported commits, as
noted in comment #0 (BPO-19466 + BPO39511), the regression doesn't occur on=
any
platform listed above.
A side note: If a VM has only one vCPU, the threading issue doesn't seem to=
be
reproducible with an unpatched version of Python 3.8.9.
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Thu, 29 Apr 2021 18:03:25 +0000
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--- Comment #13 from yocalebo@gmail.com <yocalebo@gmail.com> ---
Maybe some progress....not sure but I'm cautiously optimistic.
I analyzed 7 core dumps again to see if I spotted anything interesting. 6 of
them were py3.8 and 1 was py3.9.
100% of them have a common pattern. The threads *tstate has
lxml.etree._ParserDictionaryContext in the frames. Either the thread that w=
as
on CPU when it core dumped or some other thread. Since this is seemingly me=
mory
corruption, lxml has become my suspect since it uses it's own C bindings for
the libxml2 and libxslt libraries.
I've instrumented a somewhat complicated script that daemonizes, creates a
concurrent.futures._base.Executor class and calls methods that use lxml lib=
rary
to parse geom xml information in a while true loop.
Am I looking at a red herring?? Idk but this grabbed my attention so I'm
running the script to see if it'll tickle the problem. Maybe the version of
py-lxml we're using has a subtle issue with py3.8+. (Queue my overly dramat=
ic
rant about py3.8 changes to PyGC_Head struct.)
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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--- Comment #14 from Victor Stinner <victor.stinner@gmail.com> ---
Using the script of Comment 2, I cannot reproduce the hang with Python 3.9.=
4 on
FreeBSD 13. I used:
for i in $(seq 1 100); do python3.9 script.py || break; done
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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--- Comment #15 from yocalebo@gmail.com <yocalebo@gmail.com> ---
(In reply to Victor Stinner from comment #14)
Hi Victor, thanks for testing it out. Your results are expected since the 2
commits that fix the problem were included with python3.9. Have you tried u=
sing
python3.8?
--=20
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You are the assignee for the bug.=
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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--- Comment #16 from Victor Stinner <victor.stinner@gmail.com> ---
I can reproduce the issue with Python 3.8 on Linux.
Well, first, don't rely on implicit resource management: don't rely on
__del__() destructor.
You should use "with pool:" and then call pool.join().
--
I'm not sure if it's related, but daemon threads are evil and should be avo=
ided
if possible. It's another variant of "implicit resource management" (don't =
join
the thread, expect it to disappear magically at exit). I fixed many race
conditions in daemon threads:
* https://vstinner.github.io/daemon-threads-python-finalization-python32.ht=
ml
* https://vstinner.github.io/threading-shutdown-race-condition.html
* https://vstinner.github.io/gil-bugfixes-daemon-threads-python39.html
Python 3.9 avoids daemon threads in concurrent.futures:
https://bugs.python.org/issue39812
But multiprocessing still uses daemon threads.
--
I also fixed multiple bugs in the Python finalization to make it more relia=
ble.
My notes on that topic:
https://pythondev.readthedocs.io/finalization.html
--=20
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
Date: Fri, 30 Apr 2021 16:23:11 +0000
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--- Comment #17 from Victor Stinner <victor.stinner@gmail.com> ---
Backporting "bpo-19466: Py_Finalize() clears daemon threads earlier (GH-188=
48)"
sounds dangerous. This fix relies on many other fixes. Without the other fi=
xes,
clearing daemon threads earlier can hang or crash.
I suggest you to not rely on implicit resource management. If you really ha=
ve
to, use Python 3.9 which seems to work for your issue.
--=20
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You are the assignee for the bug.=
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Subject: [Bug 255445] lang/python 3.8/3.9 SIGSEV core dumps in libthr TrueNAS
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--- Comment #18 from yocalebo@gmail.com <yocalebo@gmail.com> ---
(In reply to Victor Stinner from comment #17)
Thanks for the tips and the links to your notes. However, the panics are st=
ill
happening on py3.9.4. Unfortunately, I've analyzed 11 core dumps at this po=
int.
10 from py3.8 and 1 from py3.9.4. All of their tstate has a reference to
lxml.etree._ParserDictionaryContext. I actually just analyzed a multiproces=
sing
core dump and it is panic'ing during garbage collection (visit_decref) but =
the
story is the same. _ParserDictionaryContext is in the thread at time of dum=
p.
--=20
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From: portscout@FreeBSD.org
To: python@freebsd.org
Subject: FreeBSD ports you maintain which are out of date
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Dear port maintainer,
The portscout new distfile checker has detected that one or more of your
ports appears to be out of date. Please take the opportunity to check
each of the ports listed below, and if possible and appropriate,
submit/commit an update. If any ports have already been updated, you can
safely ignore the entry.
You will not be e-mailed again for any of the port/version combinations
below.
Full details can be found at the following URL:
http://portscout.freebsd.org/python@freebsd.org.html
Port | Current version | New version
------------------------------------------------+-----------------+------------
devel/ipython | 7.22.0 | 7.23.0
------------------------------------------------+-----------------+------------
devel/py-pip | 20.3.4 | 21.1.1
------------------------------------------------+-----------------+------------
If any of the above results are invalid, please check the following page
for details on how to improve portscout's detection and selection of
distfiles on a per-port basis:
http://portscout.freebsd.org/info/portscout-portconfig.txt
Reported by: portscout!
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Subject: [Bug 255013] Mk/Uses/python.mk: Prepare infrastructure support for
Python 3.10
Date: Sat, 01 May 2021 16:23:51 +0000
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255013
Antoine Brodin <antoine@FreeBSD.org> changed:
What |Removed |Added
----------------------------------------------------------------------------
Flags|exp-run? |exp-run+
CC| |kai@FreeBSD.org
--- Comment #6 from Antoine Brodin <antoine@FreeBSD.org> ---
Exp-run looks fine.
@kai : can you review the patch?
--=20
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https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D255013
--- Comment #7 from Dmitry Marakasov <amdmi3@FreeBSD.org> ---
For the record, in private email wen@ has approved the patch. He also sugge=
sted
to wait with python 310 import till first beta release, but I don't see any
reason for this - we can and should start testing and improving 3.10 suppor=
t as
soon as possible.
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