[Chimera-users] Chimera on a virtualbox

chris.wood at stfc.ac.uk chris.wood at stfc.ac.uk
Thu Apr 4 03:20:38 PDT 2013


For completion, just thought I'd let anybody interested know that I have fixed this (at least, for my own setup!).  The trick is to use the version of VBox Guest Additions specifically for Ubuntu 12.* - see the final post at https://forums.virtualbox.org/viewtopic.php?f=6&t=45549:
Install Ubuntu package virtualbox-ose-guest-utils (via apt-get or synaptic) instead of the standard VB Guest Additions.

this instruction doesn't seem to be mentioned anywhere (official) on the VirtualBox website.  However, after installing this:

ccw at ccw:~$ /usr/lib/nux/unity_support_test -p
OpenGL vendor string:   Humper
OpenGL renderer string: Chromium
OpenGL version string:  2.1 Chromium 1.9

Not software rendered:    yes
Not blacklisted:          yes
GLX fbconfig:             yes
GLX texture from pixmap:  yes
GL npot or rect textures: yes
GL vertex program:        yes
GL fragment program:      yes
GL vertex buffer object:  yes
GL framebuffer object:    yes
GL version is 1.4+:       yes

Unity 3D supported:       yes

(different OpenGL info, and "Not software rendered" and "Unity 3D supported" now say 'Yes', whereas before installing this version of VBox Guest Additions these said 'no').  I can now also run Chimera, seemingly successfully (so far at least!).

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

Skype: chris_c_wood<callto://chris_c_wood/>

From: chimera-users-bounces at cgl.ucsf.edu [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Greg Couch
Sent: 06 February 2013 01:34
To: Chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Chimera on a virtualbox

(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><mailto:gregc at cgl.ucsf.edu>

To:

chris.wood at stfc.ac.uk<mailto: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<mailto: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><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/><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> [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<mailto: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



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