python crash

Discussion in 'Python' started by John Reid, Apr 10, 2009.

  1. John Reid

    John Reid Guest

    Python crashes in glibc with the following stack trace. I'm using an
    interface to R (rpy2), ipython, matplotlib, numpy, and scipy with a wx
    backend. I'm not sure if the stack trace shows which is the culprit.
    I've probably misconfigured one of their installs but knowing which one
    to recompile is a bit of a problem. They all took some time to install
    so I don't really want to start from scratch again and there's no
    knowing if that would fix it anyhow.

    I'm on 64 bit Ubuntu:
    Linux john-dell 2.6.27-11-generic #1 SMP Wed Apr 1 20:53:41 UTC 2009
    x86_64 GNU/Linux

    Python 2.5.2
    Numpy: 1.2.1
    Scipy: 0.7.0rc2
    IPython: 0.9.1
    matplotlib: 0.98.5.2
    wx: 2.8.8.0 (gtk2-unicode)

    I suspect it is something to do with matplotlib as I think it happens
    when I'm plotting stuff but its not completely reproducible.

    Also, I'm using the Ubuntu python package but I've built numpy, scipy
    and matplotlib myself. I didn't think this would be a problem though.

    Any help appreciated.

    Thanks,
    John.



    *** glibc detected *** /usr/bin/python2.5: free(): invalid pointer:
    0x00007f6e499967a0 ***
    ======= Backtrace: =========
    /lib/libc.so.6[0x7f6e6dcf1a58]
    /lib/libc.so.6(cfree+0x76)[0x7f6e6dcf40a6]
    /usr/lib/python2.5/lib-dynload/readline.so[0x7f6e6aa7fcd0]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x57e2)[0x491052]
    /usr/bin/python2.5(PyEval_EvalCodeEx+0x6ad)[0x4927cd]
    /usr/bin/python2.5[0x4dd4c2]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5[0x41fb08]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5(PyEval_CallObjectWithKeywords+0x72)[0x48a852]
    /usr/bin/python2.5(PyInstance_New+0x86)[0x422956]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x3d12)[0x48f582]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x6872)[0x4920e2]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x6872)[0x4920e2]
    /usr/bin/python2.5(PyEval_EvalCodeEx+0x6ad)[0x4927cd]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x5483)[0x490cf3]
    /usr/bin/python2.5(PyEval_EvalCodeEx+0x6ad)[0x4927cd]
    /usr/bin/python2.5[0x4dd4c2]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5[0x41fb08]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5(PyEval_CallObjectWithKeywords+0x72)[0x48a852]
    /usr/bin/python2.5(PyInstance_New+0x86)[0x422956]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x3d12)[0x48f582]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x6872)[0x4920e2]
    /usr/bin/python2.5(PyEval_EvalCodeEx+0x6ad)[0x4927cd]
    /usr/bin/python2.5(PyEval_EvalCode+0x32)[0x4929c2]
    /usr/bin/python2.5(PyRun_FileExFlags+0x108)[0x4b2678]
    /usr/bin/python2.5[0x489948]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x57e2)[0x491052]
    /usr/bin/python2.5(PyEval_EvalCodeEx+0x6ad)[0x4927cd]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x4cf8)[0x490568]
    /usr/bin/python2.5(PyEval_EvalCodeEx+0x6ad)[0x4927cd]
    /usr/bin/python2.5[0x4dd4c2]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5[0x41fb08]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x3d12)[0x48f582]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x6872)[0x4920e2]
