[gmx-users] forcefield and run in parallel

[David]

On Mon, 2002-09-02 at 21:23, Rui Qiao wrote:
> Hi, 
> 	I followed the approach David suggested and I think Gromacs is
> using the new parameters in the simulation. Thanks for all the responses!
> 	
> 	I am now trying to run Gromacs in parallel and somehow the speedup
> is not significant. The basic information is the following:
> 	# of atom: ~5000 (around 1300 water)
> 	Forces: PME, 4th order interpolation, FFT grid: 0.11nm, 
> 		vdw cut-off: 1.1nm
> 	
> 	The performance are (on P-III platinuum):
> 	1 node :		23.8h/ns
> 	4 nodes:		13.9h/ns
> 	6 nodes: 		12.8h/ns
> 	8 nodes: 		11.5h/ns
to be honest, it doesn get any better than this for small systems,
unless you have a high speed network or an IBM SP2. Erik and I plan to
work on it, if we get over our need for a couple of hours sleep a day...
> 
> 	It seems that the performance does not scale nicely with
> increasing nodes for node>=4. I realize that I am using PME and am having
> a small system, but is there a way to somehow boost the performance? 
> 
> 	While checking the log file, I found there are some information
> like:
> 
> 	Total NODE time on node 0: 922.68
> 	Average NODE time: 153.78
> 	Load imbalance reduced performance to 600% of max
> 	
> 	My simulation system has about 1200 atoms that are frozen in the
> simulation and they are allocated on node 0 in the simulations. Could this
> cause problems like load im-balancing?
> 
> ------------------------
> Rui Qiao
> Research Assistant
> Beckman Institute, UIUC
> 
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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