#3984: Sage 3.1.2.alpha1 - Linux Itanium - segfaults in chmm.pyx and hmm.pyx
------------------------+---------------------------------------------------
Reporter: mabshoff | Owner: mabshoff
Type: defect | Status: new
Priority: critical | Milestone: sage-4.3.1
Component: doctest | Keywords:
Work_issues: | Author:
Upstream: N/A | Reviewer:
Merged: |
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Changes (by was):
* upstream: => N/A
Comment:
1. I tried enabling the doctests on x86_64, and they still work fine.
2. Here's the backtrace on Itanium, where there are still segfaults:
{{{
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 2305843009213932800 (LWP 558)]
0x2000000011100c51 in
__pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel_viterbi (
__pyx_v_self=0x2000000011639f58, __pyx_v_seq=0x2000000011660098)
at sage/stats/hmm/hmm.c:6368
6368 __pyx_t_4 = PyInt_FromLong((__pyx_v_path[__pyx_t_8])); if
(unlikely(!__pyx_t_4)) {__pyx_filename = __pyx_f[1]; __pyx_lineno = 702;
__pyx_clineno = __LINE__; goto __pyx_L1_error;}
(gdb) bt
#0 0x2000000011100c51 in
__pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel_viterbi
(__pyx_v_self=0x2000000011639f58, __pyx_v_seq=0x2000000011660098)
at sage/stats/hmm/hmm.c:6368
#1 0x400000000019efc0 in PyEval_EvalFrameEx (f=0x600000000209e630,
throwflag=<value optimized out>) at Python/ceval.c:3694
#2 0x40000000001a26c0 in PyEval_EvalCodeEx (co=<value optimized out>,
globals=0x6000000002118960, locals=0x6000000002118960, args=0x0,
argcount=0, kws=0x0,
kwcount=0, defs=0x0, defcount=Cannot access memory at address 0x219a
) at Python/ceval.c:2968
#3 0x40000000001a28e0 in PyEval_EvalCode (co=0x200000001163c8a0,
globals=0x6000000002118960,
...
}}}
Using --verbose we get an example:
{{{
sage: a = hmm.DiscreteHiddenMarkovModel([[0.1,0.9],[0.1,0.9]],
[[0.9,0.1],[0.1,0.9]], [0.5,0.5])
sage: a.viterbi([1,0,0,1,0,0,1,1])
------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occured in SAGE.
This probably occured because a *compiled* component
of SAGE has a bug in it (typically accessing invalid memory)
or 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 (sorry).
------------------------------------------------------------
}}}
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/3984#comment:11>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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