VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed Jan 06 2010 - 08:58:50 CST

As a follow up, 1.8.7 did no better than 1.8.6 insofar as the memory usage
is concerned

On Wed, Jan 6, 2010 at 3:26 PM, maria goranovic <mariagoranovic_at_gmail.com>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
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen