VMD-L Mailing List

From: lam nguyen (lamvn08_at_gmail.com)
Date: Thu Nov 17 2011 - 14:20:41 CST

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
>