[gmx-users] cpu utilization

David spoel at xray.bmc.uu.se
Fri Oct 17 21:36:02 CEST 2003

On Fri, 2003-10-17 at 21:23, Dean Johnson wrote:
> > MPICH problems? Most gromacs users are using LAM. Once more, since TCP
> > communication in Linux is slow compared to Shared mem, you want to run
> > 8x2 cpus rather than 16x1.
> >
> Our experience with Amber is that 16x1 is considerably faster than 8x2, 
> which leads me to believe that its pummel the memory a little too much. 
> Whats odd is that you can run 2x16x1 decidedly faster than 1x16x2. I am 
> speculating that it gets into some self-regulating behavior and the two 
> runs stay out of each others way. Thats just a silly guess on my part.
Well, seeing is believing, so please try it all, maybe even LAM...

David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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