[gmx-users] Re: High frequency output slow down the simulation?

Jussi Lehtola jussi.lehtola at helsinki.fi
Sat Nov 8 10:31:33 CET 2008

On Sat, 2008-11-08 at 16:13 +1100, Mark Abraham wrote:
> xianghong qi wrote:
> > Hello, all:
> >  
> > I compare the two simulations with different output frequency for .xtc 
> > file in same machine. One with low frequency runs  much faster than the 
> > one with high frequency. 
> > Is that reasonable? I think the frequency shouldn't affect the 
> > simulation speed.  
> >  
> > Anyone has idea about this situation?  Thanks.  
> If that's really the only difference between the two simulations, then 
> it suggests your file system has severe problems. With modern buffered 
> I/O it's inconceivable that writing output could rate-limit GROMACS. 
> (Unless something's broken in 4.x, but you haven't said what you're using.)

It is reasonable, if you have a ridiculously high output frequency, e.g.
you write the output on each step. Also the performance of parallel
simulations may be hurt more than of serial simulations, since there is
an extra communication step to collect the data.
Jussi Lehtola, FM, Tohtorikoulutettava
Fysiikan laitos, Helsingin Yliopisto
jussi.lehtola at helsinki.fi, p. 191 50623
Mr. Jussi Lehtola, M. Sc., Doctoral Student
Department of Physics, University of Helsinki, Finland
jussi.lehtola at helsinki.fi

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