[AMBER] Regarding low %CPU efficiency while running production MD

From: <abinayar.imsc.res.in>
Date: Thu, 15 Dec 2011 17:27:42 +0530

  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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Received on Thu Dec 15 2011 - 04:00:02 PST
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