[gmx-developers] max cpu scale-up

[spitaleri.andrea at hsr.it]

Hi,
in fact I tried 128 cpu with just -s -v and I get this error:

Fatal error:
Could not find an appropriate number of separate PME nodes. i.e. >=
0.419288*#nodes (51) and <= #n
odes/2 (64) and reasonable performance wise (grid_x=144, grid_y=120).
Use the -npme option of mdrun or change the number of processors or the
grid dimensions.

Using -npme 64 it works and on 128 cpu it goes 2ns (dt=2fs) in  3h45'!
What -ddorder cartesian does? 

Anyway, really good job!

Andrea Spitaleri PhD
Dulbecco Telethon Institute 
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153

----- Original Message -----
From: Berk Hess <hessb at mpip-mainz.mpg.de>
Date: Friday, September 19, 2008 5:03 pm
Subject: Re: [gmx-developers] max cpu scale-up

> Hi,
> 
> Just try!
> 
> This depends a lot on your system.
> But with 200000 atoms you should be able to scale much further on a 
> cray 
> xt4.
> You usually don't need to use -dd option, mdrun will optimize it 
> for you.
> If you use pme, you will get far higher performance with separate 
> pme nodes,
> mdrun will automatically select this (when you do not specify -dd).
> You might need to optimize -npme.
> On a xt4 you probably want to use -ddorder cartesian
> No other options should be needed.
> 
> The only real disadvantage of an xt4 is that you can not get/select 
> you 
> processor blocks.
> Therefore 4x4x4 might fit perfectly in a torus of the machine, but 
> the 
> software
> with never give you such a nice assignment.
> 
> Berk
> 
> andrea spitaleri wrote:
> > Hi there,
> > I am using the latest cvs on hector cluster 
> (http://www.hector.ac.uk/) 
> > and normally I set the simulation to 64 cpus and -dd 4 4 4. This 
> gives 
> > to me a good performance for a simulation with ca. 200,000 atoms 
> > (6ns/day with dt=2fs).
> > How many cpus the new gromacs may scale-up? do you have any 
> optimised 
> > parameters? Do you think that 128 cpus can perform better in speed?
> >
> > thanks in advance
> >
> > regards
> >
> > andrea
> >
> 
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