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

[Herbert J. Bernstein]

You should be able to automate the set write on command by using an
external script or by redirecting stdin.  The redirected file must end
with the execution of your script and the exit command.

I'll add a command to set the screen size from the command line,
but until that is ready, it is easy to change the startup default
size in a rebuild by changing the values DefaultWide and DefaultHigh 
in graphics.h.  If you send me your screen dimensions, I'll make you
such a binary.

   -- Herbert


At 7:01 PM -0400 4/14/07, Keith McLaughlin wrote:
>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
>>>  _______________________________________________
>>>  Molvis-list mailing list
>>>  Molvis-list at bioinformatics.org
>>>  https://bioinformatics.org/mailman/listinfo/molvis-list
>>>
>>
>>
>>_______________________________________________
>>Molvis-list mailing list
>>Molvis-list at bioinformatics.org
>>https://bioinformatics.org/mailman/listinfo/molvis-list
>>
>
>
>
>--
>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
>https://bioinformatics.org/mailman/listinfo/molvis-list


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

                  +1-631-244-3035
                  yaya at dowling.edu
=====================================================