VMD-L Mailing List

From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Thu Feb 25 2010 - 15:59:32 CST

John,

When I use the Intel chip I do use the CUDA version of VMD.

And indeed "load all at once" option makes the loading extremely fast whether CUDA is enabled or not. I'm surprised that I forgot to consider this option, and I thank you for bringing it back to my brain.

Cheers,
Michel

-----Original Message-----
From: John Stone [mailto:johns_at_ks.uiuc.edu]
Sent: Thursday, February 25, 2010 3:52 PM
To: Michel Espinoza-Fonseca
Cc: 'Vmd l'
Subject: Re: vmd-l: slower trajectory loading when CUDA support is enabled

Michel,
  When you say "enabled the Intel chip" I assume you mean that you're
running the non-CUDA version of VMD yes? The CUDA code doesn't get used
during trajectory loading, this is why I suspect it to be related to the
version of the MS compilers used and not CUDA.

When you load the trajectory, what happens if you check the
"load all at once" button in the molecule file loading window?
(the default is "load in background")

I would expect that if you tell VMD to load the trajectory all at once
you will get MUCH faster loading speed, irrespective of which version
you are running.

Give that a try and let me know how it works for you.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Feb 25, 2010 at 03:48:00PM -0600, Michel Espinoza-Fonseca wrote:
> Hi John,
>
> Thank you for the clarification. Something I forgot to mention is that I still observed a slower trajectory loading even for relatively small molecules. For example, I have a 8,000-frame trajectory of a 50-residue peptide, and it loads significantly faster when I have enabled the Intel chip.
>
> But as I said, this is really not an important "problem" for me.
>
> Cheers,
> Michel
>
> -----Original Message-----
> From: John Stone [mailto:johns_at_ks.uiuc.edu]
> Sent: Thursday, February 25, 2010 3:01 PM
> To: Michel Espinoza-Fonseca
> Cc: 'Vmd l'
> Subject: Re: vmd-l: slower trajectory loading when CUDA support is enabled
>
>
> Hi Michel,
> The difference in loading speed would have nothing to do with CUDA,
> and is instead related to the difference in which version of the Microsoft
> compilers were used to compile VMD itself. This is also the reason that I
> released two versions for Windows... The use of CUDA requires that I compile
> VMD using one of the more recent Microsoft Visual Studio versions. There
> are various differences between the old MSVC6 used for the older revs of
> VMD and for the non-CUDA version of VMD 1.8.7, and the new MSVS2005
> and MSVS2008 versions I need to use for CUDA and OpenCL.
> I'm guessing that the version compiled with MSVS2005 is not running as
> fast for one of the representations you're using on your large structure.
> If you give me an example structure and a VMD saved state file for a
> visualization that you have noticed to be slower,
> I would be happy to look into what the reason might be.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Thu, Feb 25, 2010 at 02:35:18PM -0600, Michel Espinoza-Fonseca wrote:
> > Hi all,
> >
> >
> >
> > I have a laptop running under windows 7 (2.66 GHz Intel Core 2 Duo P8800
> > processor with Centrino 2) with a hybrid graphics system (Mobile Intel GMA
> > 4500MHD and NVIDIA GeForce 9300M GS 256 MB chips). The NVIDIA chip has
> > CUDA support and VMD is taking great advantage of it, something I can see
> > when using heavy drawing modes for very big molecules. However, I also
> > have noticed that loading a trajectory is significantly slower when I use
> > the NVIDIA chip compared to the times when I use the Intel one. In general
> > this situation doesn't really bother me, but I'm curious to know what
> > might be the reason for this particular behavior.
> >
> >
> >
> > Cheers,
> >
> > Michel
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ 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
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078