VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jan 06 2010 - 10:10:51 CST

Hi,
  If you're loading an XTC file, the file will be larger in memory than it
is on disk due to the way those files are compressed. VMD currently uses
12 bytes of memory per-atom per-frame, so loading a trajectory of 150,000
atoms will consume just over 1.8MB of RAM per frame, and if you load 2,000
frames, that works out to 3600MB, which is probably more than your machine
actually has available by the time your windowing system and other
services are running... If you restrict your loads to 1500 frames or so
you'll have much less trouble here.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jan 06, 2010 at 03:26:00PM +0100, maria goranovic wrote:
> Hi Axel,
>
> - I am using an x86_64 cpu, a 64-bit ubuntu, and 64-bit ubuntu (I think
> its version 8.4).
> - The swap memory is ~ 4 GB, and the physical memory is also ~ 4GB.
> - Nothing else which is memory consuming is running on the system
> (firefox, and a few shells)
> - The trajectory is gromacs .xtc format. Each frame is ~ 150,000 atoms.
>
> - When I load up such a trajectory of 2000 frames (~ 500MB), all the
> physical memory is used, but very little swap (~ 700 MB) is used. Why does
> VMD occupy more than 3 GB of physical memory if only a 500 MB trajectory
> is being loaded ?
>
> - If I load up a bigger trajectory ( ~ 1.2 GB), I do not know how much
> memory is being used, because the system freezes.
>
> Yes, the disk seems active when the machine freezes. It is a memory issue
> for sure.
>
> Thank you for the answers in advance
>
> I will try with a newer VMD,
>
> -Maria
>
> I will try installing 1.8.7 and see if that works better.
>
> On Wed, Jan 6, 2010 at 2:41 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>
> On Wed, Jan 6, 2010 at 5:32 AM, maria goranovic
> <mariagoranovic_at_gmail.com> wrote:
> > Hi,
> >
> > I am using VMD v. 1.8.6 to load up a trajectory of ~ 1.2 GB on the VMD
> GUI
> > on my linux box which has 4GB memory, and a 512 MB Nvidia card. VMD
> hangs
> > up, and freezes the entire system. Any ideas why this should happen ?
> VMD
> > also slows down considerably when I load up such large files. Any
> ideas or
> > solutions?
>
> hi maria,
>
> you are failing to provide important information, so it is
> impossible to provide useful help.
>
> what operating system are you using? what archiecture (please
> note that x86_64 cpus can run both 32-bit and 64-bit OSes and
> applications)? what _else_ is running on that machine?
> how much swap space do you have configured and how much
> is used? is the disk active when the machine "freezes"?
>
> what type of trajectory file are you loading and how many atoms
> per frame does it have? can you load a smaller chunk of it?
>
> cheers,
> axel.
>
> >
> >
> >
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen 

-- 
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