#4934: matrix1.pyx refernece related doctest crash on cicero
----------------------+-----------------------------------------------------
Reporter: mabshoff | Owner: robertwb
Type: defect | Status: new
Priority: blocker | Milestone: sage-3.2.3
Component: doctest | Keywords:
----------------------+-----------------------------------------------------
The following looks very much like a Cython reference issue: When
doctesting matrix1.pyx it segfaults at this point:
{{{
<SNIP>
sage: a = matrix([[pi, sin(x)], [cos(x), 1/e]]); a
[ pi sin(x)]
[cos(x) e^-1]
sage: a._mathematica_init_()
'{{Pi, Sin[x]}, {Cos[x], (E) ^ (-1)}}'
sage:
}}}
Valgrind says:
{{{
==26254== Invalid read of size 4
==26254== at 0x809FC3E: slot_tp_del (typeobject.c:5024)
==26254== by 0x809D32F: subtype_dealloc (typeobject.c:664)
==26254== by 0xD99F3FB:
__pyx_tp_dealloc_4sage_6matrix_21matrix_symbolic_dense_Matrix_symbolic_dense
(matrix_symbolic_dense.c:6534)
==26254== by 0x808643B: PyDict_Clear (dictobject.c:757)
==26254== by 0x8086460: dict_clear (dictobject.c:1776)
==26254== by 0x80CC54A: PyEval_EvalFrameEx (ceval.c:3557)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x8114835: function_call (funcobject.c:517)
==26254== by 0x805B126: PyObject_Call (abstract.c:1861)
==26254== by 0x806130E: instancemethod_call (classobject.c:2519)
==26254== by 0x805B126: PyObject_Call (abstract.c:1861)
==26254== by 0x80C9D85: PyEval_EvalFrameEx (ceval.c:3784)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x80CC61E: PyEval_EvalFrameEx (ceval.c:3669)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x80CC61E: PyEval_EvalFrameEx (ceval.c:3669)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x80CC61E: PyEval_EvalFrameEx (ceval.c:3669)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x80CDEB6: PyEval_EvalCode (ceval.c:494)
==26254== by 0x80EB24E: PyRun_FileExFlags (pythonrun.c:1273)
==26254== by 0x80EB519: PyRun_SimpleFileExFlags (pythonrun.c:879)
==26254== by 0x805705A: Py_Main (main.c:523)
==26254== by 0x8056431: main (python.c:23)
==26254== Address 0x68cdeac is 12 bytes inside a block of size 36 free'd
==26254== at 0x400593A: free (vg_replace_malloc.c:323)
==26254== by 0x57E1594:
__pyx_tp_dealloc_4sage_9structure_11sage_object_SageObject
(sage_object.c:7414)
==26254== by 0x6181EC3:
__pyx_tp_dealloc_4sage_9structure_7element_Element (element.c:18963)
==26254== by 0x809D4C4: subtype_dealloc (typeobject.c:709)
==26254== by 0x806185B: instancemethod_dealloc (classobject.c:2311)
==26254== by 0x809FD02: slot_tp_del (typeobject.c:5014)
==26254== by 0x809D32F: subtype_dealloc (typeobject.c:664)
==26254== by 0xD99F3FB:
__pyx_tp_dealloc_4sage_6matrix_21matrix_symbolic_dense_Matrix_symbolic_dense
(matrix_symbolic_dense.c:6534)
==26254== by 0x808643B: PyDict_Clear (dictobject.c:757)
==26254== by 0x8086460: dict_clear (dictobject.c:1776)
==26254== by 0x80CC54A: PyEval_EvalFrameEx (ceval.c:3557)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x8114835: function_call (funcobject.c:517)
==26254== by 0x805B126: PyObject_Call (abstract.c:1861)
==26254== by 0x806130E: instancemethod_call (classobject.c:2519)
==26254== by 0x805B126: PyObject_Call (abstract.c:1861)
==26254== by 0x80C9D85: PyEval_EvalFrameEx (ceval.c:3784)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x80CC61E: PyEval_EvalFrameEx (ceval.c:3669)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x80CC61E: PyEval_EvalFrameEx (ceval.c:3669)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x80CC61E: PyEval_EvalFrameEx (ceval.c:3669)
==26254== by 0x80CDCA4: PyEval_EvalCodeEx (ceval.c:2836)
==26254== by 0x80CDEB6: PyEval_EvalCode (ceval.c:494)
}}}
The segfault is in auto-generated code:
{{{
static void
__pyx_tp_dealloc_4sage_6matrix_21matrix_symbolic_dense_Matrix_symbolic_dense(PyObject
*o) {
struct
__pyx_obj_4sage_6matrix_21matrix_symbolic_dense_Matrix_symbolic_dense
*p = (struct
__pyx_obj_4sage_6matrix_21matrix_symbolic_dense_Matrix_symbolic_dense *)o;
Py_XDECREF(p->_maxima); [this is line 6534]
Py_XDECREF(p->__variables);
Py_XDECREF(p->__number_of_args);
Py_XDECREF(p->_simp);
__pyx_ptype_4sage_6matrix_12matrix_dense_Matrix_dense->tp_dealloc(o);
}
}}}
Running it all by itself is clean:
{{{
[mabsh...@cicero sage-3.2.3.final-cicero]$ ./sage -valgrind
----------------------------------------------------------------------
| Sage Version 3.2.3.final, Release Date: 2009-01-02 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
/home/mabshoff/build-3.2.3.final/sage-3.2.3.final-cicero/local/bin/sage-
ipython
Log file is /home/mabshoff/.sage/valgrind/sage-memcheck.%p
Using default flags:
--leak-resolution=high --leak-check=full --num-callers=25
--suppressions=/home/mabshoff/build-3.2.3.final/sage-3.2.3.final-cicero/
local/lib/valgrind/sage.supp
==26391== Memcheck, a memory error detector.
