New subject: Chimera on a virtualbox

5 Feb 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@cgl.ucsf.edu
To: 	chris.wood@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@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@cgl.ucsf.edu 
[mailto:chimera-users-bounces@cgl.ucsf.edu] *On Behalf Of *Greg Couch
*Sent:* 05 February 2013 23:26
*To:* Chimera-users@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@cgl.ucsf.edu mailto:gregc@cgl.ucsf.edu
*To: ***
chris.wood@stfc.ac.uk mailto:chris.wood@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@stfc.ac.uk 
mailto:chris.wood@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@stfc.ac.uk <mailto:chris.wood@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

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Re: [Chimera-users] Chimera on a virtualbox

Greg Couch

chris.wood＠stfc.ac.uk

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