[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

                   NODE (s)   Real (s)      (%)
       Time:   1581.000   1581.000    100.0
                      (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     56.376      4.515     10.930      2.196

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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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