[gmx-users] parallel computations

[fabio affinito]

I tried shorter runs, and I found out that parallel computations seems 
to be slower than serial...
I.e.:
               (Mnbf/s)   (MFlops) (ps/NODE hour) (NODE hour/ns)
serial:
Performance:      8.449    670.583      5.217    191.678
np=1 MPI:
Performance:      8.406    667.170      5.191    192.658
np=2 MPI:
Performance:      1.882    154.785      1.162    860.278

Looking inside one of the logfiles of the last simulation I found:

Total NODE time on node 1: 1268.41
Average NODE time: 271.69
Load imbalance reduced performance to 200% of max

What does it means?

Thx

Bye

Fabio



David van der Spoel wrote:

>On Tue, 2004-07-13 at 09:28, fabio affinito wrote:
>  
>
>>Hi,
>>I'm running a MPI simulation with Gromacs on 4 processors. The problem 
>>is that only one of the four logfiles seems to be advancing (and not 
>>very fast!), Is this normal?
>>
>>This is the situation of my directory this morning at 9.40
>>
>>-rw-r--r--    1 affinito G09          2351 Jul 12 14:40 Simulazione3.log
>>-rw-r--r--    1 affinito G09          2351 Jul 12 14:40 Simulazione2.log
>>-rw-r--r--    1 affinito G09          2351 Jul 12 14:40 Simulazione1.log
>>-rw-r--r--    1 affinito G09         45941 Jul 13 08:39 Simulazione0.log
>>
>>    
>>
>Yes this is normal, however you do have to check whether your
>calculation is efficient, i.e. do short test runs on 1,2,4 processors.
>
>  
>
>>Thanks again.. and bye!
>>
>>Fabio
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