[gmx-users] Re: reasons for slow computation?

[Justin A. Lemkul]

Yun Shi wrote:
> And another difference I noticed from .log files are:
> ..............
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 0.451 nm, LJ-14, atoms 3586 4808
>   multi-body bonded interactions: 0.451 nm, Proper Dih., atoms 3586 4808
> Minimum cell size due to bonded interactions: 0.496 nm
> ................
> Optimizing the DD grid for 48 cells with a minimum initial size of 0.620 nm
> The maximum allowed number of cells is: X 12 Y 12 Z 12
> Domain decomposition grid 8 x 3 x 2, separate PME nodes 24
> PME domain decomposition: 8 x 3 x 1
> Interleaving PP and PME nodes
> This is a particle-particle only node
> 
> Domain decomposition nodeid 0, coordinates 0 0 0
> 
> Using two step summing over 21 groups of on average 2.3 processes
> ...................
> 
> for the slow one, while for the fast one:
> ................
> Initial maximum inter charge-group distances:
>     two-body bonded interactions: 0.450 nm, LJ-14, atoms 2064 3014
>   multi-body bonded interactions: 0.450 nm, Proper Dih., atoms 2064 3014
> Minimum cell size due to bonded interactions: 0.494 nm
> ................
> 
> Optimizing the DD grid for 48 cells with a minimum initial size of 0.618 nm
> The maximum allowed number of cells is: X 12 Y 12 Z 12
> Domain decomposition grid 8 x 3 x 2, separate PME nodes 24
> PME domain decomposition: 8 x 3 x 1
> Interleaving PP and PME nodes
> This is a particle-particle only node
> 
> Domain decomposition nodeid 0, coordinates 0 0 0
> 
> Using two step summing over 18 groups of on average 2.7 processes
> ................
> 
> 
> Are these differences likely to generate huge performance difference?
> 

I would think these differences would not account for a threefold slowdown of 
one simulation relative to the other.  Please investigate the hardware issues I 
suggested before.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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