VMD-L Mailing List

From: Leonardo Palmieri (leopalmieri1_at_gmail.com)
Date: Tue Apr 26 2022 - 14:41:29 CDT

Well, I also found this:

I think it was from you, John.

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Feb 15 2008 - 17:03:15 CST

"...I'm also working on a future design change for the VMD internals that will
enable it to work with trajectories that are far larger than the amount
of physical memory in the machine through a new out-of-core trajectory
plugin API. I will likely implement this first using my own special
trajectory format and use mmap() and related kernel VM calls to allow
VMD to map monstrously huge MD trajectories into virtual memory.
The trick will be to add code for pre-fetching threads during trajectory
analysis and playback, and to give the OS kernel "hints" about which
timesteps need to be in-core and which ones can optionally be paged out.
Later on, I hope to have a more general implementation that can work with
any reasonable trajectory format (and without the need for mmap()), where
VMD will keep a working set of frames in-core, and will dynamically
load/free frames as analysis/visualization operations demand. This too
will attempt to use scout threads to prefetch frames on-the-fly before
they are needed so that the user "feels" like they were already in memory.
I don't have a timeline for these developments yet, I'll know more once
my experiments with my initial Unix-specific mmap() based implementation
have made significant progress."

That's I'm talking about...

2022-04-26 16:35 GMT-03:00, Leonardo Palmieri <leopalmieri1_at_gmail.com>:
> BigDCD and scripts works well, some problems sometimes...
>
> but the point is:
>
> I'm interested in use extensions from Extension > Analysis, in graphic
> mode, remotely accessing interactively a node in the computer where
> the trajectory is stored.
>
> I'm using compressed X11 forwarding to have the graphic VMD working
> remotely, but the memory available per node cannot store the entire
> trajectory and the VMD crashes when it run out of memory.
>
> That's the reason.
>
> Thanks!
>
> 2022-04-26 16:17 GMT-03:00, John Stone <johns_at_ks.uiuc.edu>:
>> Can you tell us why the bigDCD script isn't a choice for you?
>>
>> Best,
>> John
>>
>> On Tue, Apr 26, 2022 at 04:12:18PM -0300, Leonardo Palmieri wrote:
>>> Hi everybody,
>>>
>>> Is there a way to analyse a trajectory without loading the entire
>>> trajectory file in RAM's computer?
>>>
>>> I know that is possible to do choosing a sub set of frames or choosing
>>> a larger stride or scripting using BigDCD, but all of those is not a
>>> choice for me. Is there another way?
>>>
>>> Thanks in advance!
>>>
>>>
>>> --
>>> att
>>>
>>> Leonardo Palmieri
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics
>> Beckman Institute for Advanced Science and Technology
>> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>
>
> --
> att
>
> Leonardo Palmieri
>
> Pai de gente
> Pai de planta
> 

-- 
att
Leonardo Palmieri
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