[Chimera-users] Chimera on a virtualbox

Greg Couch gregc at cgl.ucsf.edu
Tue Feb 5 17:33:36 PST 2013


(No real need to involve the list, we'll figure this out and report back)


-------- Original Message --------
Subject: 	Re: [Chimera-users] Chimera on a virtualbox
Date: 	Tue, 05 Feb 2013 17:22:51 -0800
From: 	Greg Couch <gregc at cgl.ucsf.edu>
To: 	chris.wood at stfc.ac.uk



It appears as if you missed the:

     export LD_LIBRARY_PATH=$CHIMERA/lib

before running gdb because the import of libgfxinfo.so failed. And there 
should be a space between "break" and "_exit" in the gdb command.

     -- Greg

On 02/05/2013 04:38 PM, chris.wood at stfc.ac.uk wrote:
>
> Hi Greg,
>
> 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...
>
> 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
>
> $ gdb $CHIMERA/bin/python2.7
>
> GNU gdb (Ubuntu/Linaro 7.4-2012.04-0ubuntu2.1) 7.4-2012.04
>
> Copyright (C) 2012 Free Software Foundation, Inc.
>
> License GPLv3+: GNU GPL version 3 or later 
> <http://gnu.org/licenses/gpl.html>
>
> This is free software: you are free to change and redistribute it.
>
> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
>
> and "show warranty" for details.
>
> This GDB was configured as "x86_64-linux-gnu".
>
> For bug reporting instructions, please see:
>
> <http://bugs.launchpad.net/gdb-linaro/>...
>
> Reading symbols from /home/ccw/.local/chimera-1.7/bin/python2.7...done.
>
> (gdb) break_exit
>
> Undefined command: "break_exit".  Try "help".
>
> (gdb) run $CHIMERA/share/__main__.py --debug
>
> Starting program: /home/ccw/.local/chimera-1.7/bin/python2.7 
> $CHIMERA/share/__main__.py --debug
>
> [Thread debugging using libthread_db enabled]
>
> Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
>
> Traceback (most recent call last):
>
>   File "/home/ccw/.local/chimera-1.7/share/__main__.py", line 69, in 
> <module>
>
>     value = chimeraInit.init(sys.argv)
>
>   File "/home/ccw/.local/chimera-1.7/share/chimeraInit.py", line 594, 
> in init
>
>     import chimera
>
>   File "/home/ccw/.local/chimera-1.7/share/chimera/__init__.py", line 
> 16, in <module>
>
>     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
>
> ImportError: libgfxinfo.so: cannot open shared object file: No such 
> file or directory
>
> [Inferior 1 (process 4025) exited with code 01]
>
> (gdb) bt
>
> No stack.
>
> I guess the lack of libgfxinfo.so is fairly significant, and I assume 
> that the result from bt is all part of the problem?
>
> Thanks,
>
> Chris
>
> *From:*chimera-users-bounces at cgl.ucsf.edu 
> [mailto:chimera-users-bounces at cgl.ucsf.edu] *On Behalf Of *Greg Couch
> *Sent:* 05 February 2013 23:26
> *To:* Chimera-users at cgl.ucsf.edu
> *Subject:* Re: [Chimera-users] Chimera on a virtualbox
>
> (Forgot to send reply to whole list)
>
> -------- Original Message --------
>
> *Subject: ***
>
> 	
>
> Re: [Chimera-users] Chimera on a virtualbox
>
> *Date: ***
>
> 	
>
> Tue, 05 Feb 2013 13:51:47 -0800
>
> *From: ***
>
> 	
>
> Greg Couch <gregc at cgl.ucsf.edu> <mailto:gregc at cgl.ucsf.edu>
>
> *To: ***
>
> 	
>
> chris.wood at stfc.ac.uk <mailto:chris.wood at stfc.ac.uk>
>
> Hi Chris,
>
> 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.
>
> 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.
>
> 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):
>
>     % export CHIMERA=`chimera --root`
>     % export LD_LIBRARY_PATH=$CHIMERA/lib
>     % gdb $CHIMERA/bin/python2.7
>     (gdb) break_exit
>     (gdb) run $CHIMERA/share/__main__.py --debug
>     (gdb) bt
>
> 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.
>
>     HTH,
>
>     Greg
>
> On 02/05/2013 12:48 PM, chris.wood at stfc.ac.uk 
> <mailto:chris.wood at stfc.ac.uk> wrote:
>
>     Hello all,
>
>     I'm trying to run Chimera on VirtualBox. The installation
>     completes fine, but when I try and run the program (|cd| to the
>     bin directory and run |./chimera|) I see
>
>     X Error of failed request:  BadDrawable (invalid Pixmap or Window
>     parameter)
>
>     Major opcode of failed request:  72 (X_PutImage)
>
>     Resource id in failed request:  0x480006a
>
>     Serial number of failed request:  1382
>
>     Current serial number in output stream:  1388
>
>     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.
>
>     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...
>
>     **
>
>     *System:*
>
>     VirtualBox 4.2.4
>     Guest additions 4.2.4
>
>     Guest OS: Ubuntu 12.04
>     Host OS: Windows 7 professional
>
>     Thanks in advance!
>
>     Chris
>
>     -------------------
>
>     Dr Chris Wood
>
>     STFC Rutherford Appleton Laboratory
>
>     Didcot
>
>     OX11 0QX
>
>     chris.wood at stfc.ac.uk <mailto:chris.wood at stfc.ac.uk>
>     www.ccpem.ac.uk <http://www.ccpem.ac.uk>
>
>
>     Tel: +44(0)1235 567864
>
>     Tel: +44(0)7909 586624
>     Fax: +44(0)1235 567801
>
>     -- 
>     Scanned by iCritical.
>
>
> -- 
> Scanned by iCritical.
>
>



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