From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Nov 18 2012 - 22:21:22 CST

Hi,
  Out of curiosity, what configuration flags did you use when you
compiled VMD from source? Perhaps you disabled a feature that is
causing an interaction that is responsible for the freeze? What
do you get when you run this command on both your build and the
pre-packaged binary:
  vmdinfo options

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Nov 16, 2012 at 05:03:26PM -0600, Kasra Fattah wrote:
> John,
>
> Thanks for the input. Well, I could compile vmd from the source and the
> post by Andrew
> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/17060.html) really
> helped me to figure out how to do it. After building vmd from the source
> it seems that the problem has gone so I can run vmd again. But if I use
> the machine specific package as I was doing in the past I get the freezing
> issue.
>
> Best,
> Kasra.
>
> On Wed, Nov 14, 2012 at 10:20 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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

-- 
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