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.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/ -
> > ---------------------------------------------------------------
> >
> >-----------------------------------------------------------------------
> >The AMBER Mail Reflector
> >To post, send mail to amber.scripps.edu
> >To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
> >
>
> = = = = = = = = = = = = = = = = = = = =
>
>
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
>
>
--
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/ -
---------------------------------------------------------------
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 05 2007 - 06:07:45 PDT
