[Chimera-users] Chimera on a virtualbox

Greg Couch gregc at cgl.ucsf.edu
Tue Feb 5 15:25:46 PST 2013

(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>
To: 	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.



On 02/05/2013 12:48 PM, 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
> www.ccpem.ac.uk
> Tel: +44(0)1235 567864
> Tel: +44(0)7909 586624
> Fax: +44(0)1235 567801
> -- 
> Scanned by iCritical.

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