Were you using sander or pmemd? And how did you calculate this efficiency?
Also, how long were you running these simulations for?
On Thu, Dec 15, 2011 at 6:57 AM, <abinayar.imsc.res.in> wrote:
>
> Respected Sir,
> This is with regard to a small query related to AMBER11.In
> order to learn to use AMBER 11 ,I reproduced the simulations
> of " Case Study - Folding TRP Cage (Advanced analysis and
> clustering)" of your tutorial.
>
> We have a parallel processing unit of 2.2 GHz. When I roped
> in 16 processors of this processing unit, it took me 12
> long hours for the complete execution of just one Stage in
> production MD phase.The %CPU efficiency was less than 60%
> for all the processors.Is that the problem? And what can be done to make
> it 100% ?
>
> According to your tutorial, it took 27 hours in total for
> Production MD.I would like to know why it is taking so long for
> the execution of just one stage.
>
> Thanking you,
> Abinaya Raju,
> Project Student
>
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Dec 15 2011 - 05:00:03 PST