==26391== Copyright (C) 2002-2007, and GNU GPL'd, by Julian Seward et al.
==26391== Using LibVEX rev 1854, a library for dynamic binary translation.
==26391== Copyright (C) 2004-2007, and GNU GPL'd, by OpenWorks LLP.
==26391== Using valgrind-3.3.1, a dynamic binary instrumentation
framework.
==26391== Copyright (C) 2000-2007, and GNU GPL'd, by Julian Seward et al.
==26391== For more details, rerun with: -v
==26391==
Python 2.5.2 (r252:60911, Jan 3 2009, 15:33:57)
[GCC 4.3.0 20080428 (Red Hat 4.3.0-8)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
sage: a = matrix([[pi, sin(x)], [cos(x), 1/e]]); a
[ pi sin(x)]
[cos(x) e^-1]
sage: a._mathematica_init_()
'{{Pi, Sin[x]}, {Cos[x], (E) ^ (-1)}}'
sage:
Exiting SAGE (CPU time 0m5.61s, Wall time 3m4.55s).
Exiting spawned Maxima process.
==26391==
==26391== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 1321 from
1)
==26391== malloc/free: in use at exit: 24,986,088 bytes in 215,178 blocks.
==26391== malloc/free: 783,764 allocs, 568,586 frees, 100,000,527 bytes
allocated.
==26391== For counts of detected errors, rerun with: -v
==26391== searching for pointers to 215,178 not-freed blocks.
==26391== checked 30,982,372 bytes.
}}}
3.2.3.alpha0 with
{{{
[mabsh...@cicero sage-3.2.3.alpha0-cicero-gcc432]$ gcc -v
Using built-in specs.
Target: i686-pc-linux-gnu
Configured with: /usr/local/gcc-4.3.2/src/gcc-4.3.2/configure
--enable-languages=c,c++,fortran
--with-gmp=/usr/local/gmp-4.2.3/x86-Linux-fc8-gcc-4.3.1
--with-mpfr=/usr/local/mpfr-2.3.2/x86-Linux-fc8-gmp-4.2.3-gcc-4.3.1
--prefix=/usr/local/gcc-4.3.2/x86-Linux-fc8
Thread model: posix
gcc version 4.3.2 (GCC)
}}}
works fine. But 3.2.3.rc0 with
{{{
[mabsh...@cicero sage-3.2.3.alpha0-cicero-gcc432]$ gcc -v
Using built-in specs.
Target: i386-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man
--infodir=/usr/share/info --with-
bugurl=http://bugzilla.redhat.com/bugzilla
--enable-bootstrap --enable-shared --enable-threads=posix
--enable-checking=release --with-system-zlib --enable-__cxa_atexit
--disable-libunwind-exceptions --enable-
languages=c,c++,objc,obj-c++,java,fortran,ada
--enable-java-awt=gtk --disable-dssi --enable-plugin
--with-java-home=/usr/lib/jvm/java-1.5.0-gcj-1.5.0.0/jre
--enable-libgcj-multifile --enable-java-maintainer-mode
--with-ecj-jar=/usr/share/java/eclipse-ecj.jar
--disable-libjava-multilib --with-cpu=generic --build=i386-redhat-linux
Thread model: posix
gcc version 4.3.0 20080428 (Red Hat 4.3.0-8) (GCC)
}}}
has trouble.
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/4934>
Sage <http://sagemath.org/>
Sage - Open Source Mathematical Software: Building the Car Instead of
Reinventing the Wheel
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