From: Wayne Dawson (dawson_at_bi.a.u-tokyo.ac.jp)
Date: Wed Jan 06 2010 - 20:48:34 CST

Are you running some tcl script on the data?

Commands like "atomselect" do not know when you want to do clean up
(garbage collection) so they just accumulate massive amounts of memory
on a huge file like that. It would bring the OS to a halt. You need to
include "delete" somewhere in your script if that is the case.

Wayne

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
> <mailto:akohlmey_at_gmail.com>> wrote:
>
> On Wed, Jan 6, 2010 at 5:32 AM, maria goranovic
> <mariagoranovic_at_gmail.com <mailto: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 <mailto: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

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