#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: algebra | Keywords: sd31
Work_issues: | Upstream: N/A
Reviewer: François Bissey, Steven Trogdon | Author: Volker Braun,
Martin von Gagern
Merged: | Dependencies:
-----------------------------------------------+----------------------------
Changes (by vbraun):
* cc: malb, SimonKing (added)
* status: needs_work => needs_review
* component: porting => algebra
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:trac_11339_illegal_use_of__deallocate__in_libsingular.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_refcount_singular_rings.patch]
* [attachment:trac_11339_refcount_singular_polynomials.patch]
--
Comment:
Ok this should fix it now for good. The first patch introduces refcounting
for Singular ring pointers and uses it in `GroebnerStrategy`, and the
second updates `MPolynomialRing_libsingular` and
`MPolynomial_libsingular`. Please give it a try with Python-2.7...
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/11339#comment:25>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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