Bug#445851: libgl1-mesa-dri: segfault in radeon_dri.so on pymol startup
Package: libgl1-mesa-dri
Version: 7.0.1-2
The pymol application segfaults on startup right after it draws its two
windows and calls the glut main loop. Unfortunately, running it in gdb
(no matter whether locally or from remote) makes X unresponsive to X
events, I can still move around the mouse pointer, but nothing else, the
application needs to be killed remotely.
Running it with catchsegv yields this:
--8<--
PyMOL(TM) Molecular Graphics System, Version 1.0r1.
Copyright (C) 2007 by DeLano Scientific LLC.
All Rights Reserved.
Created by Warren L. DeLano, Ph.D.
Other Major Authors and Contributors:
Ralf W. Grosse-Kunstleve, Ph.D.
PyMOL is user-supported open-source software. Although some versions
are freely available, PyMOL is not in the public domain.
If PyMOL is helpful in your work or study, then please volunteer
support for our ongoing efforts to create open and affordable scientific
software by purchasing a PyMOL Maintenance and/or Support subscription.
More information can be found at "http://www.pymol.org";.
Enter "help" for a list of commands.
Enter "help <command-name>" for information on a specific command.
Hit ESC anytime to toggle between text and graphics.
Traceback (most recent call last):
File "<string>", line 1, in ?
File "/usr/lib/python2.4/UserDict.py", line 17, in __getitem__
def __getitem__(self, key): return self.data[key]
KeyError: 'PYMOL_PATH'
Traceback (most recent call last):
File "<string>", line 1, in ?
File "/usr/lib/python2.4/UserDict.py", line 17, in __getitem__
def __getitem__(self, key): return self.data[key]
KeyError: 'PYMOL_DATA'
Traceback (most recent call last):
File "<string>", line 1, in ?
File "/usr/lib/python2.4/UserDict.py", line 17, in __getitem__
def __getitem__(self, key): return self.data[key]
KeyError: 'PYMOL_PATH'
*** Segmentation fault
Register dump:
EAX: b4b92810 EBX: 08372ac8 ECX: 00000280 EDX: b2a8d008
ESI: 00000280 EDI: fffffff8 EBP: bff36e88 ESP: bff36e4c
EIP: b6bd7d5c EFLAGS: 00010292
CS: 0073 DS: 007b ES: 007b FS: 0000 GS: 0033 SS: 007b
Trap: 0000000e Error: 00000004 OldMask: 00000000
ESP/signal: bff36e4c CR2: 0000001f
FPUCW: ffff037f FPUSW: ffff4020 TAG: ffffffff
IPOFF: b6b26f98 CSSEL: 0073 DATAOFF: 082e1cc0 DATASEL: 007b
ST(0) 0000 8000000000000000 ST(1) 0000 0000000000000000
ST(2) 0000 8000000000000000 ST(3) 0000 8000000000000000
ST(4) 0000 ffff000000000000 ST(5) 0000 8000000000000000
ST(6) 0000 ffff000000000000 ST(7) 0000 8000000000000000
Backtrace:
/lib/libSegFault.so[0xb7f2304f]
??:0(??)[0xffffe420]
/usr/lib/dri/radeon_dri.so(_swrast_ReadPixels+0x10c0)[0xb6b9da10]
/usr/lib/dri/radeon_dri.so(_mesa_ReadPixels+0x12a)[0xb6bec5ca]
/var/lib/python-support/python2.4/pymol/_cmd.so(PyMOLReadPixels+0x13b)[0xb74f563b]
/var/lib/python-support/python2.4/pymol/_cmd.so(SceneCopy+0x1f7)[0xb754a0c7]
/var/lib/python-support/python2.4/pymol/_cmd.so(SceneRender+0x76e)[0xb755199e]
