AMBER Archive (2004)

Subject: Re: AMBER: amber8 performance on linux cluster

From: Lubos Vrbka (
Date: Tue Apr 27 2004 - 12:26:14 CDT

> I have tried to compile the amber8 at linux cluster
> with intel compiler and mpich, however, the
> performance is very poor for sander, usually around
> 30% or less CPU usage for each CPU. If I use only one
> CPU, the usage is above 90%. I am not sure this is
> common for parallel sander in linux? or is it problem
> from mpich?
> Thanks,
> Chen
how big is your system? i observe such behaviour for small system
simulations (~1000 atoms) on linux cluster with ethernet connection
between nodes. if your system is small, try something big (10000 atoms)
and you'll see whether this is your problem.


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