I donot think memory size is a problem, unless you are doing normal mode analysis.
I guess you are running amber within a single node. So you'd better use shared memory mode of MPI communication instead of socket communication.
Best regards,
Ye Mei
Ph. D.
ymei.itcc.nju.edu.cn
Institute of Theoretical and Computational Chemistry
Key Laboratory of Mesoscopic Chemistry of MOE
School of Chemistry and Chemical Engineering
Nanjing University
Nanjing 210093
P.R.China
2007-08-03
======= 2007-08-03 08:40:05 Ilyas Yildirim wrote=======
>Dear Ross and AMBER users,
>
>We are going to buy the following DELL system to our group to run AMBER
>9: Dell Precision Workstation 490n MiniTower, running in Red
>Hat Enterprise Linux WS v4. It has two Quad Core Intel Xeon Processor
>E5335 (2 GHz, 2X4MB L2, 1333). It is going to have 8 GB of RAM in it.
>
>I was wondering if any of you had any experience on running AMBER in this
>kind or similar system; particularly the efficiency of running sander.MPI.
>Is 8 GB of RAM enough, or can we get better speed by increasing the RAM to
>16 GB? Any ideas/suggestions are greatly appreciated.
>
>--
> Ilyas Yildirim
> ---------------------------------------------------------------
> - Department of Chemistry - -
> - University of Rochester - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
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Received on Sun Aug 05 2007 - 06:07:44 PDT
