<div>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. </div>
<div>Thanks.</div>
<div>-Xianghongh Qi</div>
<div><br><br> </div>
<div class="gmail_quote">On Sat, Nov 8, 2008 at 4:31 AM, Jussi Lehtola <span dir="ltr"><<a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="PADDING-LEFT: 1ex; MARGIN: 0px 0px 0px 0.8ex; BORDER-LEFT: #ccc 1px solid">
<div class="Ih2E3d">On Sat, 2008-11-08 at 16:13 +1100, Mark Abraham wrote:<br>> xianghong qi wrote:<br>> > Hello, all:<br>> ><br>> > I compare the two simulations with different output frequency for .xtc<br>
> > file in same machine. One with low frequency runs much faster than the<br>> > one with high frequency.<br>> > Is that reasonable? I think the frequency shouldn't affect the<br>> > simulation speed.<br>
> ><br>> > Anyone has idea about this situation? Thanks.<br>><br>> If that's really the only difference between the two simulations, then<br>> it suggests your file system has severe problems. With modern buffered<br>
> I/O it's inconceivable that writing output could rate-limit GROMACS.<br>> (Unless something's broken in 4.x, but you haven't said what you're using.)<br><br></div>It is reasonable, if you have a ridiculously high output frequency, e.g.<br>
you write the output on each step. Also the performance of parallel<br>simulations may be hurt more than of serial simulations, since there is<br>an extra communication step to collect the data.<br>--<br>------------------------------------------------------<br>
Jussi Lehtola, FM, Tohtorikoulutettava<br>Fysiikan laitos, Helsingin Yliopisto<br><a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a>, p. 191 50623<br>------------------------------------------------------<br>
Mr. Jussi Lehtola, M. Sc., Doctoral Student<br>Department of Physics, University of Helsinki, Finland<br><font color="#888888"><a href="mailto:jussi.lehtola@helsinki.fi">jussi.lehtola@helsinki.fi</a><br>------------------------------------------------------<br>
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