[Molvis-list] hardware upgrades to increase rasmol performance on very large systems.

[Keith McLaughlin]

Thanks for your feedback. I will try to monitor the memory consumption and
such and I'll update.

Closing rasmol between runs is not an option unless there is a way to make
rasmol automatically open fullscreen. Additionally, I believe the command
"set write on" needs to be entered manually. I'm not sure that it is
possible to automate this.

On 4/13/07, Dr. Christoph Gille <christoph.gille at charite.de> wrote:
>
>
> I do not think that increasing
> RAM would solve the problem.
>
> If the RAM would be a problem the entire computer would be
> frozen.
>
> Since the computer is still responsive it has sufficient memory.
>
> Nevertheless,
> can you monitor memory consumption i.e.
> calling ps aux | fgrep rasmol ... after each image
> or using top or gps or whatever monitor.
>
> As a solution, can you close the rasmol instance in your script
> and start a new one
> after 400 files ?
>
> If the number of written files is about the
> same each time
> independently of the size of the protein
> it could also be that file pointers are not closed.
>
> You could have a look at the
> source code and check whether
> the file pointers are closed.
>
>
>
> > Hello all;
> >
> > My research involves 4 million atom MD simulations and we've decided to
> use
> > rasmol for visualization. From my experiences, I have two questions and
> am
> > hoping that someone here may be able to help.
> >
> > 1. Currently I'm using version 2.7.1 because it doesn't have the
> coloring
> > problems when loading images one after another. Unfortunately, after
> about
> > 500 images rasmol gives an error and is unable to load any new images
> saying
> > that the file is not found, or something to that effect. Does anyone
> have
> > experience with handling this?
> >
> > 2. We are planning on some upgrades, and are kind of curious as to which
> > components will help the most with increasing the speed in which these
> files
> > are loaded: memory or video memory, or perhaps processor. We mostly
> suspect
> > that adding more memory would be the best choice, but I'd like to hear
> other
> > opinions.
> >
> > Thanks!
> > --
> > Keith McLaughlin
> > University of South Florida
> > Physics Dept. PHY225
> > 4202 E. Fowler Ave
> > Tampa, FL 33620
> >
> > --
> > Keith McLaughlin
> > University of South Florida
> > Physics Dept. PHY225
> > 4202 E. Fowler Ave
> > Tampa, FL 33620
> > _______________________________________________
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> > Molvis-list at bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/molvis-list
> >
>
>
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-- 
Keith McLaughlin
University of South Florida
Physics Dept. PHY225
4202 E. Fowler Ave
Tampa, FL 33620