Parallelization of a code from TCB Summer School 2003

From: Yang Yang (yang.yang_at_WMICH.EDU)
Date: Fri Apr 16 2004 - 21:54:46 CDT

Hello everybody,

I am learning to use NAMD by starting from one of the TCB summer
school tutorials, i.e. "Simulating Membrane Channels-Water channel

After successfully running it on one processor, I am trying to run
it on 3 and 8 processors. I did not alter any part of the configure
file, everything remains the same except for the command line.

I used the following to invoke NAMD

"mpirun -machinefile list -np 3 namd2 sim_short.conf", where the
list is the file containing the processor names on which the namd
will run.

It did run properly but very slowly. The CPU time is 11404.68 and
the wall clock is also 11404.68 which is much longer than the time
consumed by runnning on one processor which used CPU time/Wall clock
at 3384.39.

Questions, can I simply run it in this way for parallel computing?
Or is it because the atom number is so small, only 1320, that NAMD
can not work efficiently?

 I will appreciate any advice.


Research Assistant,CFD Lab,tel.(269-276-3433),
Department of Mechanical and Aeronautical Engineering
College of Engineering and Applied Sciences
Western Michigan University

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