VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Jan 06 2010 - 10:48:28 CST

On Wed, 2010-01-06 at 15:26 +0100, maria goranovic wrote:
> Hi Axel,

hi maria,

> - 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.

this is a problem. xtc is a compressed format. VMD expands the data
to uncompressed single precision floating point numbers (12 bytes
per atom per per frame plus other per frame overhead). this will
eat up more memory than you think...

> - 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

700MB swap is not what i would call little. with the speed difference
between hard drives and CPU/memory, being that deep into swap will
already seriously impact your performance.

> does VMD occupy more than 3 GB of physical memory if only a 500 MB
> trajectory is being loaded ?

see above.

> - If I load up a bigger trajectory ( ~ 1.2 GB), I do not know how much
> memory is being used, because the system freezes.

your machine is simply swapping to death. why do you load all the
trajectory into memory at all? you can process it in chunks only load
every 4th frame or use the bigdcd script for batch processing.

cheers,
   axel.

> 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
>
>

> --
> 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.