%timeit unpickle_all() causes a SEGABRT

[AndrewMathas]

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 ()

Component: pickling

Reviewer: Travis Scrimshaw

Issue created by migration from https://trac.sagemath.org/ticket/13636

[nbruin]

comment:2

Usually asking for the stack backtrace is one of the most interesting things:

Program received signal SIGABRT, Aborted.
0x00000031cfe36285 in raise () from /lib64/libc.so.6
...
(gdb) bt
#0  0x00000031cfe36285 in raise () from /lib64/libc.so.6
#1  0x00000031cfe37b9b in abort () from /lib64/libc.so.6
#2  0x00007fffed336797 in global_NTL_error_callback () from /usr/local/sage/5.0/local/lib/libcsage.so
#3  0x00007fffece36eaf in NTL::Error (s=0x7fffece6b6b2 "InvMod: inverse undefined") at tools.c:48
#4  0x00007fffecd8b5c6 in NTL::InvMod (a=<optimized out>, n=244) at ZZ.c:351
#5  0x00007fffecdfb18c in inv (a=<optimized out>, x=<synthetic pointer>) at ../include/NTL/lzz_p.h:278
#6  NTL::PlainRem (r=..., a=..., b=<optimized out>) at lzz_pX.c:1083
#7  0x00007fffece054c1 in NTL::GCD (d=..., u=<optimized out>, v=...) at lzz_pX1.c:558
#8  0x00007fffd99939a8 in GCD (b=..., a=...) at /usr/local/sage/5.0/local/include/NTL/lzz_pX.h:696
#9  gcd_univar_ntlp (G=..., F=...) at cf_gcd.cc:1036
#10 gcd_poly_p (f=<optimized out>, g=...) at cf_gcd.cc:546
#11 0x00007fffd998f272 in gcd_poly (f=..., g=...) at cf_gcd.cc:718
#12 0x00007fffd998f954 in gcd (f=..., g=...) at cf_gcd.cc:952
#13 0x00007fffd998fdaf in cf_content (f=..., g=...) at cf_gcd.cc:798
#14 0x00007fffd998ff58 in content (f=..., x=...) at cf_gcd.cc:851
#15 0x00007fffd998feed in content (f=..., x=...) at cf_gcd.cc:855
#16 0x00007fffd99b5966 in EZGCD_P (FF=<optimized out>, GG=<optimized out>) at cf_gcd_smallp.cc:4168
#17 0x00007fffd998f0fe in gcd_poly (f=..., g=...) at cf_gcd.cc:704
#18 0x00007fffd998e0ce in chinrem_gcd (FF=<optimized out>, GG=<optimized out>) at cf_gcd.cc:1195
#19 0x00007fffd998f156 in gcd_poly (f=..., g=...) at cf_gcd.cc:743
#20 0x00007fffd998f954 in gcd (f=..., g=...) at cf_gcd.cc:952
#21 0x00007fffd97f7a76 in singclap_gcd_r (f=0x7fffd966a328, g=0x7fffd966a1e8, r=0x7fffd96371a0) at clapsing.cc:53
#22 0x00007fffd97f7c59 in singclap_gcd (f=0x7fffd966a328, g=0x7fffd966a1e8) at clapsing.cc:109
#23 0x00007fffd9d939df in __pyx_pf_4sage_5rings_10polynomial_28multi_polynomial_libsingular_23MPolynomial_libsingular_52gcd (__pyx_v_self=0x5568500, __pyx_args=<optimized out>, __pyx_kwds=<optimized out>)
    at sage/rings/polynomial/multi_polynomial_libsingular.cpp:26669
#24 0x00007ffff7c711d3 in PyObject_Call (func=0x53a35f0, arg=<optimized out>, kw=<optimized out>)
    at Objects/abstract.c:2529
#25 0x00007ffff7d0e677 in PyEval_CallObjectWithKeywords (func=0x53a35f0, arg=0x54b8210, kw=<optimized out>)
    at Python/ceval.c:3882
#26 0x00007ffff7c87cec in methoddescr_call (descr=<optimized out>, args=0x54b8210, kwds=0x5554ab0)
    at Objects/descrobject.c:247
#27 0x00007ffff7c711d3 in PyObject_Call (func=0x1471f38, arg=<optimized out>, kw=<optimized out>)
    at Objects/abstract.c:2529
#28 0x00007ffff7d0e677 in PyEval_CallObjectWithKeywords (func=0x1471f38, arg=0x54cbdd0, kw=<optimized out>)
    at Python/ceval.c:3882
#29 0x00007fffe9f911c2 in __pyx_pf_4sage_9structure_7element_16NamedBinopMethod_1__call__ (__pyx_v_self=0x54dabd8, 
...
#91 0x00007ffff7d15bd5 in PyEval_EvalCodeEx (co=<optimized out>, globals=<optimized out>, locals=<optimized out>, 
    args=<optimized out>, argcount=1, kws=0x6f32e0, kwcount=2, defs=0x7fffee2bf068, defcount=2, closure=0x0)
    at Python/ceval.c:3253
#92 0x00007ffff7d13e51 in fast_function (nk=<optimized out>, na=1, n=<optimized out>, pp_stack=0x7fffffffd640, 
    func=0x7fffed7add70) at Python/ceval.c:4109
#93 call_function (oparg=<optimized out>, pp_stack=0x7fffffffd640) at Python/ceval.c:4034

So, the error happens in NTL. I suppose that this is an error that normally gets caught appropriately but due to %timeit doesn't? The alternative is that the whole %timeit thing happens to cause a state in NTL we aren't normally encountering.

[AndrewMathas]

comment:3

See #10705 for another seg fault associated with unpickle_all.

[nbruin]

comment:4

Replying to @AndrewAtLarge:

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.

[AndrewMathas]

comment:5

Replying to @nbruin:

Replying to @AndrewAtLarge:

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?

[tscrim]

Reviewer: Travis Scrimshaw

[tscrim]

comment:6

I agree that this is a duplicate.