/var/lib/python-support/python2.4/pymol/_cmd.so(OrthoDoDraw+0xf2d)[0xb7514fdd]
/var/lib/python-support/python2.4/pymol/_cmd.so(ExecutiveDrawNow+0x1a7)[0xb7664aa7]
/var/lib/python-support/python2.4/pymol/_cmd.so(PyMOL_Draw+0x52)[0xb76dce62]
/var/lib/python-support/python2.4/pymol/_cmd.so[0xb76f57cb]
/var/lib/python-support/python2.4/pymol/_cmd.so[0xb76f6823]
/usr/lib/libglut.so.3[0xb73785d6]
/usr/lib/libglut.so.3(fgEnumWindows+0x42)[0xb737bad2]
/usr/lib/libglut.so.3(glutMainLoopEvent+0x5b1)[0xb7378e91]
/usr/lib/libglut.so.3(glutMainLoop+0x36)[0xb7379286]
/var/lib/python-support/python2.4/pymol/_cmd.so(was_main+0x2b8)[0xb76f7d18]
/var/lib/python-support/python2.4/pymol/_cmd.so[0xb76b7a44]
/usr/bin/python2.4(PyEval_EvalFrame+0x4ca7)[0x80b9f67]
/usr/bin/python2.4(PyEval_EvalCodeEx+0x835)[0x80bb125]
/usr/bin/python2.4(PyEval_EvalFrame+0x41d2)[0x80b9492]
/usr/bin/python2.4(PyEval_EvalCodeEx+0x835)[0x80bb125]
/usr/bin/python2.4(PyEval_EvalCode+0x57)[0x80bb197]
/usr/bin/python2.4(PyRun_FileExFlags+0xca)[0x80ddfba]
/usr/bin/python2.4(PyRun_SimpleFileExFlags+0x187)[0x80de1a7]
/usr/bin/python2.4(Py_Main+0xa82)[0x8057652]
/usr/bin/python2.4(main+0x22)[0x8056ac2]
/lib/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0xb7d9d050]
??:0(_start)[0x8056a31]
Memory map:
08048000-08120000 r-xp 00000000 03:08 207956 /usr/bin/python2.4
08120000-08142000 rw-p 000d7000 03:08 207956 /usr/bin/python2.4
08142000-0866a000 rw-p 08142000 00:00 0 [heap]
b2a8d000-b2c3c000 rw-p b2a8d000 00:00 0
b2c3c000-b2c44000 r-xp 00000000 03:08 103691 /usr/lib/libXcursor.so.1.0.2
b2c44000-b2c45000 rw-p 00007000 03:08 103691 /usr/lib/libXcursor.so.1.0.2
b2c52000-b2c93000 rw-p b2c52000 00:00 0
b2c93000-b2c94000 ---p b2c93000 00:00 0
b2c94000-b34d5000 rw-p b2c94000 00:00 0
b34d5000-b34d6000 ---p b34d5000 00:00 0
b34d6000-b3cd6000 rw-p b34d6000 00:00 0
b3cd6000-b3d81000 r-xp 00000000 03:08 103039 /usr/lib/libtcl8.4.so.0
b3d81000-b3d86000 rw-p 000ab000 03:08 103039 /usr/lib/libtcl8.4.so.0
b3d86000-b3d87000 rw-p b3d86000 00:00 0
b3d87000-b3e55000 r-xp 00000000 03:08 208641 /usr/lib/libtk8.4.so.0
b3e55000-b3e61000 rw-p 000ce000 03:08 208641 /usr/lib/libtk8.4.so.0
b3e61000-b3f34000 r-xp 00000000 03:08 208306 /usr/lib/libBLT.2.4.so.8.4
b3f34000-b3f46000 rw-p 000d2000 03:08 208306 /usr/lib/libBLT.2.4.so.8.4
b3f46000-b3f88000 rw-p b3f46000 00:00 0
b3f88000-b3f8f000 r-xp 00000000 03:08 101971 /usr/lib/libXrender.so.1.3.0
b3f8f000-b3f90000 rw-p 00007000 03:08 101971 /usr/lib/libXrender.so.1.3.0
b3f90000-b3fa4000 r-xp 00000000 03:08 47902 /lib/i686/cmov/libnsl-2.6.1.so
b3fa4000-b3fa6000 rw-p 00013000 03:08 47902 /lib/i686/cmov/libnsl-2.6.1.so
b3fa6000-b3fa8000 rw-p b3fa6000 00:00 0
b3faa000-b3fac000 r-xp 00000000 03:08 214193 /usr/lib/gconv/ISO8859-15.so
b3fac000-b3fae000 rw-p 00001000 03:08 214193 /usr/lib/gconv/ISO8859-15.so
b3fae000-b3fb5000 r--s 00000000 03:08 210054 /usr/lib/gconv/gconv-modules.cache
