VMD-L Mailing List

From: Gianluca Interlandi (gianluca_at_u.washington.edu)
Date: Thu Nov 17 2011 - 16:32:09 CST

It might not add much, but I have to say that I had a similar problem
several years ago with a NVIDIA GeForce 5200 that I bought in 2001
installed in a dual pentium III. The first two VMD windows or any
application that ran openGL worked fine and the thrid was very slow. I
never had this problem with any other card. That is just my 2c.

Gianluca

On Thu, 17 Nov 2011, lam nguyen wrote:

> Here it is:
>  Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)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: 10737MB (89%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 2 available CUDA accelerators:
> Info)   [0] Quadro FX 580       4 SM_1.1 @ 1.12 GHz,  511MB RAM, KTO, OIO, ZCP
> Info)   [1] Quadro FX 580       4 SM_1.1 @ 1.12 GHz,  511MB RAM, KTO, OIO, ZCP
> Info) OpenGL renderer: Quadro FX 580/PCI/SSE2
> Info)   Features: STENCIL MSAA(16) MDE CVA MTX NPOT PP PS GLSL(OVF) 
> Info)   Full GLSL rendering mode is available.
> Info)   Textures: 2-D (8192x8192), 3-D (2048x2048x2048), Multitexture (4)
> Info) Dynamically loaded 2 plugins in directory:
> Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
> Info) File loading in progress, please wait.
> Info) Using plugin psf for structure file PG.old.psf
> psfplugin) WARNING: no dihedrals defined in PSF file.
> psfplugin) WARNING: no impropers defined in PSF file.
> psfplugin) no cross-terms defined in PSF file.
> Info) Analyzing structure ...
> Info)    Atoms: 13352
> Info)    Bonds: 19016
> Info)    Angles: 11428  Dihedrals: 0  Impropers: 0  Cross-terms: 0
> Info)    Bondtypes: 0  Angletypes: 0  Dihedraltypes: 0  Impropertypes: 0
> Info)    Residues: 994
> Info)    Waters: 0
> Info)    Segments: 3
> Info)    Fragments: 979   Protein: 0   Nucleic: 0
> Info) Using plugin pdb for coordinates from file PG.pdb
> Info) Finished with coordinate file PG.pdb.
> vmd > Info) VMD for LINUXAMD64, version 1.9 (March 14, 2011)
> Info) Exiting normally.
>
> Lam
>
> On Thu, Nov 17, 2011 at 12:13 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Lam,
>  Okay, that clearly indicates that your GPU is running out of memory
> when you have several VMD instances running.  Can you quickly send me
> the startup messages that VMD prints when you run it on your machine?
> I should be able to determine a few useful things from the OpenGL and
> CUDA messages that VMD prints when it starts up.
>
> Cheers,
>  John
>
> On Thu, Nov 17, 2011 at 12:05:18PM -0800, lam nguyen wrote:
> >    And if I have no VMD running I have:
> >            Free                    : 457 Mb
> >            Free                    : 458 Mb
> >    Lam
> >    On Thu, Nov 17, 2011 at 12:01 PM, lam nguyen <lamvn08_at_gmail.com> wrote:
> >
> >      Sorry, my reply to Peter did not go to the list.
> >      Yes, I am using Nvidia-provided driver. I have tried quite a few of
> >      them. The current version is 280.13.
> >      Here is what I have doing /usr/bin/nvidia-smi -a |grep -i free
> >      Free                    : 4 Mb
> >      Free                    : 4 Mb
> >      Lam
> >
> >
> >      On Thu, Nov 17, 2011 at 11:30 AM, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >        Hi,
> >         You didn't state what graphics driver you are using, but if you
> >        aren't
> >        running the NVIDIA-provided drivers, that would be one of the first
> >        things
> >        you should fix.  If you're using the open-source drivers that ship
> >        with
> >        ubuntu, you are surely bound to encounter various performance
> >        problems.
> >        If you have the NVIDIA drivers installed, then please run this command
> >        and tell me what it says, when you have 2 VMD sessions open and
> >        running:
> >         /usr/bin/nvidia-smi -a |grep -i free
> >
> >        Cheers,
> >         John Stone
> >         vmd_at_ks.uiuc.edu
> >        On Thu, Nov 17, 2011 at 09:16:10AM -0800, lam nguyen wrote:
> >        >    Doing this way helps a little bit. I can open 2 windows and
> >        enlarge them
> >        >    without problem. But when I open the third one, my computer
> >        almost
> >        >    freezes.
> >        >    Lam
> >        >
> >        >    On Wed, Nov 16, 2011 at 10:29 PM, Tristan Croll
> >        <tristan.croll_at_qut.edu.au>
> >        >    wrote:
> >        >
> >        >      Lam,
> >        >
> >        >      In that case, *definitely* try disabling the X11 Composite
> >        extension.
> >        >
> >        >      sudo gedit /etc/X11/xorg.conf
> >        >
> >        >      Then add to that file:
> >        >
> >        >      Section "Extensions"
> >        >      A  A  A  A Option A "Composite" "Disable"
> >        >      EndSection
> >        >
> >        >      Cheers,
> >        >
> >        >      Tristan
> >        >
> >        >      From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu]
> >        On Behalf
> >        >      Of lam nguyen
> >        >      Sent: Thursday, 17 November 2011 2:21 PM
> >        >      To: Ajasja LjubetiA:*
> >        >      Cc: vmd-l_at_ks.uiuc.edu
> >        >      Subject: Re: vmd-l: VMD slows down at multiple windows
> >        >      I have VMD 1.9. I have tried running it on ubuntu, kubuntu and
> >        mint. I
> >        >      installed these three OS' to test which one I like most. I have
> >        VMD
> >        >      slows-down problem with all three systems. My Nvidia card is
> >        quadro FX
> >        >      580. I don't think I run out of memory because I have this
> >        problem even
> >        >      right after restarting computer.
> >        >
> >        >      Lam
> >        >      On Tue, Nov 15, 2011 at 1:08 AM, Ajasja LjubetiA:*
> >        >      <ajasja.ljubetic_at_gmail.com> wrote:
> >        >      Hi,
> >        >
> >        >      I think you forgot toA mentionA some crucial information: Which
> >        OS are
> >        >      you running, what VMD version and which Nvidia card?
> >        >
> >        >      so I don't thinkA power is the problem.
> >        >
> >        >      Yes, if power would be the problem, the computer wouldA
> >        probablyA just
> >        >      reset. Perhaps you are running out of system or GPU memory?
> >        >      Ajasja
> >        >
> >        >      On Mon, Nov 14, 2011 at 23:51, lam nguyen <lamvn08_at_gmail.com>
> >        wrote:
> >        >      Hi all,
> >        >
> >        >      There is an annoying VMD problem with my desktop. If I open
> >        several VMD
> >        >      windows, from the third one they slow down a lot. It is a new
> >        machine so
> >        >      I don't think the power is the problem. Because my 4 years old
> >        laptop
> >        >      can handle many VMD windows without slowing them down. I wonder
> >        if this
> >        >      has to do with Nvidia card?
> >        >
> >        >      Is there anyone having the same trouble?
> >        >
> >        >      Lam
> >
> >        --
> >        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
>
>
>
>

-----------------------------------------------------
Gianluca Interlandi, PhD gianluca_at_u.washington.edu
                     +1 (206) 685 4435
                     http://artemide.bioeng.washington.edu/

Postdoc at the Department of Bioengineering
at the University of Washington, Seattle WA U.S.A.
-----------------------------------------------------