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
