#13636: %timeit unpickle_all() causes a SEGABRT
---------------------------------+------------------------------------------
Reporter: andrew.mathas | Owner: was
Type: defect | Status: needs_review
Priority: major | Milestone:
sage-duplicate/invalid/wontfix
Component: pickling | Resolution:
Keywords: | Work issues:
Report Upstream: N/A | Reviewers:
Authors: | Merged in:
Dependencies: | Stopgaps:
---------------------------------+------------------------------------------
Changes (by andrew.mathas):
* status: new => needs_review
* milestone: sage-5.7 => sage-duplicate/invalid/wontfix
Old description:
> The subject says it all:
> Sage gives a SEGABRT with the following:
> {{{
> sage: %timeit sage.structure.sage_object.unpickle_all()
>
> ------------------------------------------------------------------------
> Unhandled SIGABRT: An abort() occurred in Sage.
> This probably occurred because a *compiled* component of Sage has a bug
> in it and is not properly wrapped with sig_on(), sig_off(). You might
> want to run Sage under gdb with 'sage -gdb' to debug this.
> Sage will now terminate.
> ------------------------------------------------------------------------
> /usr/local/src/sage/sage-5.4.rc1/spkg/bin/sage: line 310: 60549 Abort
> trap: 6 sage-ipython "$@" -i
> }}}
> Note, however, that the following is OK:
> {{{
> sage: sage.structure.sage_object.unpickle_all()
> /usr/local/src/sage/sage-5.4.rc1/local/lib/python2.7/site-
> packages/IPython/iplib.py:2260: DeprecationWarning: This class is
> replaced by Matrix_modn_dense_float/Matrix_modn_dense_double.
> See http://trac.sagemath.org/4260 for details.
> exec code_obj in self.user_global_ns, self.user_ns
> Successfully unpickled 594 objects.
> Failed to unpickle 0 objects.
> }}}
> as is calling `unpickle()` with an argument:
> {{{
> sage: sage: dir = tmp_dir()
> sage: sage: sage.structure.sage_object.picklejar('hello', dir)
> sage: sage: sage.structure.sage_object.unpickle_all(dir)
> Successfully unpickled 1 objects.
> Failed to unpickle 0 objects.
> sage: %timeit sage.structure.sage_object.unpickle_all(dir)
> 625 loops, best of 3: 91.5 µs per loop
> }}}
>
> I get this error for versions 5.3 and 5.4.rc1 running on a macbook pro
> with lion.
>
> I initially thought that perhaps timeit did not like calling itself,
> however, this seems to be OK because the following does work:
> {{{
> sage: def fred():^J timeit('2^10000', preparse=False, number=100)
> ....:
> sage: fred()
> 100 loops, best of 3: 31 ns per loop
> sage: %timeit fred
> 625 loops, best of 3: 38.5 ns per loop
> }}}
> I tried running through sage -gdb but I don't know how to interpret the
> outout. Here is the tail of what it produces:
> {{{
> Reading symbols for shared libraries warning: .o file
> "/usr/local/src/sage/sage-5.3/devel/sage-
> main/build/temp.macosx-10.7-x86_64-2.7/sage/matrix/matrix_symbolic_dense.o"
> more recent than executable timestamp in
> "/usr/local/src/sage/sage-5.3/devel/sage-
> combinat/build/sage/matrix/matrix_symbolic_dense.so"
> warning: Could not open OSO file /usr/local/src/sage/sage-5.3/devel/sage-
> main/build/temp.macosx-10.7-x86_64-2.7/sage/matrix/matrix_symbolic_dense.o
> to scan for pubtypes for objfile /usr/local/src/sage/sage-5.3/devel/sage-
> combinat/build/sage/matrix/matrix_symbolic_dense.so
> . done
> Reading symbols for shared libraries warning: .o file
> "/usr/local/src/sage/sage-5.3/devel/sage-
> main/build/temp.macosx-10.7-x86_64-2.7/sage/rings/polynomial/symmetric_reduction.o"
> more recent than executable timestamp in
> "/usr/local/src/sage/sage-5.3/devel/sage-
> combinat/build/sage/rings/polynomial/symmetric_reduction.so"
> warning: Could not open OSO file /usr/local/src/sage/sage-5.3/devel/sage-
> main/build/temp.macosx-10.7-x86_64-2.7/sage/rings/polynomial/symmetric_reduction.o
> to scan for pubtypes for objfile /usr/local/src/sage/sage-5.3/devel/sage-
> combinat/build/sage/rings/polynomial/symmetric_reduction.so
> . done
>
> Program received signal SIGABRT, Aborted.
