charmrun setup

From: Pedro Armando Ojeda May (
Date: Sat May 05 2012 - 13:14:12 CDT


             1) Running namd2
                 TCP/namd2) using 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?

        - periodic cubic box 70x70x70
        - 33933 atoms


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