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

Herbert J. Bernstein yaya at bernstein-plus-sons.com
Fri Apr 13 10:49:37 EDT 2007

Dear Keith,

   Thank you for bringing this to my attention.  We would like to fix
it.  You have raised two problems that clearly need to be fixed in
the latest version:

   1.  You have described "coloring problems when loading images one
after the other."  Could you clarify and provide an example?
It sounds like the color maps are not getting reset properly.
Are you using a 32-bit, 16-bit or 8-bit version of RasMol?

   2.  You say that after about "500 images rasmol gives an error and
is unable to load any new images, saying that the file is not found".
Could you be more specific about the sequence of commands and data files
used, so we can reproduce this error and fix it.  it sounds like a
memory leak.

Are you running one copy of RasMol and loading and zapping multiple images
or are you running multiple copies of RasMol.  In the former case the
problem need to be addressed primarily directly in RasMol.  In the
later case, the problem needs to be adressed more at the operating
system level.  In either case, we would like to solve it.

Please specify the hardware platform and operating system you use, so
we can try to work in a similar environment.

In the meantime, I would agree with your guess that adding more memory
would help, but if you are keeping 500 copies of RasMol open and are
in a unix environment, you probably need to increase process limits
as well.  If you are in an MS windows environment, there may not be
any easy answer.


At 7:28 PM -0400 4/12/07, Keith McLaughlin wrote:
>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
>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
>Molvis-list mailing list
>Molvis-list at bioinformatics.org

  Herbert J. Bernstein, Professor of Computer Science
    Dowling College, Kramer Science Center, KSC 121
         Idle Hour Blvd, Oakdale, NY, 11769

                  yaya at dowling.edu

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