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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 <http://gnu.org/licenses/gpl.html><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"><http://bugs.launchpad.net/gdb-linaro/>...<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>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext;mso-fareast-language:EN-GB">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext;mso-fareast-language:EN-GB">
chimera-users-bounces@cgl.ucsf.edu [mailto:chimera-users-bounces@cgl.ucsf.edu] <b>
On Behalf Of </b>Greg Couch<br>
<b>Sent:</b> 05 February 2013 23:26<br>
<b>To:</b> Chimera-users@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [Chimera-users] Chimera on a virtualbox<o:p></o:p></span></p>
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<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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<p class="MsoNormal" align="right" style="text-align:right"><b>Subject: </b><b><span style="font-size:12.0pt"><o:p></o:p></span></b></p>
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<p class="MsoNormal">Re: [Chimera-users] Chimera on a virtualbox<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal" align="right" style="text-align:right"><b>Date: </b><b><span style="font-size:12.0pt"><o:p></o:p></span></b></p>
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<p class="MsoNormal">Tue, 05 Feb 2013 13:51:47 -0800<span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal" align="right" style="text-align:right"><b>From: </b><b><span style="font-size:12.0pt"><o:p></o:p></span></b></p>
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<p class="MsoNormal">Greg Couch <a href="mailto:gregc@cgl.ucsf.edu"><gregc@cgl.ucsf.edu></a><span style="font-size:12.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal" align="right" style="text-align:right"><b>To: </b><b><span style="font-size:12.0pt"><o:p></o:p></span></b></p>
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<p class="MsoNormal"><a 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>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<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 href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a> wrote:<o:p></o:p></p>
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<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 href="mailto:chris.wood@stfc.ac.uk">chris.wood@stfc.ac.uk</a><br>
<a 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>
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<br><p>--
<BR>Scanned by iCritical.
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