[gmx-users] parallel question!!!

[Erik Lindahl]

>

216 waters is an extremely small system - you only have 27 waters per  
CPU. Gromacs calculates this in a millisecond or so, and then you have  
to wait for the communication which takes more time on 8 CPUs than on  
2. A larger system will scale better.

Cheers,

Erik




> I want to test the mdrun(with mpich-iccr),but I find a strange  
> phenomenon:
> I use the two -np nodes to test how fast the parallel caculation.so I  
> use the tutor/water to test:
>
> Method 1:
> grompp -np 1 -f water.mdp -p water.top -c spc216.gro -o water.tpr
> mpirun -echo -np 1 /home/pqchen/gromacs/i686-pc-linux-gnu/bin/mdrun -s  
> water.tpr -o water.trr -c water_out.gro -v -g water.log
>
> Method 2
> grompp -np 8 -f water.mdp -p water.top -c spc216.gro -o water.tpr
> mpirun -echo -np 8 /home/pqchen/gromacs/i686-pc-linux-gnu/bin/mdrun -s  
> water.tpr -o water.trr -c water_out.gro -v -g water.log
>
> But the Method 2 consumes more time to caculate.Can anybody tell me  
> why??Can anybody help me??
>
> Thank you in advance!
>
> Sincerely yours
> ----
> PeiQuan Chen
> _______________________________________________________________________ 
> _
> PeiQuan Chen 	Department of Chemistry, Nankai University
> WeiJin Road 94, TianJin, 300071, P.R.China
> phone:	(86)2223506728		Mobile Phone: (+86)13920675030
> gromacs at 163.com	
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------------------------------------------------------------------------ 
-----
Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
Tel. 650-7250754    Fax. 650-7238464

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