#11339: Illegal use of __deallocate__ in cython (pyx) code
-----------------------------------------------+----------------------------
Reporter: gagern | Owner: drkirkby
Type: defect | Status: needs_review
Priority: major | Milestone: sage-4.7.1
Component: porting | Keywords: sd31
Work_issues: | Upstream: N/A
Reviewer: François Bissey, Steven Trogdon | Author: Volker Braun,
Martin von Gagern
Merged: | Dependencies:
-----------------------------------------------+----------------------------
Changes (by newvalueoldvalue):
* keywords: => sd31
* status: needs_work => needs_review
* author: => Volker Braun, Martin von Gagern
Old description:
> As [https://github.com/cschwan/sage-on-
> gentoo/issues/51#issuecomment-1181259 described for the Sage on Gentoo
> project], there is a problem in how parts of sage use `__deallocate__` in
> their Cython code. I've actually traced an instance of
> [http://hg.sagemath.org/sage-
> main/file/361a4ad7d52c/sage/libs/singular/groebner_strategy.pyx#l134
> groebner_strategy.pyx] causing segmentation faults under Python 2.7.
>
> What happens is that the garbage collector invokes the
> [http://docs.python.org/c-api/typeobj.html#tp_clear tp_clear] function
> for the object. Its implementation is provided by Cython, and one of its
> effects is that every python reference will be set to `None`. A bit later
> on, [http://docs.python.org/c-api/typeobj.html#tp_dealloc tp_dealloc] is
> called and invokes the `__deallocate__` method. By that time, `_parent`
> is `None`, so accessing `_parent._ring` is a bad idea, and in this case
> it turns out to be null.
>
> Others have had similar problems before. There are
> [http://stackoverflow.com/questions/4501938/how-can-c-object-lifetimes-
> be-correctly-managed-in-cython crude workarounds] floating around. I
> guess a proper solution would be twaking cython to allow custom code in
> the tp_clear function. In other words, have a "magic" mehod `__clear__`
> similar to the magic `__deallocate__`. But I'll wait for comments here
> first, before taking this to cython upstream. Perhaps people with more
> experience have better solutions to offer. And I won't mind if you decide
> to take this to Cython devs yourselves.
>
> Apply:
> * [attachment:bug11339a.patch]
New description:
As [https://github.com/cschwan/sage-on-
gentoo/issues/51#issuecomment-1181259 described for the Sage on Gentoo
project], there is a problem in how parts of sage use `__deallocate__` in
their Cython code. I've actually traced an instance of
[http://hg.sagemath.org/sage-
main/file/361a4ad7d52c/sage/libs/singular/groebner_strategy.pyx#l134
groebner_strategy.pyx] causing segmentation faults under Python 2.7.
What happens is that the garbage collector invokes the
[http://docs.python.org/c-api/typeobj.html#tp_clear tp_clear] function for
the object. Its implementation is provided by Cython, and one of its
effects is that every python reference will be set to `None`. A bit later
on, [http://docs.python.org/c-api/typeobj.html#tp_dealloc tp_dealloc] is
called and invokes the `__deallocate__` method. By that time, `_parent` is
`None`, so accessing `_parent._ring` is a bad idea, and in this case it
turns out to be null.
Others have had similar problems before. There are
[http://stackoverflow.com/questions/4501938/how-can-c-object-lifetimes-be-
correctly-managed-in-cython crude workarounds] floating around. I guess a
proper solution would be twaking cython to allow custom code in the
tp_clear function. In other words, have a "magic" mehod `__clear__`
similar to the magic `__deallocate__`. But I'll wait for comments here
first, before taking this to cython upstream. Perhaps people with more
experience have better solutions to offer. And I won't mind if you decide
to take this to Cython devs yourselves.
Apply:
*
[attachment:trac_11339_illegal_use_of__deallocate__in_libsingular.patch]
--
Comment:
In the case at hand we don't really need the Cython class
`GroebnerStrategy._parent`, only the C struct
`GroebnerStrategy._parent._ring` is used in `__deallocate__()`. I've made
a minimal patch that adds a `cdef ring *_parent_ring` data member to
`GroebnerStrategy` to keep track of the ring only. Because it refers to a
C struct, it is safe to access it the Cython destructor. Because parents
are immutable we don't have to worry about the `ring *` pointer becoming
invalid.
The patch should fix the crash, but I don't have a Sage-on-Python-2.7
install to test it. Can somebody give it a try?
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/11339#comment:16>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
--
You received this message because you are subscribed to the Google Groups
"sage-trac" group.
To post to this group, send email to [email protected].
To unsubscribe from this group, send email to
[email protected].
For more options, visit this group at
http://groups.google.com/group/sage-trac?hl=en.
