)) ok, I definitely have more CPUs than just one, but also I am also sure
that their number is not enough. the system is quite large, so I want to
have a lot of replicas covering high temperature values and the performance
good enough to see the effect of a traveling across temperature. Some kind
of exhaustive phase space search.
Maybe, it would be rather difficult [to rewrite the code], but memory data
can be saved, thus decreasing the time for restart (without dumping to
disk). I guess there is a lot of tricks here possible.
2011/8/23 Carlos Simmerling <carlos.simmerling.gmail.com>
> it usually takes programs some time before they become efficient. the
> spatial decompositino and load balancing are not ideal at the start.
> additionally, much work needs to be done to start running MD, such as
> reading and writing to disk, setting up the arrays, and so on.
> stopping the program each ps or less would be quite slow. are you in a
> situation where you have no way to access more than 1 CPU?
>
>
--
Sincerely,
Dmitry Mukha
Institute of Bioorganic Chemistry, NAS, Minsk, Belarus
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Received on Tue Aug 23 2011 - 13:00:07 PDT
