Sage 3.1.2.alpha1 - Linux Itanium - segfaults in chmm.pyx and hmm.pyx

Comma-delimited Text

 SAGE has a bug in it (typically accessing invalid memory) or is not properly wrapped with _sig_on, _sig_off. You might want to debug this. SAGE will now terminate (sorry). ------------------------------------------------------------ 

Reported by:

 Program received signal SIGSEGV, Segmentation fault. [Switching to debug this. SAGE will now terminate (sorry). ------------------------------------------------------------   A mysterious error (perphaps a block of Thread 2305843009213933088 (LWP 29797)] __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel_viterbi (__pyx_v_self=<value optimized out>, __pyx_v_seq=0x200000000dac9f38) at sage/stats/hmm/hmm.c:5310 5310        __pyx_4 = PyInt_FromLong((__pyx_v_path[__pyx_8])); if (unlikely(!__pyx_4)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 702; __pyx_clineno = __LINE__; goto __pyx_L1_error;} (gdb) bt #0  __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel_viterbi (__pyx_v_self=<value optimized out>, __pyx_v_seq=0x200000000dac9f38) at sage/stats/hmm/hmm.c:5310 #1  0x4000000000154950 in PyEval_EvalFrameEx (f=0x600000000172cec0, throwflag=<value optimized out>) at Python/ceval.c:3561 #2  0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x60000000018a78a0, locals=<value optimized out>, args=0x0, argcount=<value optimized out>, kws=0x0, kwcount=0, defs=0x0, defcount=143, closure=0xc0f005800c212018)     at Python/ceval.c:2836 #3  0x40000000001541f0 in PyEval_EvalFrameEx (f=0x600000000171b9f0, throwflag=<value optimized out>) at Python/ceval.c:494 #4  0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x20, locals=<value optimized out>, args=0x6000000001993ea0, argcount=<value optimized out>, kws=0x6000000001993ed0, kwcount=0, defs=0x0, defcount=143, closure=0xc0f005800c212018)     at Python/ceval.c:2836 #5  0x4000000000155620 in PyEval_EvalFrameEx (f=0x6000000001993cf0, throwflag=<value optimized out>) at Python/ceval.c:3669 #6  0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x10, locals=<value optimized out>, args=0x60000000000cd980, argcount=<value optimized out>, kws=0x60000000000cd9a0, kwcount=0, defs=0x20000000018b5c60, defcount=143,      closure=0xc0f005800c212018) at Python/ceval.c:2836 #7  0x4000000000154ba0 in PyEval_EvalFrameEx (f=0x60000000000cd7a0, throwflag=<value optimized out>) at Python/ceval.c:3669 #8  0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x20000000005108a0, locals=<value optimized out>, args=0x600000000006f630, argcount=<value optimized out>, kws=0x60000000000bd9d8, kwcount=3, defs=0x2000000001885bb0, defcount=143,      closure=0xc0f005800c212018) at Python/ceval.c:2836 #9  0x4000000000154ba0 in PyEval_EvalFrameEx (f=0x60000000000bd810, throwflag=<value optimized out>) at Python/ceval.c:3669 #10 0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x600000000006f630, locals=<value optimized out>, args=0x0, argcount=<value optimized out>, kws=0x0, kwcount=0, defs=0x0, defcount=143, closure=0xc0f005800c212018)     at Python/ceval.c:2836 #11 0x4000000000158eb0 in PyEval_EvalCode (co=0x20000000005160a8, globals=0x600000000006f630, locals=0x600000000006f630) at Python/ceval.c:494 #12 0x40000000001a5af0 in PyRun_FileExFlags (fp=<value optimized out>, filename=0x607ffffffef9e76d "/home/mabshoff/build-3.1.2.alpha2/sage-3.1.2.alpha1-iras-gcc-4.3.1/tmp/.doctest_hmm.py", start=<value optimized out>, globals=0x600000000006f630,      locals=0x600000000006f630, closeit=1, flags=0x607ffffffef9df70) at Python/pythonrun.c:1273 #13 0x40000000001a62e0 in PyRun_SimpleFileExFlags (fp=0x600000000004c010, filename=0x607ffffffef9e76d "/home/mabshoff/build-3.1.2.alpha2/sage-3.1.2.alpha1-iras-gcc-4.3.1/tmp/.doctest_hmm.py", closeit=1, flags=0x607ffffffef9df70) at Python/pythonrun.c:879 #14 0x4000000000016060 in Py_Main (argc=2, argv=0x607ffffffef9e2a8) at Modules/main.c:523 #15 0x4000000000014350 in main (argc=2, argv=0x607ffffffef9e2a8) at ./Modules/python.c:23 1 ==26797==    at 0x4A1CDA3: strlen (mc_replace_strmem.c:242) ==26797==    by 0x483E46: PyEval_EvalFrameEx (ceval.c:3573) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x4CC304: wrapperdescr_call (descrobject.c:304) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x1EDD5E62: __pyx_pf_4sage_5stats_3hmm_4chmm_unpickle_gaussian_hmm_v0 (chmm.c:5465)  ==26797== Invalid read of size 4 alloc"d ==26797==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x1EDD736C: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___init__ (chmm.c:2307) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784) ==26797==    by 0x45402B: wrap_init (typeobject.c:4043) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==26797==    by 0x1E9BBCF6: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel___init__ (hmm.c:1886) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784)  ==26797== Invalid read of size to run SAGE under gdb with "sage -gdb" to run SAGE under gdb with "sage -gdb" of size 10 alloc"d ==27543==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x1EDD7992: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___repr__ (chmm.c:3548) ==26797==    by 0x1EDD736C: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___init__ (chmm.c:2307) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x1EDDAE1D: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel___init__ (chmm.c:1943) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861)  ==27543== Invalid read of size 1 ==26797==    at 0x4A1CDA3: strlen (mc_replace_strmem.c:242) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x459350: type_call (typeobject.c:436) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x1EDD736C: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___init__ (chmm.c:2307) ==26797==    by 0x443669: PyObject_Repr (object.c:361) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x1EDDAFE1: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel___init__ (chmm.c:2127) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x7DEFBFE: cpm_loads (cPickle.c:5488) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x45402B: wrap_init (typeobject.c:4043) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x44DACA: PyString_FromString (stringobject.c:108) ==26797==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) 