> 0x00007fff8d58f82a in __kill ()
> }}}
New description:
**CLOSED AS DUPLICATE OF #10705**
The subject says it all:
Sage gives a SEGABRT with the following:
{{{
sage: %timeit sage.structure.sage_object.unpickle_all()
------------------------------------------------------------------------
Unhandled SIGABRT: An abort() occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off(). You might
want to run Sage under gdb with 'sage -gdb' to debug this.
Sage will now terminate.
------------------------------------------------------------------------
/usr/local/src/sage/sage-5.4.rc1/spkg/bin/sage: line 310: 60549 Abort
trap: 6 sage-ipython "$@" -i
}}}
Note, however, that the following is OK:
{{{
sage: sage.structure.sage_object.unpickle_all()
/usr/local/src/sage/sage-5.4.rc1/local/lib/python2.7/site-
packages/IPython/iplib.py:2260: DeprecationWarning: This class is replaced
by Matrix_modn_dense_float/Matrix_modn_dense_double.
See http://trac.sagemath.org/4260 for details.
exec code_obj in self.user_global_ns, self.user_ns
Successfully unpickled 594 objects.
Failed to unpickle 0 objects.
}}}
as is calling `unpickle()` with an argument:
{{{
sage: sage: dir = tmp_dir()
sage: sage: sage.structure.sage_object.picklejar('hello', dir)
sage: sage: sage.structure.sage_object.unpickle_all(dir)
Successfully unpickled 1 objects.
Failed to unpickle 0 objects.
sage: %timeit sage.structure.sage_object.unpickle_all(dir)
625 loops, best of 3: 91.5 µs per loop
}}}
I get this error for versions 5.3 and 5.4.rc1 running on a macbook pro
with lion.
I initially thought that perhaps timeit did not like calling itself,
however, this seems to be OK because the following does work:
{{{
sage: def fred():^J timeit('2^10000', preparse=False, number=100)
....:
sage: fred()
100 loops, best of 3: 31 ns per loop
sage: %timeit fred
625 loops, best of 3: 38.5 ns per loop
}}}
I tried running through sage -gdb but I don't know how to interpret the
outout. Here is the tail of what it produces:
{{{
Reading symbols for shared libraries warning: .o file
"/usr/local/src/sage/sage-5.3/devel/sage-
main/build/temp.macosx-10.7-x86_64-2.7/sage/matrix/matrix_symbolic_dense.o"
more recent than executable timestamp in
"/usr/local/src/sage/sage-5.3/devel/sage-
combinat/build/sage/matrix/matrix_symbolic_dense.so"
warning: Could not open OSO file /usr/local/src/sage/sage-5.3/devel/sage-
main/build/temp.macosx-10.7-x86_64-2.7/sage/matrix/matrix_symbolic_dense.o
to scan for pubtypes for objfile /usr/local/src/sage/sage-5.3/devel/sage-
combinat/build/sage/matrix/matrix_symbolic_dense.so
. done
Reading symbols for shared libraries warning: .o file
"/usr/local/src/sage/sage-5.3/devel/sage-
main/build/temp.macosx-10.7-x86_64-2.7/sage/rings/polynomial/symmetric_reduction.o"
more recent than executable timestamp in
"/usr/local/src/sage/sage-5.3/devel/sage-
combinat/build/sage/rings/polynomial/symmetric_reduction.so"
warning: Could not open OSO file /usr/local/src/sage/sage-5.3/devel/sage-
main/build/temp.macosx-10.7-x86_64-2.7/sage/rings/polynomial/symmetric_reduction.o
to scan for pubtypes for objfile /usr/local/src/sage/sage-5.3/devel/sage-
combinat/build/sage/rings/polynomial/symmetric_reduction.so
. done
Program received signal SIGABRT, Aborted.
0x00007fff8d58f82a in __kill ()
}}}
--
Comment:
Replying to [comment:4 nbruin]:
> Replying to [comment:3 andrew.mathas]:
> > See #10705 for another seg fault associated with unpickle_all.
> Well ... `%timeit` will run its code a couple of times to get accurate
timing information, so if (as the ticket mentions) running
`unpickle_all()` twice causes a crash then `%timeit unpickle_all()` should
too.
OK, let's close this as a duplicate then. I'll set it as needs review.
Could you please "review" it Nils?
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/13636#comment:5>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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