VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Nov 19 2012 - 17:44:27 CST

Kasra,
  I'm still traveling for the rest of this week, but I would be
happy to give you a couple of other binaries to try so we can narrow
down what was causing your problem. Indeed, I expect it is one of these
libraries.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Nov 19, 2012 at 03:10:02PM -0600, Kasra Fattah wrote:
> Hi John,
>
> This is what I get from my build:
>
> LINUXAMD64 OPENGL FLTK TK IMD TCL PYTHON PTHREADS NUMPY SILENT
>
> And this is what I get from pre-packaged binary:
>
> LINUXAMD64 OPENGL FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA XINPUT
> LIBTACHYON VRPN NETCDF TCL PYTHON PTHREADS NUMPY SILENT ICC
>
> so one of these libararies is causing the problem right? do you have any
> idea which one may cause the problem? or one has to test them one by one
> to find out?
>
> Best,
> Kasra.
>
> On Sun, Nov 18, 2012 at 10:21 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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 

-- 
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