For chmm.pyx with verbose:

 Trying:     a.viterbi([Integer(1),Integer(0),Integer(0),Integer(1),Integer(0),Integer(0),Integer(1),Integer(1)])###line 678:_sage_    >>> a.viterbi([1,0,0,1,0,0,1,1]) Expecting:     ([1, 0, 0, 1, 1, 0, 1, 1], -11.062453224772216)   ------------------------------------------------------------ Unhandled SIGSEGV: A segmentation fault occured in SAGE. This probably occured because to Trying:     m = hmm.GaussianHiddenMarkovModel([[RealNumber("0.4"),RealNumber("0.6")],[RealNumber("0.1"),RealNumber("0.9")]], [(RealNumber("0.0"),RealNumber("1.0")),(Integer(1),Integer(1))], [Integer(1),Integer(2)], "Test 1", normalize=False)###line 306:_sage_    >>> m = hmm.GaussianHiddenMarkovModel([[0.4,0.6],[0.1,0.9]], [(0.0,1.0),(1,1)], [1,2], "Test 1", normalize=False) Expecting nothing   ------------------------------------------------------------ Unhandled SIGSEGV: A segmentation fault occured in SAGE. This probably occured because a *compiled* component is not properly wrapped with _sig_on, _sig_off. You might want to run SAGE under gdb with "sage -gdb" of SAGE has a *compiled* component of run SAGE under gdb with "sage -gdb" to debug this. SAGE will now terminate (sorry). ------------------------------------------------------------ a bug in it (typically accessing invalid memory) or 

