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 <[EMAIL PROTECTED]>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 > [EMAIL PROTECTED], p. 191 50623 > ------------------------------------------------------ > Mr. Jussi Lehtola, M. Sc., Doctoral Student > Department of Physics, University of Helsinki, Finland > [EMAIL PROTECTED] > ------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Some people make the world more special just by being in it.
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