b3fb5000-b3fc3000 r-xp 00000000 03:08 246994 /usr/lib/python-support/pymol/python2.4/pymol/ExtensionClass.so
b3fc3000-b3fc4000 rw-p 0000d000 03:08 246994 /usr/lib/python-support/pymol/python2.4/pymol/ExtensionClass.so
b3fc4000-b3fe4000 r-xp 00000000 03:08 246996 /usr/lib/python-support/pymol/python2.4/pymol/sglite.so
b3fe4000-b3fe8000 rw-p 00020000 03:08 246996 /usr/lib/python-support/pymol/python2.4/pymol/sglite.so
b3fe8000-b4342000 rw-p b3fe8000 00:00 0
b4342000-b4822000 rw-s d0302000 00:0d 30226 /dev/dri/card0
b4822000-b4a22000 rw-s d0102000 00:0d 30226 /dev/dri/card0
b4a22000-b4a23000 r--s d0101000 00:0d 30226 /dev/dri/card0
b4a23000-b4a33000 r--s c0100000 00:0d 30226 /dev/dri/card0
b4a33000-b6a33000 rw-s e0000000 00:0d 30226 /dev/dri/card0
b6a33000-b6a51000 r-xp 00000000 03:08 212191 /usr/lib/libexpat.so.1.0.0
b6a51000-b6a53000 rw-p 0001d000 03:08 212191 /usr/lib/libexpat.so.1.0.0
b6a53000-b6a5d000 r-xp 00000000 03:08 223108 /usr/lib/python2.4/lib-dynload/_tkinter.so
b6a5d000-b6a5e000 rw-p 00009000 03:08 223108 /usr/lib/python2.4/lib-dynload/_tkinter.so
b6a5e000-b6a60000 rw-s f0cf9000 00:0d 30226 /dev/dri/card0
b6a60000-b6c7d000 r-xp 00000000 03:08 241145 /usr/lib/dri/radeon_dri.so
b6c7d000-b6c8c000 rw-p 0021d000 03:08 241145 /usr/lib/dri/radeon_dri.so
b6c8c000-b6d31000 rw-p b6c8c000 00:00 0
b6d32000-b6eb7000 rw-p b6d32000 00:00 0
b6eb7000-b6ebb000 r-xp 00000000 03:08 290741 /usr/lib/python2.4/lib-dynload/operator.so
b6ebb000-b6ebc000 rw-p 00004000 03:08 290741 /usr/lib/python2.4/lib-dynload/operator.so
b6ebc000-b6ecc000 r-xp 00000000 03:08 227943 /usr/lib/python2.4/lib-dynload/cPickle.so
b6ecc000-b6ecd000 rw-p 00010000 03:08 227943 /usr/lib/python2.4/lib-dynload/cPickle.so
b6ecd000-b6ed0000 r-xp 00000000 03:08 288173 /usr/lib/python2.4/lib-dynload/cStringIO.so
b6ed0000-b6ed1000 rw-p 00003000 03:08 288173 /usr/lib/python2.4/lib-dynload/cStringIO.so
b6ed1000-b6f12000 rw-p b6ed1000 00:00 0
b6f12000-b7043000 r-xp 00000000 03:08 223303 /usr/lib/i686/cmov/libcrypto.so.0.9.8
b7043000-b7059000 rw-p 00131000 03:08 223303 /usr/lib/i686/cmov/libcrypto.so.0.9.8
b7059000-b705c000 rw-p b7059000 00:00 0
b705c000-b709a000 r-xp 00000000 03:08 255920 /usr/lib/i686/cmov/libssl.so.0.9.8
b709a000-b709e000 rw-p 0003d000 03:08 255920 /usr/lib/i686/cmov/libssl.so.0.9.8
b709e000-b70a0000 r-xp 00000000 03:08 287757 /usr/lib/python2.4/lib-dynload/_random.so
b70a0000-b70a1000 rw-p 00002000 03:08 287757 /usr/lib/python2.4/lib-dynload/_random.so
b70a1000-b70a5000 r-xp 00000000 03:08 288175 /usr/lib/python2.4/lib-dynload/binascii.so
b70a5000-b70a6000 rw-p 00003000 03:08 288175 /usr/lib/python2.4/lib-dynload/binascii.so
b70a6000-b70aa000 r-xp 00000000 03:08 290745 /usr/lib/python2.4/lib-dynload/struct.so
b70aa000-b70ab000 rw-p 00004000 03:08 290745 /usr/lib/python2.4/lib-dynload/struct.so
b70ab000-b70ae000 r-xp 00000000 03:08 228077 /usr/lib/python2.4/lib-dynload/_ssl.so