changed from

 Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 2305843009213933088 (LWP 29739)] __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel__initialize_state (__pyx_v_self=<value optimized out>, __pyx_v_pi=0x200000000d6e9998) at sage/stats/hmm/chmm.c:2748 2748          ((__pyx_v_state->out_a[0])[__pyx_v_j]) = __pyx_6; (gdb) bt #0  __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel__initialize_state (__pyx_v_self=<value optimized out>, __pyx_v_pi=0x200000000d6e9998) at sage/stats/hmm/chmm.c:2748 #1  0x4000000000215400 in PyCFunction_Call (func=<value optimized out>, arg=0x200000000b73d390, kw=0x0) at Objects/methodobject.c:82 #2  0x400000000001fe10 in PyObject_Call (func=0x200000000db0b0a8, arg=0x200000000b73d390, kw=0x0) at Objects/abstract.c:1861 #3  0x200000000d9113a0 in __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___init__ (__pyx_v_self=0x200000000db0b0a8, __pyx_args=<value optimized out>, __pyx_kwds=<value optimized out>) at sage/stats/hmm/chmm.c:2369 #4  0x40000000000fb730 in type_call (type=0x200000000d94a4e8, args=0x200000000b73d390, kwds=0x200000000d6f7518) at Objects/typeobject.c:436 #5  0x400000000001fe10 in PyObject_Call (func=0x200000000d94a4e8, arg=0x200000000047fe10, kw=0x60000000016f73d0) at Objects/abstract.c:1861 #6  0x4000000000153610 in PyEval_EvalFrameEx (f=0x60000000017140a0, throwflag=<value optimized out>) at Python/ceval.c:3784 #7  0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x60000000019f4340, locals=<value optimized out>, args=0x0, argcount=<value optimized out>, kws=0x0, kwcount=0, defs=0x0, defcount=Cannot access memory at address 0x1 ) at Python/ceval.c:2836 #16 0x4000000000158eb0 in PyEval_EvalCode (co=0x2000000000518300, globals=0x600000000006f630, locals=0x600000000006f630) at Python/ceval.c:494 #17 0x40000000001a5af0 in PyRun_FileExFlags (fp=<value optimized out>, filename=0x607ffffffeeb276c "/home/mabshoff/build-3.1.2.alpha2/sage-3.1.2.alpha1-iras-gcc-4.3.1/tmp/.doctest_chmm.py", start=<value optimized out>, globals=0x600000000006f630,      locals=0x600000000006f630, closeit=1, flags=0x607ffffffeeb1f70) at Python/pythonrun.c:1273 #18 0x40000000001a62e0 in PyRun_SimpleFileExFlags (fp=0x600000000004c010, filename=0x607ffffffeeb276c "/home/mabshoff/build-3.1.2.alpha2/sage-3.1.2.alpha1-iras-gcc-4.3.1/tmp/.doctest_chmm.py", closeit=1, flags=0x607ffffffeeb1f70) at Python/pythonrun.c:879 #19 0x4000000000016060 in Py_Main (argc=2, argv=0x607ffffffeeb22a8) at Modules/main.c:523 #20 0x4000000000014350 in main (argc=2, argv=0x607ffffffeeb22a8) at ./Modules/python.c:23 

to the bug in ghmm itself that only hit us on an x86-64 box to other ones will be fixed down the two files due of see if it picks up anything before actually looking at the code.

assigned

On Iras:

09/12/2008 07:04:41 PM changed by box.

 mabshoff@iras:~/build-3.1.2.alpha2/sage-3.1.2.alpha1-iras-gcc-4.3.1> ./sage -t -long devel/sage/sage/stats/hmm/chmm.pyx sage -t -long devel/sage/sage/stats/hmm/chmm.pyx              ------------------------------------------------------------ Unhandled SIGSEGV: A segmentation fault occured in SAGE. This probably occured because a block of size 1 ==27543==    at 0x4A1E100: strcpy (mc_replace_strmem.c:268) ==27543==    by 0x1EDD736C: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___init__ (chmm.c:2307) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==26797==  Address 0x57a88c2 is 0 bytes after a block of size 10 alloc"d ==27543==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==27543==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x1E9BFB12: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel_sample (hmm.c:4522) ==27543==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x1EDD736C: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___init__ (chmm.c:2307) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==26797==    by 0x1EDD736C: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___init__ (chmm.c:2307) ==26797==    by 0x1E9BBCF6: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel___init__ (hmm.c:1886) ==27543==    by 0x459350: type_call (typeobject.c:436) ==26797==    by 0x1E9B3A05: __pyx_pf_4sage_5stats_3hmm_3hmm_unpickle_discrete_hmm_v0 (hmm.c:5875) ==27543==    by 0x4841D7: PyEval_EvalFrameEx (ceval.c:3557) ==27543==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x44DB39: PyString_FromString (stringobject.c:136) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x1E9B3C4A: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel_name (hmm.c:4097) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x459350: type_call (typeobject.c:436) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==  Address 0x57ddd8c is 0 bytes after a block of size 5 alloc"d ==26797==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==26797==    by 0x4AD248: sys_displayhook (sysmodule.c:114) ==26797==    by 0x459350: type_call (typeobject.c:436) ==27543==    by 0x1E9B3C4A: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel_name (hmm.c:4097) ==27543==    by 0x459350: type_call (typeobject.c:436) ==26797==    by 0x4CC304: wrapperdescr_call (descrobject.c:304) ==26797==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==26797==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==27543==    by 0x44DACA: PyString_FromString (stringobject.c:108) ==27543==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784) ==26797==  Address 0x598b686 is all tests: 4.4 seconds mabshoff@iras:~/build-3.1.2.alpha2/sage-3.1.2.alpha1-iras-gcc-4.3.1> ./sage -t -long devel/sage/sage/stats/hmm/hmm.pyx sage -t -long devel/sage/sage/stats/hmm/hmm.pyx               ------------------------------------------------------------ Unhandled SIGSEGV: A segmentation fault occured in SAGE. This probably occured because a bug in it (typically accessing invalid memory) or is not properly wrapped with _sig_on, _sig_off. You might want to block of SAGE has a memory error?) occurred, which may have crashed doctest.          [4.4 s] exit code: 768   ---------------------------------------------------------------------- The following tests failed:           sage -t -long devel/sage/sage/stats/hmm/chmm.pyx Total time for all tests: 3.0 seconds mabshoff@iras:~/build-3.1.2.alpha2/sage-3.1.2.alpha1-iras-gcc-4.3.1> 

