VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 14 2012 - 22:20:11 CST

Kasra,
  Although your other OpenGL apps don't cause the freeze, that doesn't
mean anything. Unless they use the same OpenGL features that VMD does,
they may not push OpenGL very hard. Recompiling VMD from source will make
no difference, as VMD is not the source of your problem. As I said before
it is your video driver, X11, kernel, or combination of the above that
are causing this problem since you only started having the problem after
you ran a linux update...

By the way, the compilation steps you had below aren't
entirely correct. After running the configure script, you need to
cd to the src directory, and then do "make" there. After that completes,
you would then "cd ..", then run "./make_distrib LINUXAMD64 opengl"
or do a "make install", whichever you prefer.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 12, 2012 at 06:44:02PM -0600, Kasra Fattah wrote:
> Thank you John for the clear explanation. I'm still trying to make it work
> and I did everything you suggested, the problem is that only vmd shows
> this behavior and all other packages using Opengl are fine. I also tested
> the graphics with Phoronix and it came out to be fine, no freezing or
> crashes. Anyways, for the last thing I wanted to build vmd from source
> again. in the past I used the specific the platform specific package but
> this time I tried making it from scratch using "Source Code" on the
> download page. I read the manual and document so I took following steps
> (right?):
> 1. from plugins directory: make LINUXAMD64
> 2. export PLUGINDIR = path to vmd-1.9.1 directory
> 3. make distrib
> 4. cd to vmd-1.9.1 directory
> 5. ./configure LINUXAMD64
> After all these a new LINUXAMD64 directory is created in vmd-1.9.1
> directory but it's empty and it doesn't have the vmd_LINUXAMD64 in it! So
> if I do make install from src it complains about that. Am I missing
> something in these steps? Will you please guide me on building vmd from
> "source code"?
> Best,
> Kasra.
>
> On Fri, Nov 9, 2012 at 1:32 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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 

-- 
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