    /usr/bin/python2.5(PyEval_EvalCodeEx+0x6ad)[0x4927cd]
    /usr/bin/python2.5[0x4dd4c2]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5[0x41fb08]
    /usr/bin/python2.5(PyObject_Call+0x13)[0x418c33]
    /usr/bin/python2.5(PyEval_CallObjectWithKeywords+0x72)[0x48a852]
    /usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core_.so(_ZN12wxPyCallback12EventThunkerER7wxEvent+0x107)[0x7f6e662099d7]
    /usr/lib/libwx_baseu-2.8.so.0(_ZN12wxEvtHandler21ProcessEventIfMatchesERK21wxEventTableEntryBasePS_R7wxEvent+0x89)[0x7f6e64556ca9]
    /usr/lib/libwx_baseu-2.8.so.0(_ZN12wxEvtHandler23SearchDynamicEventTableER7wxEvent+0x54)[0x7f6e64556e54]
    /usr/lib/libwx_baseu-2.8.so.0(_ZN12wxEvtHandler12ProcessEventER7wxEvent+0x92)[0x7f6e64557f42]
    /usr/lib/libwx_gtk2u_core-2.8.so.0(_ZN11wxTimerBase6NotifyEv+0x66)[0x7f6e64ee51d6]
    /usr/lib/libwx_gtk2u_core-2.8.so.0[0x7f6e64dec3cb]
    /usr/lib/libglib-2.0.so.0[0x7f6e623a551b]
    /usr/lib/libglib-2.0.so.0(g_main_context_dispatch+0x23b)[0x7f6e623a4d5b]
    /usr/lib/libglib-2.0.so.0[0x7f6e623a852d]
    /usr/lib/libglib-2.0.so.0(g_main_loop_run+0x1cd)[0x7f6e623a8a5d]
    /usr/lib/libgtk-x11-2.0.so.0(gtk_main+0xa7)[0x7f6e63fb17a7]
    /usr/lib/libwx_gtk2u_core-2.8.so.0(_ZN11wxEventLoop3RunEv+0x48)[0x7f6e64de3d18]
    /usr/lib/libwx_gtk2u_core-2.8.so.0(_ZN9wxAppBase8MainLoopEv+0x4b)[0x7f6e64e6cf4b]
    /usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core_.so(_ZN7wxPyApp8MainLoopEv+0x37)[0x7f6e66208cd7]
    /usr/lib/python2.5/site-packages/wx-2.8-gtk2-unicode/wx/_core_.so[0x7f6e6626707e]
    /usr/bin/python2.5(PyEval_EvalFrameEx+0x562b)[0x490e9b]
    ======= Memory map: ========
    00400000-00525000 r-xp 00000000 08:05 4825998
    /usr/bin/python2.5
    00724000-00725000 r--p 00124000 08:05 4825998
    /usr/bin/python2.5
    00725000-00757000 rw-p 00125000 08:05 4825998
    /usr/bin/python2.5
    00757000-0075f000 rw-p 00757000 00:00 0
    018e9000-0d5d6000 rw-p 018e9000 00:00 0
    [heap]
    405bc000-405bd000 ---p 405bc000 00:00 0
    405bd000-40dbd000 rwxp 405bd000 00:00 0
    40dbd000-40dbf000 rwxp 00000000 00:0e 696
    /dev/zero
    40dbf000-40dc0000 ---p 40dbf000 00:00 0
    40dc0000-415c0000 rwxp 40dc0000 00:00 0
    41cb3000-41cb4000 ---p 41cb3000 00:00 0
    41cb4000-424b4000 rwxp 41cb4000 00:00 0
    7f6e487a6000-7f6e4880b000 r-xp 00000000 08:05 5318973
    /usr/local/lib64/R/library/stats/libs/stats.so
    7f6e4880b000-7f6e48a0a000 ---p 00065000 08:05 5318973
    /usr/local/lib64/R/library/stats/libs/stats.so
    7f6e48a0a000-7f6e48a0c000 r--p 00064000 08:05 5318973
    /usr/local/lib64/R/library/stats/libs/stats.so
    7f6e48a0c000-7f6e48a0e000 rw-p 00066000 08:05 5318973
    /usr/local/lib64/R/library/stats/libs/stats.so
    7f6e48a0e000-7f6e48a2c000 r-xp 00000000 08:05 5441873
    /usr/local/lib64/R/library/grDevices/libs/grDevices.so
    7f6e48a2c000-7f6e48c2b000 ---p 0001e000 08:05 5441873
    /usr/local/lib64/R/library/grDevices/libs/grDevices.so
    7f6e48c2b000-7f6e48c2c000 r--p 0001d000 08:05 5441873
    /usr/local/lib64/R/library/grDevices/libs/grDevices.so
    7f6e48c2c000-7f6e48c2d000 rw-p 0001e000 08:05 5441873
