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

[xianghong qi]

thanks lot for your reply. My high frequency is every 0.1ps, low frequency
is every 100ps. I am not sure whether every 0.1ps is extremly high or not. I
am running with Gromacs 4.0. Up to now, I can see the only difference is the
speed between high frequency simulation and low frequency simulation.
Thanks.
-Xianghongh Qi



On Sat, Nov 8, 2008 at 4:31 AM, Jussi Lehtola <jussi.lehtola at helsinki.fi>wrote:

> 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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