b70ae000-b70af000 rw-p 00003000 03:08 228077 /usr/lib/python2.4/lib-dynload/_ssl.so
b70af000-b70b3000 r-xp 00000000 03:08 211566 /usr/lib/libXdmcp.so.6.0.0
b70b3000-b70b4000 rw-p 00003000 03:08 211566 /usr/lib/libXdmcp.so.6.0.0
b70b4000-b70b6000 r-xp 00000000 03:08 211564 /usr/lib/libXau.so.6.0.0
b70b6000-b70b7000 rw-p 00001000 03:08 211564 /usr/lib/libXau.so.6.0.0
b70b7000-b70c1000 r-xp 00000000 03:08 48224 /lib/libgcc_s.so.1
b70c1000-b70c2000 rw-p 00009000 03:08 48224 /lib/libgcc_s.so.1
b70c2000-b71a2000 r-xp 00000000 03:08 215928 /usr/lib/libstdc++.so.6.0.9
b71a2000-b71a5000 r--p 000e0000 03:08 215928 /usr/lib/libstdc++.so.6.0.9
b71a5000-b71a7000 rw-p 000e3000 03:08 215928 /usr/lib/libstdc++.so.6.0.9
b71a7000-b71ad000 rw-p b71a7000 00:00 0
b71ad000-b71b5000 r-xp 00000000 03:08 217294 /usr/lib/libdrm.so.2.3.0
b71b5000-b71b6000 rw-p 00008000 03:08 217294 /usr/lib/libdrm.so.2.3.0
b71b6000-b71ba000 r-xp 00000000 03:08 211572 /usr/lib/libXfixes.so.3.1.0
b71ba000-b71bb000 rw-p 00003000 03:08 211572 /usr/lib/libXfixes.so.3.1.0
b71bb000-b71bd000 r-xp 00000000 03:08 217296 /usr/lib/libXdamage.so.1.1.0
b71bd000-b71be000 rw-p 00001000 03:08 217296 /usr/lib/libXdamage.so.1.1.0
b71be000-b71c2000 r-xp 00000000 03:08 217298 /usr/lib/libXxf86vm.so.1.0.0
b71c2000-b71c3000 rw-p 00003000 03:08 217298 /usr/lib/libXxf86vm.so.1.0.0
b71c3000-b71d0000 r-xp 00000000 03:08 208356 /usr/lib/libXext.so.6.4.0
b71d0000-b71d1000 rw-p 0000c000 03:08 208356 /usr/lib/libXext.so.6.4.0
b71d1000-b72b9000 r-xp 00000000 03:08 209871 /usr/lib/libX11.so.6.2.0
b72b9000-b72bd000 rw-p 000e8000 03:08 209871 /usr/lib/libX11.so.6.2.0
b72bd000-b7328000 r-xp 00000000 03:08 207346 /usr/lib/libfreetype.so.6.3.16
b7328000-b732c000 rw-p 0006a000 03:08 207346 /usr/lib/libfreetype.so.6.3.16
b732c000-b7340000 r-xp 00000000 03:08 207365 /usr/lib/libz.so.1.2.3.3
b7340000-b7341000 rw-p 00013000 03:08 207365 /usr/lib/libz.so.1.2.3.3
b7341000-b7363000 r-xp 00000000 03:08 217311 /usr/lib/libpng12.so.0.15.0
b7363000-b7364000 rw-p 00021000 03:08 217311 /usr/lib/libpng12.so.0.15.0
b7364000-b7392000 r-xp 00000000 03:08 207268 /usr/lib/libglut.so.3.8.0
b7392000-b7397000 rw-p 0002e000 03:08 207268 /usr/lib/libglut.so.3.8.0
b7397000-b7416000 r-xp 00000000 03:08 207743 /usr/lib/libGLU.so.1.3.070001
b7416000-b7417000 rw-p 0007f000 03:08 207743 /usr/lib/libGLU.so.1.3.070001
b7417000-b7474000 r-xp 00000000 03:08 207742 /usr/lib/libGL.so.1.2
b7474000-b7476000 rw-p 0005d000 03:08 207742 /usr/lib/libGL.so.1.2
b7476000-b7477000 rw-p b7476000 00:00 0
b7477000-b7481000 r-xp 00000000 03:08 288172 /usr/lib/python2.4/lib-dynload/_socket.so
b7481000-b7484000 rw-p 00009000 03:08 288172 /usr/lib/python2.4/lib-dynload/_socket.so
b7484000-b7718000 r-xp 00000000 03:08 246995 /usr/lib/python-support/pymol/python2.4/pymol/_cmd.so
b7718000-b7b47000 rw-p 00294000 03:08 246995 /usr/lib/python-support/pymol/python2.4/pymol/_cmd.so