    /usr/local/lib64/R/library/grDevices/libs/grDevices.so
    7f6e48c2d000-7f6e48c33000 r-xp 00000000 08:05 5400895
    /usr/local/lib64/R/library/methods/libs/methods.so
    7f6e48c33000-7f6e48e33000 ---p 00006000 08:05 5400895
    /usr/local/lib64/R/library/methods/libs/methods.so
    7f6e48e33000-7f6e48e34000 r--p 00006000 08:05 5400895
    /usr/local/lib64/R/library/methods/libs/methods.so
    7f6e48e34000-7f6e48e35000 rw-p 00007000 08:05 5400895
    /usr/local/lib64/R/library/methods/libs/methods.so
    7f6e48e35000-7f6e48e63000 r-xp 00000000 08:05 5145219
    /usr/local/lib64/R/lib/libRblas.so
    7f6e48e63000-7f6e49062000 ---p 0002e000 08:05 5145219
    /usr/local/lib64/R/lib/libRblas.so
    7f6e49062000-7f6e49063000 r--p 0002d000 08:05 5145219
    /usr/local/lib64/R/lib/libRblas.so
    7f6e49063000-7f6e49064000 rw-p 0002e000 08:05 5145219
    /usr/local/lib64/R/lib/libRblas.so
    7f6e49064000-7f6e491df000 r-xp 00000000 08:05 5145229
    /usr/local/lib64/R/lib/libRlapack.so
    7f6e491df000-7f6e493df000 ---p 0017b000 08:05 5145229
    /usr/local/lib64/R/lib/libRlapack.so
    7f6e493df000-7f6e493e0000 r--p 0017b000 08:05 5145229
    /usr/local/lib64/R/lib/libRlapack.so
    7f6e493e0000-7f6e493e1000 rw-p 0017c000 08:05 5145229
    /usr/local/lib64/R/lib/libRlapack.so
    7f6e493e1000-7f6e4945d000 rw-p 7f6e493e1000 00:00 0
    7f6e4945d000-7f6e496ea000 r-xp 00000000 08:05 5145224
    /usr/local/lib64/R/lib/libR.so
    7f6e496ea000-7f6e498ea000 ---p 0028d000 08:05 5145224
    /usr/local/lib64/R/lib/libR.so
    7f6e498ea000-7f6e498ef000 r--p 0028d000 08:05 5145224
    /usr/local/lib64/R/lib/libR.so
    7f6e498ef000-7f6e498ff000 rw-p 00292000 08:05 5145224
    /usr/local/lib64/R/lib/libR.so
    7f6e498ff000-7f6e49998000 rw-p 7f6e498ff000 00:00 0
    7f6e49998000-7f6e499a4000 r-xp 00000000 08:05 4909357
    /usr/lib/python2.5/site-packages/_rpy2081.so
    7f6e499a4000-7f6e49ba3000 ---p 0000c000 08:05 4909357
    /usr/lib/python2.5/site-packages/_rpy2081.so
    7f6e49ba3000-7f6e49ba4000 r--p 0000b000 08:05 4909357
    /usr/lib/python2.5/site-packages/_rpy2081.so
    7f6e49ba4000-7f6e49ba5000 rw-p 0000c000 08:05 4909357
    /usr/lib/python2.5/site-packages/_rpy2081.so
    7f6e49ba5000-7f6e49dae000 rw-p 7f6e49ba5000 00:00 0
    7f6e49dae000-7f6e49db1000 r-xp 00000000 08:05 2900033
    /lib/libgpg-error.so.0.3.0
    7f6e49db1000-7f6e49fb0000 ---p 00003000 08:05 2900033
    /lib/libgpg-error.so.0.3.0
    7f6e49fb0000-7f6e49fb1000 rw-p 00002000 08:05 2900033
    /lib/libgpg-error.so.0.3.0
    7f6e49fb1000-7f6e4a016000 r-xp 00000000 08:05 2900031
    /lib/libgcrypt.so.11.4.4
    7f6e4a016000-7f6e4a215000 ---p 00065000 08:05 2900031
    /lib/libgcrypt.so.11.4.4
    7f6e4a215000-7f6e4a216000 r--p 00064000 08:05 2900031
    /lib/libgcrypt.so.11.4.4
    7f6e4a216000-7f6e4a218000 rw-p 00065000 08:05 2900031
    /lib/libgcrypt.so.11.4.4
    7f6e4a218000-7f6e4a228000 r-xp 00000000 08:05 4827546
    /usr/lib/libtasn1.so.3.0.15
    7f6e4a228000-7f6e4a427000 ---p 00010000 08:05 4827546
    /usr/lib/libtasn1.so.3.0.15
    7f6e4a427000-7f6e4a429000 rw-p 0000f000 08:05 4827546 Aborted
     
    John Reid, Apr 10, 2009
    #1
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