VMD-L Mailing List

From: Kasra Fattah (kasra.fattah_at_gmail.com)
Date: Fri Nov 09 2012 - 11:07:12 CST

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.
>>
>
>