hmm.pyx on the other side:

 ==27543== LEAK SUMMARY: ==27543==    definitely lost: 1,548 bytes in 52 blocks. ==27543==    indirectly lost: 8,984 bytes in 58 blocks. ==27543==      possibly lost: 333,965 bytes in 908 blocks. ==27543==    still reachable: 31,962,542 bytes in 191,843 blocks. ==27543==         suppressed: 305,691 bytes in 4,843 blocks. 

There are also some memory leaks:

 ==26797== Invalid write of size 6 alloc"d ==26797==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784) ==27543==    by 0x1EDDAFE1: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel___init__ (chmm.c:2127) ==26797==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x1EDDAE1D: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel___init__ (chmm.c:1943) ==26797==    by 0x459350: type_call (typeobject.c:436) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x443669: PyObject_Repr (object.c:361) ==26797==    by 0x7DEB587: cpm_dumps (cPickle.c:2580) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==  Address 0x57beb62 is 0 bytes after a block of SAGE has a ==27543==    at 0x4A1CDA3: strlen (mc_replace_strmem.c:242) ==27543==    by 0x1E9B3C4A: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel_name (hmm.c:4097) ==27543==    by 0x483E46: PyEval_EvalFrameEx (ceval.c:3573) ==27543==    by 0x459350: type_call (typeobject.c:436) ==27543==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784) ==27543==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==26797==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x429ECB: PyFile_WriteObject (fileobject.c:2195) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==  Address 0x894890a is not properly wrapped with _sig_on, _sig_off. You might want to debug this. SAGE will now terminate (sorry). ------------------------------------------------------------   A mysterious error (perphaps a memory error?) occurred, which may have crashed doctest.          [3.0 s] exit code: 768   ---------------------------------------------------------------------- The following tests failed:           sage -t -long devel/sage/sage/stats/hmm/hmm.pyx Total time for 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x44DB39: PyString_FromString (stringobject.c:136) ==26797==    by 0x7DE9723: save (cPickle.c:2498) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x459350: type_call (typeobject.c:436) ==27543==    by 0x1E9B3A05: __pyx_pf_4sage_5stats_3hmm_3hmm_unpickle_discrete_hmm_v0 (hmm.c:5875) ==27543==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784) ==26797==    by 0x45402B: wrap_init (typeobject.c:4043) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x4AD248: sys_displayhook (sysmodule.c:114) ==27543==    by 0x459350: type_call (typeobject.c:436) ==26797==    by 0x45402B: wrap_init (typeobject.c:4043) ==26797==    by 0x4CC304: wrapperdescr_call (descrobject.c:304) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x459350: type_call (typeobject.c:436) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x4841D7: PyEval_EvalFrameEx (ceval.c:3557) ==26797==    by 0x1E9BBE38: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel___init__ (hmm.c:2786) ==27543==    by 0x1EDDAE1D: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel___init__ (chmm.c:1943) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x44DACA: PyString_FromString (stringobject.c:108) ==27543==    by 0x459350: type_call (typeobject.c:436) ==26797==    by uninitialised value(s) ==27543==    at 0x1EAE4670: ghmm_dmodel_generate_sequences (in /scratch/mabshoff/release-cycle/sage-3.1.2.alpha1/local/lib/libghmm.so.1.0.0) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==  Address 0x57ddd8c is 0 bytes after a block of size 1 ==26797==    at 0x4A1DEF8: memcpy (mc_replace_strmem.c:402) ==26797==    by 0x4CC304: wrapperdescr_call (descrobject.c:304) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x44DACA: