improving parallel on mac cluster

Date: Mon Feb 09 2004 - 11:44:31 CST

I've managed to run my simulation in parallel on a couple of G5 mac computers
but i've noticed that my performance does not increase after three nodes. I am
guessing the possible reason for this to be:
1. simulation is bottlenecked by the ethernet connection
2. my molecule is not configured properly to take advantage of mutiple sys...
i have my cutoff set to a large number(essentially no cutoff) but if i change
it to smaller number with switching on the simulation seems to be distributed
between the systems better.
3. patch size...i think this is related to reason #2. because number of
patches namd creates seems to be dependent of the conf file and simulation
speed seems to be dependent on the number of patches.

could anyone provide some insight into my situation.


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