b7b47000-b7b4b000 r-xp 00000000 03:08 290744 /usr/lib/python2.4/lib-dynload/strop.so
b7b4b000-b7b4d000 rw-p 00003000 03:08 290744 /usr/lib/python2.4/lib-dynload/strop.so
b7b4d000-b7b8e000 rw-p b7b4d000 00:00 0
b7b8f000-b7d03000 r--p 00000000 03:08 224060 /usr/lib/locale/locale-archive
b7d03000-b7d87000 rw-p b7d03000 00:00 0
b7d87000-b7ec9000 r-xp 00000000 03:08 47896 /lib/i686/cmov/libc-2.6.1.so
b7ec9000-b7eca000 r--p 00142000 03:08 47896 /lib/i686/cmov/libc-2.6.1.so
b7eca000-b7ecc000 rw-p 00143000 03:08 47896 /lib/i686/cmov/libc-2.6.1.so
b7ecc000-b7ecf000 rw-p b7ecc000 00:00 0
b7ecf000-b7ef2000 r-xp 00000000 03:08 47900 /lib/i686/cmov/libm-2.6.1.so
b7ef2000-b7ef4000 rw-p 00023000 03:08 47900 /lib/i686/cmov/libm-2.6.1.so
b7ef4000-b7ef6000 r-xp 00000000 03:08 48435 /lib/i686/cmov/libutil-2.6.1.so
b7ef6000-b7ef8000 rw-p 00001000 03:08 48435 /lib/i686/cmov/libutil-2.6.1.so
b7ef8000-b7efa000 r-xp 00000000 03:08 47899 /lib/i686/cmov/libdl-2.6.1.so
b7efa000-b7efc000 rw-p 00001000 03:08 47899 /lib/i686/cmov/libdl-2.6.1.so
b7efc000-b7efd000 rw-p b7efc000 00:00 0
b7efd000-b7f10000 r-xp 00000000 03:08 48148 /lib/i686/cmov/libpthread-2.6.1.so
b7f10000-b7f12000 rw-p 00013000 03:08 48148 /lib/i686/cmov/libpthread-2.6.1.so
b7f12000-b7f14000 rw-p b7f12000 00:00 0
b7f15000-b7f17000 r-xp 00000000 03:08 290739 /usr/lib/python2.4/lib-dynload/math.so
b7f17000-b7f18000 rw-p 00002000 03:08 290739 /usr/lib/python2.4/lib-dynload/math.so
b7f18000-b7f1b000 r-xp 00000000 03:08 227937 /usr/lib/python2.4/lib-dynload/collections.so
b7f1b000-b7f1c000 rw-p 00003000 03:08 227937 /usr/lib/python2.4/lib-dynload/collections.so
b7f1c000-b7f1f000 r-xp 00000000 03:08 290749 /usr/lib/python2.4/lib-dynload/time.so
b7f1f000-b7f21000 rw-p 00002000 03:08 290749 /usr/lib/python2.4/lib-dynload/time.so
b7f21000-b7f24000 r-xp 00000000 03:08 48384 /lib/libSegFault.so
b7f24000-b7f26000 rw-p 00002000 03:08 48384 /lib/libSegFault.so
b7f26000-b7f28000 rw-p b7f26000 00:00 0
b7f28000-b7f44000 r-xp 00000000 03:08 47810 /lib/ld-2.6.1.so
b7f44000-b7f46000 rw-p 0001b000 03:08 47810 /lib/ld-2.6.1.so
bff22000-bff41000 rw-p bff22000 00:00 0 s
ffffe000-fffff000 r-xp 00000000 00:00 0 s
--8<--
I will try to get a gdb backtrace somehow, if possible.
This is on a testing box, for the record.
Michael
-- System Information:
Debian Release: lenny/sid
APT prefers testing
APT policy: (500, 'testing')
Architecture: i386 (i686)
Kernel: Linux 2.6.22-2-686 (SMP w/1 CPU core)
Locale: LANG=POSIX, LC_CTYPE=de_DE.ISO-8859-15@euro
(charmap=ISO-8859-15)
Shell: /bin/sh linked to /bin/bash
Versions of packages libgl1-mesa-dri depends on:
ii libc6 2.6.1-1+b1 GNU C Library: Shared libraries
ii libdrm2 2.3.0-4 Userspace interface to kernel DRM
ii libexpat1 1.95.8-4 XML parsing C library - runtime li
ii libgl1-mesa-glx 7.0.1-2 A free implementation of the OpenG
libgl1-mesa-dri recommends no packages.
-- debconf-show failed
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