VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Jan 06 2010 - 08:26:00 CST

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