[gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)

[Florian Haberl]

On Thursday 14 September 2006 09:53, Mark Abraham wrote:
> Qiao Baofu wrote:
> > Hi,
> >
> > Thanks. I have test different cpus. Our institute has two clusters: one
> > is each node has 4 cpu (A), one is one node has only 1 cpu (B).   I made
> > different tests on the two clusters and my local computer using the same
> > system. See the following result:
> >
> >  A     (For 1 hour)
> >     # of cpus   ;    MD steps
> >       4             finished (200000steps for 26:21)
> >       8             finished (200000steps for 40:57)
> >      12             87950
> >      20             42749
> >      44             5962   !!!!!
> >  B   (For 1 hour)
> >      # of cpu           ; MD steps
> >        1                156991  for 56:12
> >        2                179820
> >        3                200,000 for 54:20
> >        4                200,000 for 51:12
> >  c. Local(single cpu), 200000 steps  For 1h52:38
> >
> > One can see that
> > 1. On cluster A, one nodes(4 cpu) is just as 4 times fast as my local
> > computer.
> > 2. More than one nodes will decrease the performancs the gromacs,
> > 3. On cluster B, the more cpu used, the faster gromacs runs. But the
> > difference of speed is not apparent.
> > 4. Cluster B with 4 cpus is slow as half as that Cluster A with 1 node
> > (4 cpus)
> >
> > I wonder if anyone can tell the bottlenack: the hardware on the cluster
> > or gromacs?
>
> Probably your interconnects between nodes are using carrier pigeons or
> something :-) I expect that 1 cpu on machine A will require around four
> times as long as 1 4-cpu node, which you can presumably test for yourself.
>
> For next time, if you want to compare hardware like this, either use the
> same length of time or the same number of MD steps for all of your runs.
> Also when reporting runtimes, make it clear whether you are reporting
> walltime or some time * number_of_cpus, etc. :-)

Search the mailing list i have post several times benchmark results for 
different systems with standard benchmark suite.

http://www.gromacs.org/pipermail/gmx-developers/2006-January/001473.html


>
> Mark
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Greetings,

Florian 

-- 
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 Florian Haberl                        
 Computer-Chemie-Centrum   
 Universitaet Erlangen/ Nuernberg
 Naegelsbachstr 25
 D-91052 Erlangen
 Telephone:  	+49(0) − 9131 − 85 26581
 Mailto: florian.haberl AT chemie.uni-erlangen.de
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