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(No real need to involve the list, we'll figure this out and report
back)<br>
<div class="moz-forward-container"><br>
<br>
-------- Original Message --------
<table class="moz-email-headers-table" border="0" cellpadding="0"
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<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Subject:
</th>
<td>Re: [Chimera-users] Chimera on a virtualbox</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">Date: </th>
<td>Tue, 05 Feb 2013 17:22:51 -0800</td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">From: </th>
<td>Greg Couch <a class="moz-txt-link-rfc2396E" href="mailto:gregc@cgl.ucsf.edu"><gregc@cgl.ucsf.edu></a></td>
</tr>
<tr>
<th nowrap="nowrap" valign="BASELINE" align="RIGHT">To: </th>
<td><a class="moz-txt-link-abbreviated" href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a></td>
</tr>
</tbody>
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<div class="moz-cite-prefix">It appears as if you missed the:<br>
<br>
export LD_LIBRARY_PATH=$CHIMERA/lib<br>
<br>
before running gdb because the import of libgfxinfo.so failed.
And there should be a space between "break" and "_exit" in the
gdb command.<br>
<br>
-- Greg<br>
<br>
On 02/05/2013 04:38 PM, <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a>
wrote:<br>
</div>
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<p class="MsoNormal"><span style="color:windowtext">Hi Greg,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">I know
that doing anything with graphics within virtual machines
is not always a brilliant idea, but I have seen Chimera
work in VirtualBox and I wanted to get to the bottom of
why mine doesn’t…<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">I’ve got
the latest graphics driver on my host (and I run Chimera
successfully on it anyway). I’ve run the commands you
suggested, with the following output<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">$ gdb
$CHIMERA/bin/python2.7<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">GNU gdb
(Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Copyright
(C) 2012 Free Software Foundation, Inc.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">License
GPLv3+: GNU GPL version 3 or later <a
moz-do-not-send="true" class="moz-txt-link-rfc2396E"
href="http://gnu.org/licenses/gpl.html"><http://gnu.org/licenses/gpl.html></a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">This is
free software: you are free to change and redistribute it.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">There is
NO WARRANTY, to the extent permitted by law. Type "show
copying"<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">and "show
warranty" for details.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">This GDB
was configured as "x86_64-linux-gnu".<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">For bug
reporting instructions, please see:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><a
moz-do-not-send="true" class="moz-txt-link-rfc2396E"
href="http://bugs.launchpad.net/gdb-linaro/"><http://bugs.launchpad.net/gdb-linaro/></a>...<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Reading
symbols from
/home/ccw/.local/chimera-1.7/bin/python2.7...done.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">(gdb)
break_exit<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Undefined
command: "break_exit". Try "help".<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">(gdb) run
$CHIMERA/share/__main__.py --debug<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Starting
program: /home/ccw/.local/chimera-1.7/bin/python2.7
$CHIMERA/share/__main__.py --debug<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">[Thread
debugging using libthread_db enabled]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Using host
libthread_db library
"/lib/x86_64-linux-gnu/libthread_db.so.1".<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Traceback
(most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"> File
"/home/ccw/.local/chimera-1.7/share/__main__.py", line 69,
in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"> value
= chimeraInit.init(sys.argv)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"> File
"/home/ccw/.local/chimera-1.7/share/chimeraInit.py", line
594, in init<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"> import
chimera<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"> File
"/home/ccw/.local/chimera-1.7/share/chimera/__init__.py",
line 16, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"> from
_chimera import BBox, Camera, Color, ColorGroup,
DirectionalLight, LODControl, Lens, LensViewer, Light,
Material, MaterialColor, Model, NoGuiViewer, OGLFont,
OSLAbbreviation, OpenModels, OpenState, PathFinder,
PixelMap, Plane, Point, PositionalLight, Selectable,
SharedState, SpotLight, Sphere, Texture, TextureColor,
TrackChanges, Vector, Viewer, X3DScene, Xform<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">ImportError:
libgfxinfo.so: cannot open shared object file: No such
file or directory<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">[Inferior
1 (process 4025) exited with code 01]<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">(gdb) bt<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">No stack.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">I guess
the lack of libgfxinfo.so is fairly significant, and I
assume that the result from bt is all part of the problem?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Chris<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<div>
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1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext;mso-fareast-language:EN-GB"
lang="EN-US">From:</span></b><span
style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext;mso-fareast-language:EN-GB"
lang="EN-US"> <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:chimera-users-bounces@cgl.ucsf.edu">chimera-users-bounces@cgl.ucsf.edu</a>
[<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="mailto:chimera-users-bounces@cgl.ucsf.edu">mailto:chimera-users-bounces@cgl.ucsf.edu</a>]
<b> On Behalf Of </b>Greg Couch<br>
<b>Sent:</b> 05 February 2013 23:26<br>
<b>To:</b> <a moz-do-not-send="true"
class="moz-txt-link-abbreviated"
href="mailto:Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>
<b>Subject:</b> Re: [Chimera-users] Chimera on a
virtualbox<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">(Forgot to send reply to whole list)<o:p></o:p></p>
<div>
<p class="MsoNormal">-------- Original Message -------- <o:p></o:p></p>
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cellspacing="0">
