VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Oct 01 2011 - 21:26:37 CDT

Hi,

On Sat, Oct 01, 2011 at 05:37:43PM +0400, Dmitry Osolodkin wrote:
> On 10/01/2011 04:58 PM, Axel Kohlmeyer wrote:
> >you want to do simulations of 20,000,000 atom systems
> >on a single workstation?
>
> Obviously not :)
>
> >the first thing you have to worry about for visualization
> >is not the GPU, but having sufficient RAM.

This is a very important point. I'm working on adding the
ability for VMD work with trajectory data entirely out-of-core, but
in the short term until these features are completed, you will need
enough system RAM to work with the portions of your simultion trajectory
data that you need to view/analyze.

> And does the GPU RAM matter? I'm planning to start with Intel i7 CPU and
> 16 Gb RAM, and I have spare $1K for additional memory and GPU. What else
> should I take in mind when selecting GPU hardware? My aim is smooth
> interaction with large cartoon rendered system, its rotation etc.

If you want to use the new GPU accelerated features of VMD,
then yes, the amount of GPU memory you have will be very important.
All of the new MD trajectory analysis features of VMD require
enough GPU RAM to hold the equivalent of a few timesteps worth of
coordinates. If you're working with 20M atom systems,
then you need at least 1GB of unused GPU memory to do much of anything,
but that memory also gets used by the windowing system, by
recent versions of web browsers like Chrome, and so on. For things
like time-averaging of coordinates, you might need 20 trajectory frames
in memory at once. I have a big batch of new GPU analysis features
coming in the next version of VMD this fall, and they will need
GPUs with a decent amount of memory.

You can of course use VMD without any of the GPU features, but if
you want the GPU accelerated features, you'll need some GPU memory
matched to the size of the structures you're working with.
At least 12 bytes per atom, per timestep, plus various overhead...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

> >a trajectory
> >for systems of this size can become very large and as soon
> >as your workstation will begin to swap, everything will
> >become very slow.
>
> Yes, I know. The trajectory will be preprocessed before visualisation.
>
> >the choice between nvidia or amd/ati depends
> >a bit on the operating system. if you are using linux
> >(which i would recommended) then the support for nvidia
> >GPU is significantly better (using the nvidia provided
> >drivers).
>
> Yes, I'm using OpenSuse linux.
>
> >high-performance quadro cards are very expensive,
> >but most of the features that they offer over geforce
> >cards are not exploited by VMD.
> Just to make clear: which specific features of quadro cards are
> exploited by VMD? It's sort of curiosity.
>
> > so you are probably best
> > off with a GeForce GTX 580 card.
>
> Looks OK.
>
> >
> >cheers,
> > axel.
> >
> >>Thanks in advance and best regards,
> >>Dmitry Osolodkin
> >
> >
>
> --
> Dmitry Osolodkin, PhD
> Researcher
> Group of Computational Molecular Design
> Department of Chemistry
> Moscow State University
> Moscow 119991 Russia
> e-mail: dmitry_o_at_qsar.chem.msu.ru
> Phone: +7-495-9393557
> Fax: +7-495-9390290 

-- 
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