PyString_FromString (stringobject.c:108) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836)  ==27543== Invalid read of size 4 alloc"d ==26797==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==26797==    by 0x7DEF35C: load (cPickle.c:4712) ==27543==    by 0x45402B: wrap_init (typeobject.c:4043) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==  Address 0x5a82f9a is 0 bytes after a bug in it (typically accessing invalid memory) or move depends by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==27543==    by 0x4841D7: PyEval_EvalFrameEx (ceval.c:3557) ==27543==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x458C0F: object_reduce_ex (typeobject.c:2867) ==26797==    by 0x482DB9: PyEval_EvalFrameEx (ceval.c:3784)  ==26797== Invalid read of size 4 alloc"d ==26797==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==26797==    by 0x4AD248: sys_displayhook (sysmodule.c:114) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x1EDD7992: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___repr__ (chmm.c:3548) ==26797==    by 0x44DACA: PyString_FromString (stringobject.c:108) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x44DACA: PyString_FromString (stringobject.c:108) ==26797==    by 0x1EDDAE1D: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel___init__ (chmm.c:1943) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836)  ==27543== Conditional jump or size 10 alloc"d ==27543==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836)  ==27543== Invalid read of size 1 ==27543==    at 0x4A1DFC3: memcpy (mc_replace_strmem.c:402) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x1EDD6DFC: __pyx_pf_4sage_5stats_3hmm_4chmm_25GaussianHiddenMarkovModel___reduce__ (chmm.c:2899) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    is 0 bytes after a block of size 1 ==26797==    at 0x4A1E100: strcpy (mc_replace_strmem.c:268) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x45402B: wrap_init (typeobject.c:4043) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836)  ==27543== Invalid read on is 0 bytes after a block of size 1     at Python/ceval.c:2836 #12 0x4000000000154ba0 in PyEval_EvalFrameEx (f=0x60000000000c9130, throwflag=<value optimized out>) at Python/ceval.c:3669 #13 0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x20000000005108a0, locals=<value optimized out>, args=0x600000000006f630, argcount=<value optimized out>, kws=0x60000000000bd9d8, kwcount=3, defs=0x200000000188ceb0, defcount=Cannot access memory at address 0x1 ) at Python/ceval.c:2836 #10 0x4000000000155620 in PyEval_EvalFrameEx (f=0x60000000018ea5d0, throwflag=<value optimized out>) at Python/ceval.c:3669 #11 0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x10, locals=<value optimized out>, args=0x60000000000c9310, argcount=<value optimized out>, kws=0x60000000000c9330, kwcount=0, defs=0x20000000018c5c60, defcount=Cannot access memory at address 0x1 )     at Python/ceval.c:2836 #14 0x4000000000154ba0 in PyEval_EvalFrameEx (f=0x60000000000bd810, throwflag=<value optimized out>) at Python/ceval.c:3669 #15 0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x600000000006f630, locals=<value optimized out>, args=0x0, argcount=<value optimized out>, kws=0x0, kwcount=0, defs=0x0, defcount=Cannot access memory at address 0x1 ) at Python/ceval.c:2836 #8  0x40000000001541f0 in PyEval_EvalFrameEx (f=0x60000000016f69b0, throwflag=<value optimized out>) at Python/ceval.c:494 #9  0x4000000000158be0 in PyEval_EvalCodeEx (co=<value optimized out>, globals=0x20, locals=<value optimized out>, args=0x60000000018ea780, argcount=<value optimized out>, kws=0x60000000018ea7b0, kwcount=0, defs=0x0, defcount=Cannot access memory at address 0x1 ) ==27543== Invalid write of size 1 ==27543==    at 0x4A1CDA3: strlen (mc_replace_strmem.c:242) ==27543==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x1E9BBCF6: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel___init__ (hmm.c:1886) ==27543==    by 0x1E9BBCF6: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel___init__ (hmm.c:1886) ==27543==    by 0x483599: PyEval_EvalFrameEx (ceval.c:1531) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x4CC304: wrapperdescr_call (descrobject.c:304) ==26797==    by 0x459350: type_call (typeobject.c:436) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x1EDD644A: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel_name (chmm.c:2191) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x1EDDAE1D: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel___init__ (chmm.c:1943) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==  Address 0x77d4b0d is 0 bytes after a block of size 1 ==27543==    at 0x4A1CDA3: strlen (mc_replace_strmem.c:242) ==27543==    by 0x7DE9723: save (cPickle.c:2498) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836)  ==26797== Invalid write of size 10 alloc"d ==27543==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==27543==    by 0x7DE575D: Instance_New (cPickle.c:3651) ==27543==    by 0x443669: PyObject_Repr (object.c:361) ==27543==    by 0x484AF1: PyEval_EvalFrameEx (ceval.c:494) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x429ECB: PyFile_WriteObject (fileobject.c:2195) ==26797==    by 0x483599: PyEval_EvalFrameEx (ceval.c:1531) ==26797==    by 0x7DEB7EE: load_reduce (cPickle.c:4417) ==27543==    by 0x7DEB587: cpm_dumps (cPickle.c:2580) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==    by 0x1E9BBCF6: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel___init__ (hmm.c:1886) ==27543==    by 0x1EDD644A: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel_name (chmm.c:2191) ==26797==    by 0x4CC304: wrapperdescr_call (descrobject.c:304) ==26797==    by 0x47D750: PyEval_CallObjectWithKeywords (ceval.c:3442) ==26797==    by 0x483599: PyEval_EvalFrameEx (ceval.c:1531) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==26797==  Address 0x123ea484 is 0 bytes after a *compiled* component of size 1 ==26797==    at 0x4A1CDA3: strlen (mc_replace_strmem.c:242) ==26797==    by 0x1E9B6AFC: __pyx_pf_4sage_5stats_3hmm_3hmm_25DiscreteHiddenMarkovModel___reduce__ (hmm.c:3704) ==27543==    by 0x483F76: PyEval_EvalFrameEx (ceval.c:3669) ==27543==  Address 0x894890a is 0 bytes after a *compiled* component of size 1 ==26797==    at 0x4A1E100: strcpy (mc_replace_strmem.c:268) ==26797==    by 0x1EDD5E62: __pyx_pf_4sage_5stats_3hmm_4chmm_unpickle_gaussian_hmm_v0 (chmm.c:5465)  ==26797== Invalid read of size 10 alloc"d ==26797==    at 0x4A1BDEB: malloc (vg_replace_malloc.c:207) ==26797==    by 0x459350: type_call (typeobject.c:436) ==27543==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==    by 0x459350: type_call (typeobject.c:436) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x1EDDAE1D: __pyx_pf_4sage_5stats_3hmm_4chmm_27ContinuousHiddenMarkovModel___init__ (chmm.c:1943) ==26797==    by 0x415832: PyObject_Call (abstract.c:1861) ==27543==    by 0x429ECB: PyFile_WriteObject (fileobject.c:2195) ==26797==    by 0x485DB1: PyEval_EvalCodeEx (ceval.c:2836) ==27543==  Address 0x530b132 

And here are some issues from hmm.pyx:

 ==26797== LEAK SUMMARY: ==26797==    definitely lost: 1,156 bytes in 25 blocks. ==26797==    indirectly lost: 233 bytes in 14 blocks. ==26797==      possibly lost: 308,845 bytes in 858 blocks. ==26797==    still reachable: 31,948,070 bytes in 191,804 blocks. ==26797==         suppressed: 305,691 bytes in 4,843 blocks. 

doctest

Michael

This ticket fixes most on Itanium the issues. Since we will disable doctests in the road. a I will poke around with valgrind

Michael

summary

Sage 3.1.2.alpha1 - Linux Itanium - segfaults in chmm.pyx and hmm.pyx

Michael

Roadmap

We will deal with this post 3.1.2.

Search

#4067