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<p class="MsoNormal" style="text-align:right"
align="right"><b>Subject: </b><b><span
style="font-size:12.0pt"><o:p></o:p></span></b></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p class="MsoNormal">Re: [Chimera-users] Chimera on
a virtualbox<span style="font-size:12.0pt"><o:p></o:p></span></p>
</td>
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valign="top">
<p class="MsoNormal" style="text-align:right"
align="right"><b>Date: </b><b><span
style="font-size:12.0pt"><o:p></o:p></span></b></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p class="MsoNormal">Tue, 05 Feb 2013 13:51:47 -0800<span
style="font-size:12.0pt"><o:p></o:p></span></p>
</td>
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<td style="padding:0cm 0cm 0cm 0cm" nowrap="nowrap"
valign="top">
<p class="MsoNormal" style="text-align:right"
align="right"><b>From: </b><b><span
style="font-size:12.0pt"><o:p></o:p></span></b></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p class="MsoNormal">Greg Couch <a
moz-do-not-send="true"
href="mailto:gregc@cgl.ucsf.edu"><gregc@cgl.ucsf.edu></a><span
style="font-size:12.0pt"><o:p></o:p></span></p>
</td>
</tr>
<tr>
<td style="padding:0cm 0cm 0cm 0cm" nowrap="nowrap"
valign="top">
<p class="MsoNormal" style="text-align:right"
align="right"><b>To: </b><b><span
style="font-size:12.0pt"><o:p></o:p></span></b></p>
</td>
<td style="padding:0cm 0cm 0cm 0cm">
<p class="MsoNormal"><a moz-do-not-send="true"
href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a><span
style="font-size:12.0pt"><o:p></o:p></span></p>
</td>
</tr>
</tbody>
</table>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Hi Chris,<br>
<br>
So what are you trying to do with Chimera inside a
virtual machine? Presumably, you're not trying to use
it graphically because virtualized graphics performance
is usually abysmal. Chimera benefits immensely from
direct access to the graphics hardware. So that leaves
using Chimera as a server, and for that the headless
version of Chimera is usually better -- the headless
version uses a software implementation of OpenGL and
thus avoids any driver issues.<br>
<br>
That said, this bug is still likely to be related to
OpenGL support in VirtualBox. Make sure the computer
that VirtualBox is running on has an up-to-date OpenGL
graphics driver. It doesn't matter what VirtualBox does
if the underlying system has a bad graphics driver.<br>
<br>
To confirm that the bug is in the graphics driver, get a
backtrace of where the error occurs by using gdb as
follows in a Terminal window (and assuming there is a
symbolic link to the chimera binary on your path):<br>
<br>
% export CHIMERA=`chimera --root`<br>
% export LD_LIBRARY_PATH=$CHIMERA/lib<br>
% gdb $CHIMERA/bin/python2.7<br>
(gdb) break_exit<br>
(gdb) run $CHIMERA/share/__main__.py --debug<br>
(gdb) bt<br>
<br>
The '%' and '(gdb)' parts are the shell and gdb prompts,
respectively. The output from the bt command will
probably be in Chimera's molecular drawing code (as
opposed to drawing the UI). If you need help
interpreting the chimera backtrace, you can send it to
me. <br>
<br>
HTH,<br>
<br>
Greg<br>
<br>
On 02/05/2013 12:48 PM, <a moz-do-not-send="true"
href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a>
wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hello all,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I'm trying to run Chimera on
VirtualBox. The installation completes fine, but when I
try and run the program (<code><span
style="font-size:10.0pt;font-family:"Calibri","sans-serif"">cd</span></code>
to the bin directory and run <code><span
style="font-size:10.0pt">./chimera</span></code>) I
see<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt">X
Error of failed request: BadDrawable (invalid Pixmap
or Window parameter)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt">Major
opcode of failed request: 72 (X_PutImage)</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt">Resource
id in failed request: 0x480006a</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt">Serial
number of failed request: 1382</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:10.0pt">Current
serial number in output stream: 1388</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I've tried enabling / disabling
hardware virtualization & 3D acceleration, but to no
avail. Although people do seem to have problems with
chimera on a virtualbox, it normally seems to be a
problem with OpenGL, which this doesn't seem to be.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Has anyone seen this error before? Is
there anything else I'm missing? I can’t even work out
if it's a hardware, VirtualBox, or OS problem…<o:p></o:p></p>
<p class="MsoNormal"><strong><span
style="font-size:10.0pt;font-family:"Verdana","sans-serif""> </span></strong><o:p></o:p></p>
<p class="MsoNormal"><strong><span
style="font-size:10.0pt;font-family:"Verdana","sans-serif"">System:</span></strong><o:p></o:p></p>
<p class="MsoNormal">VirtualBox 4.2.4<br>
Guest additions 4.2.4<o:p></o:p></p>
<p class="MsoNormal">Guest OS: Ubuntu 12.04<br>
Host OS: Windows 7 professional<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thanks in advance!<o:p></o:p></p>
<p class="MsoNormal">Chris<o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB">-------------------</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB">Dr Chris Wood</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB">STFC Rutherford
Appleton Laboratory</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB">Didcot</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB">OX11 0QX</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB"> </span><o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB"><a
moz-do-not-send="true"
href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a><br>
<a moz-do-not-send="true"
href="http://www.ccpem.ac.uk">www.ccpem.ac.uk</a></span><o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB"><br>
Tel: +44(0)1235 567864</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="mso-fareast-language:EN-GB">Tel: +44(0)7909
586624<br>
Fax: +44(0)1235 567801</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif";mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p>-- <br>
Scanned by iCritical.<o:p></o:p></p>
</blockquote>
<p class="MsoNormal" style="margin-bottom:12.0pt"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif";mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif";mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
</div>
<br>
<p>-- <br>
Scanned by iCritical. </p>
<br>
</blockquote>
<br>
<br>
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