[gmx-users] Re: Question about parallazing Gromacs (Qiao Baofu)
Qiao Baofu
qiaobf at gmail.com
Thu Sep 14 12:45:07 CEST 2006
2006/9/14, Mark Abraham <Mark.Abraham at anu.edu.au>:
>
>
> 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.
It is forbidden to run only one cpu on the cluster A in my inisititute.
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. :-)
For all the jobs (except the one on my local computer) , I set
walltime=1hour, and nsteps= 200,000,dt=0.001.
The running time are taken from the end of the .log file. See the following
example.
NODE (s) Real (s) (%)
Time: 1581.000 1581.000 100.0
26:21
(Mnbf/s) (GFlops) (ns/day) (hour/ns)
Performance: 56.376 4.515 10.930 2.196
Mark
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--
Sincerely yours,
**********************************************
Baofu Qiao, PhD
Frankfurt Institute for Advanced Studies
Max-von-Laue-Str. 1
60438 Frankfurt am Main, Germany TEL:+49-69-7984-7529
**********************************************
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