VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 09 2012 - 13:32:35 CST

Hi,
  The problem you have is almost certainly completely unrelated to
VMD itself, so this is going to turn into a Linux / OpenGL debugging issue.

Given that the problems started with your Ubuntu update, the most
likely causes for such a problem are:
  1) video driver
  2) changes to X11
  3) kernel update that creates a problem with specific video driver version

If it were me, I would roll back the changes to the video driver, X11,
and possibly also the linux kernel itself.

I myself have seen problems that are caused by particular combinations
of kernel and video driver. I have a machine that has a particular kernel
version that is stable with a certain range of video driver versions,
and is unstable with more recent video drivers. Other nearly-identical
machines that have a slightly newer kernel version are stable with the
very driver versions that freeze the other machine. So, these are things
I think you should consider first and foremost.

Cheers,
  John Stone

On Fri, Nov 09, 2012 at 11:07:12AM -0600, Kasra Fattah wrote:
> Axel,
> Is there any chance to debug and fix the problem while I'm on the local
> machine now? I already sent the glxinfo and behavior of VMD on the local
> machine.
> I'd appreciate any help
>
> Best,
> Kasra.
>
> On Thu, Nov 8, 2012 at 10:46 AM, Kasra Fattah <kasra.fattah_at_gmail.com>
> wrote:
>
> I tried to run VMD on the machine locally but still the same problem
> exists. I tried run it right after rebooting the system and it was fine
> I closed it and reopen and it was fine, did the same thing again vmd
> writes out its first few lines of info in the terminal as usual:
>
> rlwrap: Command not found.
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 8 CPUs detected.
> Info) Free system memory: 29345MB (97%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 2 available CUDA accelerators:
> Info) [0] Tesla C2075 14 SM_2.0 @ 1.15 GHz, 5.2GB RAM, OIO, ZCP
> Info) [1] GeForce GTX 460 v2 7 SM_2.1 @ 1.65 GHz, 1.0GB RAM, KTO, OIO,
> ZCP
> Warning) Detected X11 'Composite' extension: if incorrect display occurs
> Warning) try disabling this optional X server feature.
>
> But it freezes after that. I get those warnings even when it runs
> without freezing. Freezing can happen for the first run if I execute vmd
> a while after system startup (not right after). Even running vmd in the
> text mode ( vmd -dispdev text) shows the same pattern. I have attached
> the glxinfo of the local machine where no trace of mesa opengl
> libararies are seen in this one. Any clue as to what is going on?
>
> Thank you,
> Kasra.
>
> On Thu, Nov 8, 2012 at 12:15 AM, Axel Kohlmeyer <akohlmey_at_gmail.com>
> wrote:
>
> the glxinfo output indicates that you are running VMD on a remote
> machine
> and thus use OpenGL over X (GLX). that is a very tricky configuration
> on
> linux. you probably need to update the nvidia drivers on the remote
> machine.
> also you should very carefully check whether the driver update has
> worked
> properly. it looks as if there are some library inconsistencies where
> part of
> what you use are the default (mesa based) opengl libraries and some
> other
> part are the libraries shipped by nvidia. this is also *very*
> problematic.
> this is near impossible to debug and fix from remote.
> axel.
>
> On Thu, Nov 8, 2012 at 6:03 AM, Kasra Fattah <kasra.fattah_at_gmail.com>
> wrote:
>
> Here is more information about the system I'm running VMD on, just
> in case:
> Linux 3.2.0-32-generic #51-Ubuntu SMP Wed Sep 26 21:33:09 UTC 2012
> x86_64 x86_64 x86_64 GNU/Linux
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
> Distributor ID: Ubuntu
> Description: Ubuntu 12.04.1 LTS
> Release: 12.04
> Codename: precise
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
> nvidia driver version 304.43
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
> Package: xserver-xorg-core
> Version: 2:1.11.4-0ubuntu10.6
> ---------------------------------------------------------------------------------------------------------------------------------------------------------------
> I have also attached the output of glxinfo.
> Best,
> Kasra.
>
> On Wed, Nov 7, 2012 at 7:18 PM, Kasra Fattah
> <kasra.fattah_at_gmail.com> wrote:
>
> Hi everybody,
>
> After a recent update of my workstation Ubuntu 12.04, VMD causes
> the system to freeze. After rebooting the system I can run VMD
> with no problem but if I close it and reopen it several times
> (like 2 or 3 times) then it'll lockup with following output of vmd
> ~$ vmd
> rlwrap: Command not found.
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
>
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>
> Info) Please include this reference in published work using VMD:
>
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
>
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1,
> 33-38.
> Info)
> -------------------------------------------------------------
> Info) Multithreading available, 8 CPUs detected.
> Info) Free system memory: 29004MB (96%)
> Info) Creating CUDA device pool and initializing hardware...
> This can happen even after first try to run VMD if it's I try to
> run it after a while of start up of the system. However, I still
> can ssh to the system! My video card is a nvidia GTX 460 card and
> I updated the drivers of the video card when I saw this behaviour
> but it didn't solve the problem, I also tried to downgrade the
> xserver-xorg-core to see if it's causing the problem but that even
> didn't solve it. Would you please help how I can solve this issue.
> Thank you,
> Kasra.
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078