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

[Mark Abraham]

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. :-)

Mark