AMBER Archive (2007)

Subject: Re: AMBER: Any experience on Dell two quad core system?

From: Ye Mei (ymei_at_itcc.nju.edu.cn)
Date: Thu Aug 02 2007 - 22:57:00 CDT

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_at_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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