AMBER Archive (2007)

Subject: Re: AMBER: amber on AMD opteron-250

From: David LeBard (david.lebard_at_asu.edu)
Date: Wed Dec 05 2007 - 14:29:22 CST

Hi Servaas,

This is generally due to your network, which you did not mention so I assume
we are talking about the gigabit ethernet, and to the number of CPU's per
node, which also you neglected to specify. However, with my experience on
dual CPU opterons (240's and 248's) and a gigabit ethernet these numbers
seem about right. Unfortunately you may only be able to get good scaling
for 20k atoms upto 32 CPUs, but only if you have a faster network like
infiniband or myirnet or the like.

Good luck,
David LeBard

On 12/5/07, servaas michielssens <servaas.michielssens_at_student.kuleuven.be>
wrote:
>
> I ran a 20ps simulation of a system of 20000 atoms on an AMD opteron 250
> cluster with 8 processors, I used amber8 and pmemd for the simulation. I
> found some strange results:
> proc time(min)
> 2 31
> 3 29
> 4 20
> 5 23
> 6 24
> 7 20
> 8 21
>
> 4 processors gives the optimum, it seems to be independent of how I
> adress the processors. So for 5 processors 1-2-3-4-5 or 1-2-3-4-7 gives
> the same results, always on for processors there is an optimum. Anyone
> who experienced this scaling problem?
>
> kind regards,
>
> servaas michielssens
>
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