[gmx-users] Load balancing between PME and PP on more than 12 processors

[XAvier Periole]

Hi,

Have a look at g_tunepme on the gromacs web site or on google. It does  
this fine tuning for you.

It is pretty good

On Feb 10, 2010, at 21:09, Warren Gallin <wgallin at ualberta.ca> wrote:

> I have a question about the procedure for running a parallel  
> simulation on more than 12 processors using GROMACS 4.0.7.
>
> I understand that partitioning the PME calculations and PP  
> calculations improves performance, and that there is an initial  
> automated "guess" at deciding how many processors to devote to PME  
> vs. PP calculations.
>
> When I ran a simulation of a system on 16 processors, GROMACS  
> automatically devoted 6 processors to PMA calculations and 10 to PP  
> calculations.  A 1 nsec simulation using 2 fs steps took only  
> marginally less time (5 h 12 m) as runningthe same simulation on 8  
> processors (6 h 45 m), without the separation of PME and PP  
> calculations and the following note was in the log file:
>
>
> NOTE: 35.7 % performance was lost because the PME nodes
>      had more work to do than the PP nodes.
>      You might want to increase the number of PME nodes
>      or increase the cut-off and the grid spacing.
>
>
> I reran the same simulation, this time including -npme 8 in the  
> mdrun call, and the simulation completed in 4 h 19 min, with the  
> following note in the log file:
>
> NOTE: 16.8 % performance was lost because the PME nodes
>      had more work to do than the PP nodes.
>      You might want to increase the number of PME nodes
>      or increase the cut-off and the grid spacing.
>
>
> So I conclude that I need to increase cut-off and grid spacing,  
> since this is recommended in the manual and in the paper describing  
> the GROMACS 4 algoithm changes.
>
> Unfortunately
> a) I am unclear on which parameters in the .mdp file represent cut- 
> off and grid spacing
>
> and
>
> b) When the manual says "For changing the electrostatics settings it  
> is useful to know the accuracy of the electrostatics remains nearly  
> constant when the Coulomb cut-off and the PME grid spacing are  
> scaled by the same factor."
> Does this mean that cut-off and grid-spacing parameters need to be  
> changed by the same proportion?
>
> I hope this is sufficiently specific a question - if not, let me  
> knwo what I need to be clearer on.
>
> Thanks,
>
> Warren Gallin
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