AMBER Archive (2007)

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

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Aug 02 2007 - 23:23:17 CDT

Dear Ye Mei,

Thanks for your reply. I was also wondering if I can get an almost fully
efficient CPU usage in this kind of a machine. I am assuming that because
the two Quad Core is on the same motherboard, I can get an almost perfect
efficient usage of the CPUs, if I run a simulation in parallel mode; but I
might be wrong. Thanks again.

On Fri, 3 Aug 2007, Ye Mei wrote:

> 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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-- 
  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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