From: Kasra Fattah (kasra.fattah_at_gmail.com)
Date: Mon Nov 12 2012 - 18:44:02 CST

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
>