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

Qiao Baofu qiaobf at gmail.com
Thu Sep 14 09:27:45 CEST 2006


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
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

I wonder if anyone can tell the bottlenack: the hardware on the cluster or

2006/9/14, Mark Abraham <mark.abraham at anu.edu.au>:
> > You have to
> > find your optimum making some tests with your settings. To do that you
> can
> > start your simulation and interrupt after a while to have some data
> logged
> > in the log file. Then, from the information in that log file you can
> > estimate the time that the whole task will take and compare using more
> or
> > less number of processors until you find your optimum value.
> Of course, that "while" should be at least of the order of several
> minutes. There is a set-up cost borne once at the start of the calculation
> which is not proportional to the length of the calculation, so you need to
> run long enough to get out of the time period during which it dominates
> the linear component.
> Mark
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Sincerely yours,
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
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