From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Sat May 05 2012 - 13:37:05 CDT
See
http://www.ks.uiuc.edu/Research/namd/wiki/?NamdPerformanceTuning
On 5/5/2012 8:14 PM, Pedro Armando Ojeda May wrote:
> Hi,
>
> FACTS:
> 1) Running namd2
> (/N/soft/linux-rhel4-x86_64/namd-2.7b2/NAMD_2.7b2_Linux-x86_64-
> TCP/namd2) using charmrun
> (/soft/linux-rhel4-x86_64/namd-2.7b2/
> NAMD_2.7b2_Linux-x86_64-TCP/charmrun).
>
> 2) Launch the run as follows:
>
> charmrun namd2 ++remote-shell ssh ++verbose
> +netpoll ++nodelist nodelist2
> ++ppn 8 ++p 16 inputfile
>
> my nodefile looks like:
> group main
> host x087
> host x089
> host x093
>
> Each node has 8 processors. Running on the command
> line (not with torque or any
> other queue system).
>
>
> It works fine in the sense that my program finishes for the number of
> steps I assigned. My concern is regarding to the simulation time, if I
> use "++p 8" the time this run lasts is 22min (measured with "time"
> command), but if I use "++p 16" the time for the run is 20min.
> I expected the simulation time to be reduce at least for a half, but
> it is almost the same time.
> Does anyone has a comment about this issue?
>
>
> SIMULATION DETAILS:
> - periodic cubic box 70x70x70
> - 33933 atoms
>
>
> thanks.
>
>
>
>
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