python crash

John Reid j.reid at mail.cryst.bbk.ac.uk
Fri Apr 10 19:05:24 CEST 2009


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




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