[gmx-users] cpu utilization

[David]

On Fri, 2003-10-17 at 19:37, Dean Johnson wrote:
> Howdy all,
> I have started running some benchmarks using the latest of all the 
> required software (with vanilla MPICH). Its a 16 node Dell dual 1.7 & 
> 1.8Ghz xeons with gigE. When I am running Amber I get pretty much full 
> cpu utillization when I run two 16 cpu (16x1) jobs and slightly less 
> with a single 32 cpu (16x2)  job. Running GROMACS, I can only get 
> utilization up close to 40% when I try larger jobs. The nodes have 
> plenty of memory and the systems are pretty quiet. Is this consistent 
> with what people are seeing?
Which benchmark?

I'd suggest using the DPPC benchmark and run grompp -shuffle. 
Furthermore for other benchmarks you have to have a reasonable ratio of
computation/communication, e.g. at least 3000-5000 atoms per processor
to scale. It would be interesting to see some scaling benchmarks using
Amber and Gromacs for the same calculation.


> 
> Also, perhaps a bit of evidence, it has a real hard time cleaning up 
> after itself. The output indicating performance and stuff comes *way* 
> before the jobs eventually die and some never die. I had to write a 
> simple  'killgro' command to nuke everything for good. Any ideas?
> 
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.


> 	-Dean
> 
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-- 
David.
________________________________________________________________________
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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